Starting phenix.real_space_refine on Mon Jul 28 19:20:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqa_38571/07_2025/8xqa_38571.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6924 2.51 5 N 1758 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5301 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 17, 'TRANS': 660} Chain breaks: 2 Chain: "B" Number of atoms: 5301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5301 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 17, 'TRANS': 660} Chain breaks: 2 Time building chain proxies: 6.47, per 1000 atoms: 0.61 Number of scatterers: 10602 At special positions: 0 Unit cell: (101.52, 109.08, 116.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1860 8.00 N 1758 7.00 C 6924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 88.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 4.262A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.099A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.557A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 223 through 253 Processing helix chain 'A' and resid 260 through 292 Proline residue: A 276 - end of helix removed outlier: 3.725A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.892A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.614A pdb=" N ALA A 379 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 376 through 380' Processing helix chain 'A' and resid 381 through 413 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.434A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.899A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.768A pdb=" N ASP A 520 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.849A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.509A pdb=" N LEU A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.622A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.759A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 854 Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.830A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 Processing helix chain 'B' and resid 75 through 95 removed outlier: 4.405A pdb=" N VAL B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 4.203A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.551A pdb=" N GLU B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.551A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.707A pdb=" N VAL B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 223 through 253 Processing helix chain 'B' and resid 260 through 291 Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 297 through 317 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.524A pdb=" N ALA B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 removed outlier: 3.538A pdb=" N VAL B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 3.970A pdb=" N VAL B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 413 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.633A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 481 removed outlier: 4.288A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 522 through 530 removed outlier: 4.071A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 600 Processing helix chain 'B' and resid 604 through 621 removed outlier: 4.010A pdb=" N GLU B 621 " --> pdb=" O VAL B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 639 through 653 removed outlier: 4.201A pdb=" N SER B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 855 removed outlier: 4.527A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.870A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 4.286A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 909 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.17 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3331 1.34 - 1.46: 1932 1.46 - 1.58: 5423 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10798 Sorted by residual: bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.549 -0.014 6.80e-03 2.16e+04 4.40e+00 bond pdb=" C ILE A 818 " pdb=" N PRO A 819 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.28e-02 6.10e+03 2.61e+00 bond pdb=" C LEU A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.57e+00 bond pdb=" CA ILE A 488 " pdb=" C ILE A 488 " ideal model delta sigma weight residual 1.520 1.533 -0.014 8.80e-03 1.29e+04 2.45e+00 bond pdb=" CB PRO B 144 " pdb=" CG PRO B 144 " ideal model delta sigma weight residual 1.492 1.416 0.076 5.00e-02 4.00e+02 2.33e+00 ... (remaining 10793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 14528 3.15 - 6.30: 97 6.30 - 9.44: 12 9.44 - 12.59: 0 12.59 - 15.74: 1 Bond angle restraints: 14638 Sorted by residual: angle pdb=" C SER A 487 " pdb=" N ILE A 488 " pdb=" CA ILE A 488 " ideal model delta sigma weight residual 120.24 125.31 -5.07 6.30e-01 2.52e+00 6.48e+01 angle pdb=" C SER B 487 " pdb=" N ILE B 488 " pdb=" CA ILE B 488 " ideal model delta sigma weight residual 120.24 123.59 -3.35 6.30e-01 2.52e+00 2.83e+01 angle pdb=" CA LEU A 405 " pdb=" CB LEU A 405 " pdb=" CG LEU A 405 " ideal model delta sigma weight residual 116.30 132.04 -15.74 3.50e+00 8.16e-02 2.02e+01 angle pdb=" CA TRP A 635 " pdb=" CB TRP A 635 " pdb=" CG TRP A 635 " ideal model delta sigma weight residual 113.60 121.40 -7.80 1.90e+00 2.77e-01 1.68e+01 angle pdb=" C ILE A 640 " pdb=" N TYR A 641 " pdb=" CA TYR A 641 " ideal model delta sigma weight residual 120.09 124.44 -4.35 1.25e+00 6.40e-01 1.21e+01 ... (remaining 14633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5782 17.82 - 35.64: 481 35.64 - 53.46: 143 53.46 - 71.28: 33 71.28 - 89.10: 5 Dihedral angle restraints: 6444 sinusoidal: 2522 harmonic: 3922 Sorted by residual: dihedral pdb=" CA ILE B 853 " pdb=" C ILE B 853 " pdb=" N ILE B 854 " pdb=" CA ILE B 854 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU A 220 " pdb=" C LEU A 220 " pdb=" N GLY A 221 " pdb=" CA GLY A 221 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA THR B 258 " pdb=" C THR B 258 " pdb=" N SER B 259 " pdb=" CA SER B 259 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1007 0.034 - 0.067: 518 0.067 - 0.101: 145 0.101 - 0.135: 81 0.135 - 0.168: 21 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA LEU A 143 " pdb=" N LEU A 143 " pdb=" C LEU A 143 " pdb=" CB LEU A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA ASN A 830 " pdb=" N ASN A 830 " pdb=" C ASN A 830 " pdb=" CB ASN A 830 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE B 486 " pdb=" CA ILE B 486 " pdb=" CG1 ILE B 486 " pdb=" CG2 ILE B 486 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1769 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 467 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C LEU A 467 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 467 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 468 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 467 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.16e+00 pdb=" C LEU B 467 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 467 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL B 468 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 271 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C VAL B 271 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL B 271 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA B 272 " -0.014 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2635 2.79 - 3.32: 10575 3.32 - 3.85: 18310 3.85 - 4.37: 20137 4.37 - 4.90: 35202 Nonbonded interactions: 86859 Sorted by model distance: nonbonded pdb=" O VAL A 468 " pdb=" OG1 THR A 472 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 631 " pdb=" OG SER A 634 " model vdw 2.271 3.040 nonbonded pdb=" O ALA B 307 " pdb=" OG1 THR B 311 " model vdw 2.320 3.040 nonbonded pdb=" O VAL B 468 " pdb=" OG1 THR B 472 " model vdw 2.322 3.040 nonbonded pdb=" O GLY B 369 " pdb=" OG1 THR B 373 " model vdw 2.322 3.040 ... (remaining 86854 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.910 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10798 Z= 0.253 Angle : 0.762 15.739 14638 Z= 0.438 Chirality : 0.048 0.168 1772 Planarity : 0.007 0.057 1796 Dihedral : 14.998 89.102 3904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.62 % Allowed : 11.50 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.20), residues: 1344 helix: -0.55 (0.13), residues: 1140 sheet: None (None), residues: 0 loop : -1.16 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 635 HIS 0.004 0.001 HIS B 889 PHE 0.021 0.002 PHE B 455 TYR 0.015 0.002 TYR A 191 ARG 0.004 0.000 ARG A 583 Details of bonding type rmsd hydrogen bonds : bond 0.10345 ( 909) hydrogen bonds : angle 5.68188 ( 2718) covalent geometry : bond 0.00527 (10798) covalent geometry : angle 0.76164 (14638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 471 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8323 (m) cc_final: 0.7904 (m) REVERT: A 112 ILE cc_start: 0.8385 (mt) cc_final: 0.8020 (mm) REVERT: A 116 VAL cc_start: 0.8318 (p) cc_final: 0.8083 (p) REVERT: A 124 GLU cc_start: 0.7502 (tp30) cc_final: 0.6559 (tp30) REVERT: A 147 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7868 (mt) REVERT: A 160 MET cc_start: 0.7722 (mmm) cc_final: 0.7334 (mmt) REVERT: A 168 ILE cc_start: 0.7750 (tt) cc_final: 0.7546 (tp) REVERT: A 186 MET cc_start: 0.6658 (mtp) cc_final: 0.6416 (mtp) REVERT: A 188 LEU cc_start: 0.8553 (tp) cc_final: 0.8219 (tt) REVERT: A 205 MET cc_start: 0.7655 (mmm) cc_final: 0.6965 (mpp) REVERT: A 209 ASP cc_start: 0.6253 (m-30) cc_final: 0.5960 (m-30) REVERT: A 213 VAL cc_start: 0.8983 (t) cc_final: 0.8782 (t) REVERT: A 217 LEU cc_start: 0.8228 (mt) cc_final: 0.7954 (mt) REVERT: A 218 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7685 (mtmt) REVERT: A 229 ILE cc_start: 0.8531 (mm) cc_final: 0.8323 (mm) REVERT: A 236 LEU cc_start: 0.8031 (mm) cc_final: 0.7642 (mp) REVERT: A 237 ASN cc_start: 0.7930 (t0) cc_final: 0.7692 (t0) REVERT: A 245 PHE cc_start: 0.8209 (t80) cc_final: 0.7993 (t80) REVERT: A 257 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7733 (pp) REVERT: A 292 HIS cc_start: 0.8355 (m-70) cc_final: 0.7819 (m-70) REVERT: A 312 TYR cc_start: 0.8300 (t80) cc_final: 0.8078 (t80) REVERT: A 361 ASN cc_start: 0.8537 (m-40) cc_final: 0.8092 (m110) REVERT: A 367 MET cc_start: 0.7709 (mtp) cc_final: 0.7504 (mtm) REVERT: A 372 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 431 ARG cc_start: 0.8511 (mmt-90) cc_final: 0.8116 (mmt90) REVERT: A 454 LYS cc_start: 0.8299 (mttm) cc_final: 0.7808 (mttm) REVERT: A 477 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8405 (tt) REVERT: A 479 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7241 (ttp80) REVERT: A 481 LEU cc_start: 0.8568 (mt) cc_final: 0.8222 (mt) REVERT: A 499 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7090 (ttp80) REVERT: A 506 ASN cc_start: 0.7983 (m110) cc_final: 0.7650 (m110) REVERT: A 531 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6846 (mm-30) REVERT: A 578 MET cc_start: 0.8108 (ttm) cc_final: 0.7812 (ttm) REVERT: A 579 MET cc_start: 0.7926 (mmm) cc_final: 0.7371 (mmm) REVERT: A 585 ARG cc_start: 0.8246 (ttp-170) cc_final: 0.7986 (ttp-170) REVERT: A 597 GLN cc_start: 0.7513 (mt0) cc_final: 0.7268 (mt0) REVERT: A 613 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 645 LYS cc_start: 0.8969 (tptp) cc_final: 0.8402 (tptp) REVERT: A 843 TYR cc_start: 0.8550 (t80) cc_final: 0.7757 (t80) REVERT: A 848 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 849 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7820 (mm-30) REVERT: A 852 LYS cc_start: 0.8216 (mttp) cc_final: 0.7928 (mttp) REVERT: A 862 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8357 (mmtm) REVERT: A 866 GLU cc_start: 0.7209 (tp30) cc_final: 0.6985 (tp30) REVERT: A 875 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7245 (tpt90) REVERT: A 880 LYS cc_start: 0.8221 (tptp) cc_final: 0.7777 (tptp) REVERT: A 900 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7405 (tp40) REVERT: A 925 MET cc_start: 0.7843 (mmm) cc_final: 0.7507 (mmm) REVERT: A 938 MET cc_start: 0.8412 (mmm) cc_final: 0.8201 (mmm) REVERT: B 77 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 84 SER cc_start: 0.8179 (t) cc_final: 0.7691 (p) REVERT: B 109 LEU cc_start: 0.7963 (mt) cc_final: 0.7711 (mt) REVERT: B 122 LEU cc_start: 0.8412 (mt) cc_final: 0.8199 (mm) REVERT: B 124 GLU cc_start: 0.7383 (tp30) cc_final: 0.6744 (tp30) REVERT: B 145 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7904 (m) REVERT: B 149 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6857 (tm-30) REVERT: B 152 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8066 (t80) REVERT: B 195 PHE cc_start: 0.7476 (t80) cc_final: 0.7179 (t80) REVERT: B 249 MET cc_start: 0.7435 (tmm) cc_final: 0.7027 (tmm) REVERT: B 278 TRP cc_start: 0.8410 (t-100) cc_final: 0.8103 (t-100) REVERT: B 292 HIS cc_start: 0.8309 (m-70) cc_final: 0.7988 (m-70) REVERT: B 335 ASN cc_start: 0.8253 (t0) cc_final: 0.7813 (t0) REVERT: B 337 GLU cc_start: 0.7754 (mp0) cc_final: 0.7383 (mp0) REVERT: B 338 LYS cc_start: 0.8071 (mttm) cc_final: 0.7846 (mttm) REVERT: B 388 LEU cc_start: 0.8568 (tt) cc_final: 0.8351 (tt) REVERT: B 390 ILE cc_start: 0.8477 (mm) cc_final: 0.8256 (mm) REVERT: B 397 ILE cc_start: 0.8215 (mm) cc_final: 0.7896 (mm) REVERT: B 443 GLU cc_start: 0.7639 (tp30) cc_final: 0.7166 (tp30) REVERT: B 454 LYS cc_start: 0.7981 (tppt) cc_final: 0.7758 (mmtm) REVERT: B 499 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7343 (ptp90) REVERT: B 500 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7449 (tpt90) REVERT: B 527 THR cc_start: 0.8232 (p) cc_final: 0.7805 (p) REVERT: B 531 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6368 (mm-30) REVERT: B 579 MET cc_start: 0.7803 (mmm) cc_final: 0.7372 (mmm) REVERT: B 586 MET cc_start: 0.7762 (tmm) cc_final: 0.6380 (tmm) REVERT: B 588 LYS cc_start: 0.8256 (ttpp) cc_final: 0.7540 (ttpp) REVERT: B 590 GLU cc_start: 0.7631 (mm-30) cc_final: 0.6320 (mm-30) REVERT: B 591 LYS cc_start: 0.8232 (mtmp) cc_final: 0.7930 (mtmp) REVERT: B 595 TRP cc_start: 0.7943 (m100) cc_final: 0.7704 (m100) REVERT: B 613 GLN cc_start: 0.7518 (tm-30) cc_final: 0.6922 (tm-30) REVERT: B 645 LYS cc_start: 0.8496 (tptp) cc_final: 0.7904 (tptp) REVERT: B 841 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8260 (mtpp) REVERT: B 843 TYR cc_start: 0.8324 (t80) cc_final: 0.7460 (t80) REVERT: B 847 GLU cc_start: 0.7855 (tp30) cc_final: 0.7497 (tp30) REVERT: B 848 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 852 LYS cc_start: 0.8626 (mttp) cc_final: 0.8235 (mttp) REVERT: B 876 LEU cc_start: 0.8167 (mt) cc_final: 0.7946 (mt) REVERT: B 880 LYS cc_start: 0.7972 (tmmt) cc_final: 0.7725 (tmmt) REVERT: B 907 ASN cc_start: 0.7574 (m-40) cc_final: 0.6487 (m-40) REVERT: B 908 HIS cc_start: 0.7707 (m-70) cc_final: 0.7172 (m-70) REVERT: B 911 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6632 (mt-10) REVERT: B 913 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 915 GLU cc_start: 0.7599 (tt0) cc_final: 0.7209 (tt0) REVERT: B 928 HIS cc_start: 0.7140 (t70) cc_final: 0.6846 (t70) REVERT: B 943 ASN cc_start: 0.7286 (p0) cc_final: 0.7046 (p0) outliers start: 76 outliers final: 25 residues processed: 513 average time/residue: 0.2699 time to fit residues: 185.3083 Evaluate side-chains 477 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 443 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 0.0980 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 374 GLN A 421 ASN A 502 HIS A 506 ASN A 917 GLN B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 421 ASN B 502 HIS B 506 ASN B 624 GLN B 877 GLN B 886 GLN B 917 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105418 restraints weight = 19566.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108732 restraints weight = 9128.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110756 restraints weight = 5291.220| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10798 Z= 0.139 Angle : 0.555 10.979 14638 Z= 0.297 Chirality : 0.038 0.264 1772 Planarity : 0.004 0.052 1796 Dihedral : 8.162 70.929 1503 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.75 % Allowed : 17.16 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.22), residues: 1344 helix: 0.95 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 523 HIS 0.004 0.001 HIS B 889 PHE 0.025 0.001 PHE B 163 TYR 0.015 0.001 TYR B 594 ARG 0.005 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 909) hydrogen bonds : angle 4.40018 ( 2718) covalent geometry : bond 0.00273 (10798) covalent geometry : angle 0.55497 (14638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 465 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7492 (mmtm) cc_final: 0.7236 (mmtm) REVERT: A 85 CYS cc_start: 0.8352 (m) cc_final: 0.8020 (m) REVERT: A 112 ILE cc_start: 0.8369 (mt) cc_final: 0.8038 (mm) REVERT: A 124 GLU cc_start: 0.7635 (tp30) cc_final: 0.6708 (tp30) REVERT: A 128 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7405 (ttp-170) REVERT: A 160 MET cc_start: 0.7769 (mmm) cc_final: 0.7380 (mmt) REVERT: A 168 ILE cc_start: 0.7709 (tt) cc_final: 0.7495 (tp) REVERT: A 186 MET cc_start: 0.6748 (mtp) cc_final: 0.6469 (mtp) REVERT: A 197 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7060 (mt-10) REVERT: A 205 MET cc_start: 0.7622 (mmm) cc_final: 0.7296 (mpp) REVERT: A 217 LEU cc_start: 0.8457 (mt) cc_final: 0.8206 (mt) REVERT: A 218 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7643 (mtmt) REVERT: A 237 ASN cc_start: 0.7932 (t0) cc_final: 0.7723 (t0) REVERT: A 257 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7580 (pp) REVERT: A 292 HIS cc_start: 0.8279 (m-70) cc_final: 0.7741 (m-70) REVERT: A 335 ASN cc_start: 0.8675 (t0) cc_final: 0.8325 (t0) REVERT: A 401 MET cc_start: 0.7212 (mtm) cc_final: 0.7000 (mtm) REVERT: A 406 PHE cc_start: 0.7698 (m-80) cc_final: 0.7474 (m-80) REVERT: A 454 LYS cc_start: 0.8407 (mttm) cc_final: 0.8079 (mttm) REVERT: A 477 LEU cc_start: 0.8598 (tt) cc_final: 0.8208 (tt) REVERT: A 479 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7416 (ttp80) REVERT: A 481 LEU cc_start: 0.8546 (mt) cc_final: 0.8267 (mt) REVERT: A 486 ILE cc_start: 0.8471 (mt) cc_final: 0.8187 (tt) REVERT: A 499 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7115 (ttp80) REVERT: A 502 HIS cc_start: 0.7798 (t-90) cc_final: 0.7202 (t-90) REVERT: A 506 ASN cc_start: 0.7953 (m-40) cc_final: 0.7407 (m-40) REVERT: A 578 MET cc_start: 0.8166 (ttm) cc_final: 0.7887 (ttm) REVERT: A 579 MET cc_start: 0.7977 (mmm) cc_final: 0.7395 (mmm) REVERT: A 596 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7798 (tmmt) REVERT: A 597 GLN cc_start: 0.7500 (mt0) cc_final: 0.7261 (mt0) REVERT: A 613 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 622 LYS cc_start: 0.7954 (tttp) cc_final: 0.7701 (tttp) REVERT: A 645 LYS cc_start: 0.8934 (tptp) cc_final: 0.8320 (tptp) REVERT: A 843 TYR cc_start: 0.8599 (t80) cc_final: 0.7844 (t80) REVERT: A 848 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 852 LYS cc_start: 0.8182 (mttp) cc_final: 0.7945 (mttp) REVERT: A 862 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8378 (mmtm) REVERT: A 866 GLU cc_start: 0.7263 (tp30) cc_final: 0.7041 (tp30) REVERT: A 868 LYS cc_start: 0.8642 (mmmm) cc_final: 0.7858 (mmmm) REVERT: A 875 ARG cc_start: 0.7650 (tpt90) cc_final: 0.7171 (tpt90) REVERT: A 880 LYS cc_start: 0.8221 (tptp) cc_final: 0.7778 (tptp) REVERT: A 900 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: A 912 THR cc_start: 0.8423 (m) cc_final: 0.8219 (p) REVERT: A 925 MET cc_start: 0.7930 (mmm) cc_final: 0.7605 (mmm) REVERT: A 931 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 77 VAL cc_start: 0.8284 (t) cc_final: 0.7965 (m) REVERT: B 84 SER cc_start: 0.8065 (t) cc_final: 0.7666 (p) REVERT: B 109 LEU cc_start: 0.7937 (mt) cc_final: 0.7639 (mt) REVERT: B 124 GLU cc_start: 0.7427 (tp30) cc_final: 0.7161 (tp30) REVERT: B 149 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6957 (tm-30) REVERT: B 233 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 249 MET cc_start: 0.7536 (tmm) cc_final: 0.7069 (tmm) REVERT: B 278 TRP cc_start: 0.8374 (t-100) cc_final: 0.8043 (t-100) REVERT: B 300 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 337 GLU cc_start: 0.7687 (mp0) cc_final: 0.7406 (mp0) REVERT: B 351 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8074 (tpp-160) REVERT: B 384 ASP cc_start: 0.6993 (m-30) cc_final: 0.6742 (m-30) REVERT: B 390 ILE cc_start: 0.8500 (mm) cc_final: 0.8269 (mm) REVERT: B 420 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7742 (mtm-85) REVERT: B 443 GLU cc_start: 0.7664 (tp30) cc_final: 0.7212 (tp30) REVERT: B 499 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7246 (ptp90) REVERT: B 500 ARG cc_start: 0.7795 (tpt90) cc_final: 0.7412 (tpt90) REVERT: B 512 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 517 PHE cc_start: 0.7542 (m-10) cc_final: 0.7286 (m-80) REVERT: B 527 THR cc_start: 0.8257 (p) cc_final: 0.7548 (p) REVERT: B 579 MET cc_start: 0.7803 (mmm) cc_final: 0.7435 (mmm) REVERT: B 581 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6018 (pp20) REVERT: B 586 MET cc_start: 0.7679 (tmm) cc_final: 0.6006 (tmm) REVERT: B 588 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7782 (ttpp) REVERT: B 590 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6747 (mm-30) REVERT: B 591 LYS cc_start: 0.8202 (mtmp) cc_final: 0.7951 (mtmp) REVERT: B 595 TRP cc_start: 0.7987 (m100) cc_final: 0.7718 (m100) REVERT: B 596 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8162 (mmmt) REVERT: B 613 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6977 (tm-30) REVERT: B 635 TRP cc_start: 0.5412 (m100) cc_final: 0.5189 (m100) REVERT: B 645 LYS cc_start: 0.8522 (tptp) cc_final: 0.7949 (tptp) REVERT: B 825 VAL cc_start: 0.8408 (t) cc_final: 0.8179 (p) REVERT: B 826 ASN cc_start: 0.7894 (t0) cc_final: 0.7551 (m110) REVERT: B 841 LYS cc_start: 0.8501 (ttmm) cc_final: 0.7984 (ttmm) REVERT: B 843 TYR cc_start: 0.8276 (t80) cc_final: 0.7614 (t80) REVERT: B 847 GLU cc_start: 0.7893 (tp30) cc_final: 0.7514 (tp30) REVERT: B 848 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 876 LEU cc_start: 0.8200 (mt) cc_final: 0.7968 (mt) REVERT: B 881 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6772 (mm-30) REVERT: B 889 HIS cc_start: 0.7993 (m90) cc_final: 0.7057 (m90) REVERT: B 907 ASN cc_start: 0.7614 (m-40) cc_final: 0.6509 (m-40) REVERT: B 908 HIS cc_start: 0.7857 (m-70) cc_final: 0.7264 (m-70) REVERT: B 911 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6662 (mp0) REVERT: B 913 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8758 (mt) REVERT: B 915 GLU cc_start: 0.7676 (tt0) cc_final: 0.7272 (tt0) REVERT: B 928 HIS cc_start: 0.7128 (t70) cc_final: 0.6830 (t70) REVERT: B 938 MET cc_start: 0.7807 (tpp) cc_final: 0.7598 (tpp) outliers start: 66 outliers final: 34 residues processed: 495 average time/residue: 0.3251 time to fit residues: 217.4078 Evaluate side-chains 489 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 449 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 913 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 108 optimal weight: 0.0170 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 900 GLN B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 421 ASN B 506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105036 restraints weight = 19821.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108381 restraints weight = 9247.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110453 restraints weight = 5342.402| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10798 Z= 0.145 Angle : 0.582 13.547 14638 Z= 0.299 Chirality : 0.039 0.241 1772 Planarity : 0.004 0.047 1796 Dihedral : 7.181 67.055 1483 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.75 % Allowed : 19.43 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1344 helix: 1.42 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.59 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 523 HIS 0.009 0.001 HIS B 502 PHE 0.021 0.001 PHE A 457 TYR 0.014 0.001 TYR A 392 ARG 0.005 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 909) hydrogen bonds : angle 4.24409 ( 2718) covalent geometry : bond 0.00293 (10798) covalent geometry : angle 0.58164 (14638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 457 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7467 (mmtm) cc_final: 0.7043 (mmtm) REVERT: A 85 CYS cc_start: 0.8344 (m) cc_final: 0.8026 (m) REVERT: A 112 ILE cc_start: 0.8396 (mt) cc_final: 0.8064 (mm) REVERT: A 124 GLU cc_start: 0.7649 (tp30) cc_final: 0.6772 (tp30) REVERT: A 125 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 128 ARG cc_start: 0.7664 (ttp-170) cc_final: 0.7433 (ttp-170) REVERT: A 160 MET cc_start: 0.7749 (mmm) cc_final: 0.7383 (mmt) REVERT: A 186 MET cc_start: 0.6697 (mtp) cc_final: 0.6454 (mtp) REVERT: A 199 MET cc_start: 0.7692 (mmm) cc_final: 0.7311 (mmm) REVERT: A 205 MET cc_start: 0.7602 (mmm) cc_final: 0.7372 (mmm) REVERT: A 217 LEU cc_start: 0.8339 (mt) cc_final: 0.8102 (mt) REVERT: A 237 ASN cc_start: 0.7937 (t0) cc_final: 0.7708 (t0) REVERT: A 257 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7605 (pp) REVERT: A 292 HIS cc_start: 0.8269 (m-70) cc_final: 0.7731 (m-70) REVERT: A 337 GLU cc_start: 0.7310 (mp0) cc_final: 0.6727 (mp0) REVERT: A 387 TYR cc_start: 0.7980 (m-10) cc_final: 0.7674 (m-10) REVERT: A 454 LYS cc_start: 0.8412 (mttm) cc_final: 0.8198 (mttm) REVERT: A 477 LEU cc_start: 0.8589 (tt) cc_final: 0.8267 (tt) REVERT: A 479 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7492 (ttp80) REVERT: A 481 LEU cc_start: 0.8519 (mt) cc_final: 0.8257 (mt) REVERT: A 486 ILE cc_start: 0.8520 (mt) cc_final: 0.8298 (tt) REVERT: A 499 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7160 (ttp80) REVERT: A 502 HIS cc_start: 0.7809 (t-90) cc_final: 0.7333 (t-90) REVERT: A 506 ASN cc_start: 0.7956 (m-40) cc_final: 0.7471 (m-40) REVERT: A 514 SER cc_start: 0.8258 (p) cc_final: 0.8017 (p) REVERT: A 578 MET cc_start: 0.8141 (ttm) cc_final: 0.7896 (ttm) REVERT: A 579 MET cc_start: 0.7897 (mmm) cc_final: 0.7314 (mmm) REVERT: A 585 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7964 (ttt180) REVERT: A 596 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7783 (tmmt) REVERT: A 597 GLN cc_start: 0.7497 (mt0) cc_final: 0.7247 (mt0) REVERT: A 611 LEU cc_start: 0.8295 (tp) cc_final: 0.8055 (tp) REVERT: A 613 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7656 (tm-30) REVERT: A 616 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 622 LYS cc_start: 0.7992 (tttp) cc_final: 0.7629 (tttp) REVERT: A 645 LYS cc_start: 0.8966 (tptp) cc_final: 0.8691 (tptp) REVERT: A 843 TYR cc_start: 0.8611 (t80) cc_final: 0.7867 (t80) REVERT: A 848 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 849 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 862 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8400 (mmtm) REVERT: A 866 GLU cc_start: 0.7229 (tp30) cc_final: 0.6990 (tp30) REVERT: A 868 LYS cc_start: 0.8619 (mmmm) cc_final: 0.7822 (mmmm) REVERT: A 875 ARG cc_start: 0.7697 (tpt90) cc_final: 0.7183 (tpt90) REVERT: A 880 LYS cc_start: 0.8254 (tptp) cc_final: 0.7798 (tptp) REVERT: A 900 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7489 (tp40) REVERT: A 925 MET cc_start: 0.7885 (mmm) cc_final: 0.7572 (mmm) REVERT: A 940 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7504 (ttm-80) REVERT: B 81 ILE cc_start: 0.7932 (mt) cc_final: 0.7637 (mt) REVERT: B 84 SER cc_start: 0.8026 (t) cc_final: 0.7626 (p) REVERT: B 109 LEU cc_start: 0.7949 (mt) cc_final: 0.7637 (mt) REVERT: B 124 GLU cc_start: 0.7513 (tp30) cc_final: 0.7171 (tp30) REVERT: B 140 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7584 (mm110) REVERT: B 149 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6996 (tm-30) REVERT: B 152 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 199 MET cc_start: 0.7599 (tpp) cc_final: 0.7263 (mmm) REVERT: B 233 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 249 MET cc_start: 0.7581 (tmm) cc_final: 0.7056 (tmm) REVERT: B 269 LEU cc_start: 0.8006 (tp) cc_final: 0.7657 (tp) REVERT: B 278 TRP cc_start: 0.8376 (t-100) cc_final: 0.8070 (t-100) REVERT: B 284 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7839 (mmmm) REVERT: B 288 PHE cc_start: 0.7858 (t80) cc_final: 0.7635 (t80) REVERT: B 300 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6916 (mt-10) REVERT: B 320 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6946 (mm-30) REVERT: B 337 GLU cc_start: 0.7681 (mp0) cc_final: 0.7408 (mp0) REVERT: B 361 ASN cc_start: 0.8164 (m-40) cc_final: 0.7950 (m-40) REVERT: B 384 ASP cc_start: 0.7042 (m-30) cc_final: 0.6840 (m-30) REVERT: B 390 ILE cc_start: 0.8483 (mm) cc_final: 0.8275 (mm) REVERT: B 399 ARG cc_start: 0.8554 (ttt90) cc_final: 0.8247 (tpt170) REVERT: B 420 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7480 (mtm-85) REVERT: B 438 LEU cc_start: 0.8147 (mt) cc_final: 0.7817 (mp) REVERT: B 443 GLU cc_start: 0.7685 (tp30) cc_final: 0.7325 (tm-30) REVERT: B 499 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7256 (ptp90) REVERT: B 500 ARG cc_start: 0.7803 (tpt90) cc_final: 0.7423 (tpp80) REVERT: B 512 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8116 (tp) REVERT: B 527 THR cc_start: 0.8064 (p) cc_final: 0.7516 (p) REVERT: B 531 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6123 (mm-30) REVERT: B 579 MET cc_start: 0.7818 (mmm) cc_final: 0.7431 (mmm) REVERT: B 581 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6034 (pp20) REVERT: B 586 MET cc_start: 0.7757 (tmm) cc_final: 0.6122 (tmm) REVERT: B 588 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7838 (ttpp) REVERT: B 590 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6730 (mm-30) REVERT: B 591 LYS cc_start: 0.8131 (mtmp) cc_final: 0.7906 (mtmp) REVERT: B 595 TRP cc_start: 0.8016 (m100) cc_final: 0.7724 (m100) REVERT: B 596 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8222 (mmmt) REVERT: B 613 GLN cc_start: 0.7482 (tm-30) cc_final: 0.6975 (tm-30) REVERT: B 645 LYS cc_start: 0.8531 (tptp) cc_final: 0.8017 (tptp) REVERT: B 825 VAL cc_start: 0.8440 (t) cc_final: 0.8212 (p) REVERT: B 826 ASN cc_start: 0.7905 (t0) cc_final: 0.7511 (m110) REVERT: B 837 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: B 841 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8108 (ttmm) REVERT: B 843 TYR cc_start: 0.8223 (t80) cc_final: 0.7749 (t80) REVERT: B 847 GLU cc_start: 0.7879 (tp30) cc_final: 0.7532 (tp30) REVERT: B 848 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 850 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.8060 (p) REVERT: B 872 GLU cc_start: 0.8169 (tp30) cc_final: 0.7018 (tp30) REVERT: B 876 LEU cc_start: 0.8257 (mt) cc_final: 0.7645 (mt) REVERT: B 881 GLU cc_start: 0.7544 (mm-30) cc_final: 0.6723 (mm-30) REVERT: B 907 ASN cc_start: 0.7653 (m-40) cc_final: 0.6569 (m-40) REVERT: B 908 HIS cc_start: 0.7913 (m-70) cc_final: 0.7479 (m-70) REVERT: B 911 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6693 (mt-10) REVERT: B 913 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8777 (mt) REVERT: B 915 GLU cc_start: 0.7628 (tt0) cc_final: 0.7216 (tt0) REVERT: B 924 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7690 (pp20) REVERT: B 928 HIS cc_start: 0.7116 (t70) cc_final: 0.6819 (t70) outliers start: 66 outliers final: 41 residues processed: 482 average time/residue: 0.2796 time to fit residues: 178.0453 Evaluate side-chains 500 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 450 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 624 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105041 restraints weight = 19915.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108370 restraints weight = 9231.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110436 restraints weight = 5341.631| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10798 Z= 0.156 Angle : 0.566 13.872 14638 Z= 0.296 Chirality : 0.038 0.219 1772 Planarity : 0.004 0.046 1796 Dihedral : 6.795 59.847 1480 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.79 % Allowed : 20.38 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1344 helix: 1.65 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.50 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 523 HIS 0.003 0.000 HIS A 614 PHE 0.016 0.001 PHE A 457 TYR 0.017 0.001 TYR A 392 ARG 0.006 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 909) hydrogen bonds : angle 4.17280 ( 2718) covalent geometry : bond 0.00318 (10798) covalent geometry : angle 0.56585 (14638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 450 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7432 (mmtm) cc_final: 0.7147 (mmtm) REVERT: A 85 CYS cc_start: 0.8346 (m) cc_final: 0.8016 (m) REVERT: A 112 ILE cc_start: 0.8410 (mt) cc_final: 0.8069 (mm) REVERT: A 124 GLU cc_start: 0.7652 (tp30) cc_final: 0.6758 (tp30) REVERT: A 125 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 128 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7463 (ttp-170) REVERT: A 160 MET cc_start: 0.7724 (mmm) cc_final: 0.7337 (mmt) REVERT: A 186 MET cc_start: 0.6568 (mtp) cc_final: 0.6366 (mtp) REVERT: A 205 MET cc_start: 0.7612 (mmm) cc_final: 0.7231 (mmm) REVERT: A 217 LEU cc_start: 0.8345 (mt) cc_final: 0.8104 (mt) REVERT: A 237 ASN cc_start: 0.7954 (t0) cc_final: 0.7719 (t0) REVERT: A 292 HIS cc_start: 0.8224 (m-70) cc_final: 0.7650 (m-70) REVERT: A 319 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6607 (mt) REVERT: A 335 ASN cc_start: 0.8664 (t0) cc_final: 0.8400 (t0) REVERT: A 337 GLU cc_start: 0.7315 (mp0) cc_final: 0.6733 (mp0) REVERT: A 387 TYR cc_start: 0.7973 (m-10) cc_final: 0.7641 (m-10) REVERT: A 431 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8076 (mmt180) REVERT: A 454 LYS cc_start: 0.8432 (mttm) cc_final: 0.8129 (mttm) REVERT: A 477 LEU cc_start: 0.8588 (tt) cc_final: 0.8263 (tt) REVERT: A 479 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7534 (ttp80) REVERT: A 481 LEU cc_start: 0.8527 (mt) cc_final: 0.8252 (mt) REVERT: A 499 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7173 (ttp80) REVERT: A 502 HIS cc_start: 0.7838 (t-90) cc_final: 0.7381 (t-90) REVERT: A 506 ASN cc_start: 0.7981 (m-40) cc_final: 0.7492 (m-40) REVERT: A 514 SER cc_start: 0.8292 (p) cc_final: 0.8058 (p) REVERT: A 578 MET cc_start: 0.8225 (ttm) cc_final: 0.7979 (ttm) REVERT: A 579 MET cc_start: 0.7978 (mmm) cc_final: 0.7400 (mmm) REVERT: A 596 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7793 (tmmt) REVERT: A 597 GLN cc_start: 0.7472 (mt0) cc_final: 0.7235 (mt0) REVERT: A 611 LEU cc_start: 0.8261 (tp) cc_final: 0.7998 (tp) REVERT: A 613 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 645 LYS cc_start: 0.8998 (tptp) cc_final: 0.8354 (tptp) REVERT: A 826 ASN cc_start: 0.7462 (t0) cc_final: 0.7099 (t0) REVERT: A 843 TYR cc_start: 0.8629 (t80) cc_final: 0.7857 (t80) REVERT: A 848 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 849 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 862 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8396 (mmtm) REVERT: A 866 GLU cc_start: 0.7293 (tp30) cc_final: 0.7026 (tp30) REVERT: A 868 LYS cc_start: 0.8599 (mmmm) cc_final: 0.7812 (mmmm) REVERT: A 875 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7470 (tpt90) REVERT: A 880 LYS cc_start: 0.8278 (tptp) cc_final: 0.7829 (tptp) REVERT: A 881 GLU cc_start: 0.7516 (mm-30) cc_final: 0.6922 (tm-30) REVERT: A 900 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: A 925 MET cc_start: 0.7991 (mmm) cc_final: 0.7739 (mmm) REVERT: A 931 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 938 MET cc_start: 0.8514 (mmm) cc_final: 0.8265 (mmm) REVERT: A 940 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7473 (ttm-80) REVERT: B 81 ILE cc_start: 0.7949 (mt) cc_final: 0.7642 (mt) REVERT: B 84 SER cc_start: 0.8031 (t) cc_final: 0.7621 (p) REVERT: B 109 LEU cc_start: 0.7924 (mt) cc_final: 0.7600 (mt) REVERT: B 124 GLU cc_start: 0.7550 (tp30) cc_final: 0.7156 (tp30) REVERT: B 149 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 152 PHE cc_start: 0.8263 (t80) cc_final: 0.7924 (t80) REVERT: B 199 MET cc_start: 0.7549 (tpp) cc_final: 0.7253 (tpp) REVERT: B 233 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7093 (tm-30) REVERT: B 246 ASN cc_start: 0.8151 (m-40) cc_final: 0.7918 (m-40) REVERT: B 249 MET cc_start: 0.7559 (tmm) cc_final: 0.7077 (tmm) REVERT: B 269 LEU cc_start: 0.8001 (tp) cc_final: 0.7680 (tp) REVERT: B 278 TRP cc_start: 0.8391 (t-100) cc_final: 0.8087 (t-100) REVERT: B 300 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6831 (mt-10) REVERT: B 335 ASN cc_start: 0.8272 (t0) cc_final: 0.7995 (t0) REVERT: B 337 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 351 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8083 (tpp-160) REVERT: B 384 ASP cc_start: 0.7105 (m-30) cc_final: 0.6692 (m-30) REVERT: B 390 ILE cc_start: 0.8527 (mm) cc_final: 0.8299 (mm) REVERT: B 399 ARG cc_start: 0.8512 (ttt90) cc_final: 0.8185 (tpt170) REVERT: B 420 ARG cc_start: 0.8045 (mtm180) cc_final: 0.7509 (mtm-85) REVERT: B 443 GLU cc_start: 0.7726 (tp30) cc_final: 0.7143 (tp30) REVERT: B 475 GLN cc_start: 0.7479 (tp40) cc_final: 0.7177 (tp40) REVERT: B 499 ARG cc_start: 0.7580 (ptp90) cc_final: 0.7279 (ptp90) REVERT: B 500 ARG cc_start: 0.7840 (tpt90) cc_final: 0.7491 (tpp80) REVERT: B 527 THR cc_start: 0.8182 (p) cc_final: 0.7485 (p) REVERT: B 531 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6241 (mm-30) REVERT: B 579 MET cc_start: 0.7769 (mmm) cc_final: 0.7320 (mmm) REVERT: B 581 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5981 (pp20) REVERT: B 586 MET cc_start: 0.7758 (tmm) cc_final: 0.6053 (tmm) REVERT: B 588 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7866 (ttpp) REVERT: B 590 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6702 (mm-30) REVERT: B 591 LYS cc_start: 0.8092 (mtmp) cc_final: 0.7881 (mtmp) REVERT: B 595 TRP cc_start: 0.7981 (m100) cc_final: 0.7685 (m100) REVERT: B 596 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8228 (mmmt) REVERT: B 613 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 645 LYS cc_start: 0.8571 (tptp) cc_final: 0.8032 (tptp) REVERT: B 825 VAL cc_start: 0.8499 (t) cc_final: 0.8267 (p) REVERT: B 826 ASN cc_start: 0.7871 (OUTLIER) cc_final: 0.7523 (m110) REVERT: B 837 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: B 841 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8206 (ttmm) REVERT: B 843 TYR cc_start: 0.8168 (t80) cc_final: 0.7836 (t80) REVERT: B 847 GLU cc_start: 0.7855 (tp30) cc_final: 0.7587 (tp30) REVERT: B 848 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 850 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8017 (p) REVERT: B 872 GLU cc_start: 0.7997 (tp30) cc_final: 0.7481 (tp30) REVERT: B 875 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7426 (ttt-90) REVERT: B 876 LEU cc_start: 0.8117 (mt) cc_final: 0.7806 (mt) REVERT: B 881 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 885 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7640 (pp) REVERT: B 907 ASN cc_start: 0.7655 (m-40) cc_final: 0.6597 (m-40) REVERT: B 908 HIS cc_start: 0.7936 (m-70) cc_final: 0.7517 (m-70) REVERT: B 911 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6697 (mt-10) REVERT: B 928 HIS cc_start: 0.7114 (t70) cc_final: 0.6844 (t70) REVERT: B 929 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7283 (mtpp) outliers start: 78 outliers final: 49 residues processed: 480 average time/residue: 0.2718 time to fit residues: 173.1547 Evaluate side-chains 504 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 446 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105414 restraints weight = 19862.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108770 restraints weight = 9225.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110838 restraints weight = 5362.114| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10798 Z= 0.143 Angle : 0.575 14.377 14638 Z= 0.296 Chirality : 0.039 0.225 1772 Planarity : 0.004 0.045 1796 Dihedral : 6.474 58.038 1471 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.45 % Allowed : 21.17 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.23), residues: 1344 helix: 1.81 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.59 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.002 0.000 HIS B 458 PHE 0.013 0.001 PHE A 245 TYR 0.018 0.001 TYR A 392 ARG 0.006 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 909) hydrogen bonds : angle 4.11188 ( 2718) covalent geometry : bond 0.00299 (10798) covalent geometry : angle 0.57525 (14638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 448 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7402 (mmtm) cc_final: 0.7121 (mmtm) REVERT: A 85 CYS cc_start: 0.8326 (m) cc_final: 0.8007 (m) REVERT: A 112 ILE cc_start: 0.8402 (mt) cc_final: 0.8059 (mm) REVERT: A 124 GLU cc_start: 0.7596 (tp30) cc_final: 0.6918 (tp30) REVERT: A 125 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7152 (mt-10) REVERT: A 128 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7469 (ttp-170) REVERT: A 160 MET cc_start: 0.7723 (mmm) cc_final: 0.7335 (mmt) REVERT: A 186 MET cc_start: 0.6575 (mtp) cc_final: 0.6359 (mtp) REVERT: A 199 MET cc_start: 0.7780 (mmm) cc_final: 0.7432 (mmm) REVERT: A 205 MET cc_start: 0.7593 (mmm) cc_final: 0.7368 (mpp) REVERT: A 217 LEU cc_start: 0.8341 (mt) cc_final: 0.8101 (mt) REVERT: A 218 LYS cc_start: 0.7837 (ttmt) cc_final: 0.7497 (ttmt) REVERT: A 237 ASN cc_start: 0.7948 (t0) cc_final: 0.7702 (t0) REVERT: A 292 HIS cc_start: 0.8198 (m-70) cc_final: 0.7604 (m-70) REVERT: A 319 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6540 (mt) REVERT: A 335 ASN cc_start: 0.8658 (t0) cc_final: 0.8391 (t0) REVERT: A 337 GLU cc_start: 0.7290 (mp0) cc_final: 0.6685 (mp0) REVERT: A 387 TYR cc_start: 0.7930 (m-10) cc_final: 0.7620 (m-10) REVERT: A 431 ARG cc_start: 0.8237 (mmt180) cc_final: 0.8009 (mmt180) REVERT: A 454 LYS cc_start: 0.8423 (mttm) cc_final: 0.8116 (mttm) REVERT: A 477 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 479 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7555 (ttp80) REVERT: A 481 LEU cc_start: 0.8511 (mt) cc_final: 0.8236 (mt) REVERT: A 499 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7158 (ttp80) REVERT: A 502 HIS cc_start: 0.7898 (t-90) cc_final: 0.7396 (t-90) REVERT: A 506 ASN cc_start: 0.7978 (m-40) cc_final: 0.7466 (m-40) REVERT: A 578 MET cc_start: 0.8221 (ttm) cc_final: 0.7965 (ttm) REVERT: A 579 MET cc_start: 0.7975 (mmm) cc_final: 0.7404 (mmm) REVERT: A 596 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7774 (tmmt) REVERT: A 597 GLN cc_start: 0.7459 (mt0) cc_final: 0.7207 (mt0) REVERT: A 611 LEU cc_start: 0.8254 (tp) cc_final: 0.7973 (tp) REVERT: A 613 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 622 LYS cc_start: 0.7869 (tttp) cc_final: 0.7515 (tttp) REVERT: A 645 LYS cc_start: 0.8989 (tptp) cc_final: 0.8392 (tptp) REVERT: A 843 TYR cc_start: 0.8639 (t80) cc_final: 0.7919 (t80) REVERT: A 848 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 849 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7963 (mm-30) REVERT: A 852 LYS cc_start: 0.8324 (mttp) cc_final: 0.8036 (tttp) REVERT: A 862 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8390 (mmtm) REVERT: A 866 GLU cc_start: 0.7297 (tp30) cc_final: 0.7001 (tp30) REVERT: A 875 ARG cc_start: 0.7702 (tpt90) cc_final: 0.7388 (tpt90) REVERT: A 880 LYS cc_start: 0.8273 (tptp) cc_final: 0.7821 (tptp) REVERT: A 881 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6935 (tm-30) REVERT: A 900 GLN cc_start: 0.8134 (tm130) cc_final: 0.7924 (tp40) REVERT: A 910 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7762 (ttm-80) REVERT: A 925 MET cc_start: 0.8050 (mmm) cc_final: 0.7767 (mmm) REVERT: A 931 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7329 (mm-30) REVERT: A 938 MET cc_start: 0.8531 (mmm) cc_final: 0.8256 (mmm) REVERT: B 81 ILE cc_start: 0.7923 (mt) cc_final: 0.7640 (mt) REVERT: B 84 SER cc_start: 0.8025 (t) cc_final: 0.7611 (p) REVERT: B 109 LEU cc_start: 0.7928 (mt) cc_final: 0.7614 (mt) REVERT: B 124 GLU cc_start: 0.7503 (tp30) cc_final: 0.7181 (tp30) REVERT: B 149 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7056 (tm-30) REVERT: B 152 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7914 (t80) REVERT: B 246 ASN cc_start: 0.8096 (m-40) cc_final: 0.7883 (m-40) REVERT: B 249 MET cc_start: 0.7532 (tmm) cc_final: 0.7038 (tmm) REVERT: B 269 LEU cc_start: 0.7992 (tp) cc_final: 0.7666 (tp) REVERT: B 278 TRP cc_start: 0.8384 (t-100) cc_final: 0.8065 (t-100) REVERT: B 300 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 337 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 351 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8051 (tpp-160) REVERT: B 361 ASN cc_start: 0.8172 (m-40) cc_final: 0.7674 (m110) REVERT: B 387 TYR cc_start: 0.7852 (m-10) cc_final: 0.7441 (m-10) REVERT: B 390 ILE cc_start: 0.8522 (mm) cc_final: 0.8300 (mm) REVERT: B 399 ARG cc_start: 0.8497 (ttt90) cc_final: 0.8123 (tpt170) REVERT: B 420 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7513 (mtm-85) REVERT: B 443 GLU cc_start: 0.7739 (tp30) cc_final: 0.7164 (tp30) REVERT: B 475 GLN cc_start: 0.7475 (tp40) cc_final: 0.7172 (tp40) REVERT: B 499 ARG cc_start: 0.7593 (ptp90) cc_final: 0.7286 (ptp90) REVERT: B 500 ARG cc_start: 0.7843 (tpt90) cc_final: 0.7469 (tpp80) REVERT: B 512 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8145 (tp) REVERT: B 527 THR cc_start: 0.8184 (p) cc_final: 0.7452 (p) REVERT: B 579 MET cc_start: 0.7765 (mmm) cc_final: 0.7319 (mmm) REVERT: B 581 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6001 (pp20) REVERT: B 586 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6027 (tmm) REVERT: B 588 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7874 (ttpp) REVERT: B 590 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6674 (mm-30) REVERT: B 591 LYS cc_start: 0.8084 (mtmp) cc_final: 0.7874 (mtmp) REVERT: B 595 TRP cc_start: 0.7998 (m100) cc_final: 0.7699 (m100) REVERT: B 613 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 645 LYS cc_start: 0.8568 (tptp) cc_final: 0.8038 (tptp) REVERT: B 825 VAL cc_start: 0.8509 (t) cc_final: 0.8278 (p) REVERT: B 826 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7529 (m110) REVERT: B 837 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7057 (m-80) REVERT: B 841 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8179 (ttmm) REVERT: B 847 GLU cc_start: 0.7837 (tp30) cc_final: 0.7566 (tp30) REVERT: B 848 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7838 (mt-10) REVERT: B 850 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 872 GLU cc_start: 0.7998 (tp30) cc_final: 0.7516 (tp30) REVERT: B 876 LEU cc_start: 0.8119 (mt) cc_final: 0.7810 (mt) REVERT: B 880 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7677 (tmmt) REVERT: B 881 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 885 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7546 (pp) REVERT: B 907 ASN cc_start: 0.7664 (m-40) cc_final: 0.6562 (m110) REVERT: B 908 HIS cc_start: 0.7937 (m-70) cc_final: 0.7524 (m-70) REVERT: B 911 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6695 (mt-10) REVERT: B 916 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8350 (tt) REVERT: B 928 HIS cc_start: 0.7103 (t70) cc_final: 0.6821 (t70) REVERT: B 929 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7250 (mtpp) outliers start: 74 outliers final: 48 residues processed: 471 average time/residue: 0.2816 time to fit residues: 175.1656 Evaluate side-chains 505 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 443 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 626 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 943 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.123712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104739 restraints weight = 19994.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108072 restraints weight = 9271.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110150 restraints weight = 5399.128| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10798 Z= 0.166 Angle : 0.583 14.582 14638 Z= 0.304 Chirality : 0.040 0.261 1772 Planarity : 0.004 0.054 1796 Dihedral : 5.932 59.409 1465 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.36 % Allowed : 22.21 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.23), residues: 1344 helix: 1.79 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.42 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.002 0.000 HIS B 292 PHE 0.013 0.001 PHE A 517 TYR 0.014 0.001 TYR B 837 ARG 0.006 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 909) hydrogen bonds : angle 4.14204 ( 2718) covalent geometry : bond 0.00342 (10798) covalent geometry : angle 0.58306 (14638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 448 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7405 (mmtm) cc_final: 0.7168 (mmtm) REVERT: A 85 CYS cc_start: 0.8358 (m) cc_final: 0.8025 (m) REVERT: A 124 GLU cc_start: 0.7573 (tp30) cc_final: 0.6986 (tp30) REVERT: A 125 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 128 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7468 (ttp-170) REVERT: A 160 MET cc_start: 0.7750 (mmm) cc_final: 0.7369 (mmt) REVERT: A 186 MET cc_start: 0.6595 (mtp) cc_final: 0.6367 (mtp) REVERT: A 199 MET cc_start: 0.7718 (mmm) cc_final: 0.7356 (mmm) REVERT: A 205 MET cc_start: 0.7597 (mmm) cc_final: 0.7369 (mpp) REVERT: A 217 LEU cc_start: 0.8357 (mt) cc_final: 0.8103 (mt) REVERT: A 218 LYS cc_start: 0.7877 (ttmt) cc_final: 0.7529 (ttmt) REVERT: A 237 ASN cc_start: 0.7936 (t0) cc_final: 0.7708 (t0) REVERT: A 250 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7466 (mtmm) REVERT: A 292 HIS cc_start: 0.8224 (m-70) cc_final: 0.7679 (m-70) REVERT: A 319 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6577 (mt) REVERT: A 335 ASN cc_start: 0.8662 (t0) cc_final: 0.8398 (t0) REVERT: A 337 GLU cc_start: 0.7304 (mp0) cc_final: 0.6701 (mp0) REVERT: A 387 TYR cc_start: 0.7933 (m-10) cc_final: 0.7554 (m-10) REVERT: A 431 ARG cc_start: 0.8272 (mmt180) cc_final: 0.8056 (mmt180) REVERT: A 454 LYS cc_start: 0.8381 (mttm) cc_final: 0.8094 (mttm) REVERT: A 477 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8244 (tt) REVERT: A 479 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7559 (ttp80) REVERT: A 481 LEU cc_start: 0.8563 (mt) cc_final: 0.8296 (mt) REVERT: A 491 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7465 (ttm110) REVERT: A 499 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7107 (ttp80) REVERT: A 502 HIS cc_start: 0.7852 (t-90) cc_final: 0.7355 (t-90) REVERT: A 506 ASN cc_start: 0.7961 (m-40) cc_final: 0.7452 (m-40) REVERT: A 512 LEU cc_start: 0.8605 (tp) cc_final: 0.8237 (tt) REVERT: A 578 MET cc_start: 0.8151 (ttm) cc_final: 0.7926 (ttm) REVERT: A 579 MET cc_start: 0.7947 (mmm) cc_final: 0.7390 (mmm) REVERT: A 596 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7710 (tmmt) REVERT: A 597 GLN cc_start: 0.7459 (mt0) cc_final: 0.7194 (mt0) REVERT: A 611 LEU cc_start: 0.8260 (tp) cc_final: 0.7974 (tp) REVERT: A 613 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7636 (tm-30) REVERT: A 645 LYS cc_start: 0.8965 (tptp) cc_final: 0.8361 (tptp) REVERT: A 843 TYR cc_start: 0.8640 (t80) cc_final: 0.7950 (t80) REVERT: A 848 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 849 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 852 LYS cc_start: 0.8296 (mttp) cc_final: 0.8031 (tttp) REVERT: A 862 LYS cc_start: 0.8678 (mmtm) cc_final: 0.8430 (mmtm) REVERT: A 866 GLU cc_start: 0.7271 (tp30) cc_final: 0.6984 (tp30) REVERT: A 875 ARG cc_start: 0.7710 (tpt90) cc_final: 0.7418 (tpt90) REVERT: A 880 LYS cc_start: 0.8289 (tptp) cc_final: 0.7832 (tptp) REVERT: A 881 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6947 (tm-30) REVERT: A 900 GLN cc_start: 0.8196 (tm130) cc_final: 0.7969 (tp40) REVERT: A 925 MET cc_start: 0.8039 (mmm) cc_final: 0.7801 (mmm) REVERT: A 931 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7487 (mm-30) REVERT: A 938 MET cc_start: 0.8519 (mmm) cc_final: 0.8226 (mmm) REVERT: B 81 ILE cc_start: 0.7937 (mt) cc_final: 0.7635 (mt) REVERT: B 84 SER cc_start: 0.8040 (t) cc_final: 0.7608 (p) REVERT: B 109 LEU cc_start: 0.7947 (mt) cc_final: 0.7683 (mt) REVERT: B 120 VAL cc_start: 0.8498 (t) cc_final: 0.8083 (p) REVERT: B 149 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7058 (tm-30) REVERT: B 188 LEU cc_start: 0.8117 (tp) cc_final: 0.7398 (tt) REVERT: B 199 MET cc_start: 0.7740 (mmm) cc_final: 0.7019 (tpt) REVERT: B 246 ASN cc_start: 0.8108 (m-40) cc_final: 0.7884 (m-40) REVERT: B 269 LEU cc_start: 0.8021 (tp) cc_final: 0.7700 (tp) REVERT: B 278 TRP cc_start: 0.8401 (t-100) cc_final: 0.8091 (t-100) REVERT: B 300 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6959 (mt-10) REVERT: B 337 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: B 351 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8084 (tpp-160) REVERT: B 366 MET cc_start: 0.8141 (tpp) cc_final: 0.7843 (tpp) REVERT: B 384 ASP cc_start: 0.7079 (m-30) cc_final: 0.6827 (m-30) REVERT: B 387 TYR cc_start: 0.7884 (m-10) cc_final: 0.7412 (m-10) REVERT: B 420 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7501 (mtm-85) REVERT: B 425 MET cc_start: 0.7721 (ttm) cc_final: 0.7517 (ttt) REVERT: B 443 GLU cc_start: 0.7728 (tp30) cc_final: 0.7110 (tp30) REVERT: B 475 GLN cc_start: 0.7475 (tp40) cc_final: 0.7185 (tp40) REVERT: B 499 ARG cc_start: 0.7615 (ptp90) cc_final: 0.7281 (ptp90) REVERT: B 500 ARG cc_start: 0.7849 (tpt90) cc_final: 0.7495 (tpp80) REVERT: B 512 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 527 THR cc_start: 0.8045 (p) cc_final: 0.7524 (p) REVERT: B 531 GLU cc_start: 0.6380 (mm-30) cc_final: 0.6023 (mm-30) REVERT: B 579 MET cc_start: 0.7755 (mmm) cc_final: 0.7380 (mmm) REVERT: B 581 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5908 (pp20) REVERT: B 586 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6049 (tmm) REVERT: B 588 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7980 (ttpp) REVERT: B 590 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 595 TRP cc_start: 0.8034 (m100) cc_final: 0.7724 (m100) REVERT: B 613 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 645 LYS cc_start: 0.8558 (tptp) cc_final: 0.8002 (tptp) REVERT: B 825 VAL cc_start: 0.8510 (t) cc_final: 0.8272 (p) REVERT: B 826 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7528 (m110) REVERT: B 837 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: B 847 GLU cc_start: 0.7765 (tp30) cc_final: 0.7490 (tp30) REVERT: B 848 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 850 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7950 (p) REVERT: B 872 GLU cc_start: 0.7944 (tp30) cc_final: 0.7577 (tp30) REVERT: B 876 LEU cc_start: 0.8090 (mt) cc_final: 0.7821 (mt) REVERT: B 880 LYS cc_start: 0.8048 (tmmt) cc_final: 0.7708 (tmmt) REVERT: B 881 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 885 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7537 (pp) REVERT: B 904 THR cc_start: 0.7791 (p) cc_final: 0.7376 (t) REVERT: B 907 ASN cc_start: 0.7659 (m-40) cc_final: 0.6558 (m110) REVERT: B 908 HIS cc_start: 0.7932 (m-70) cc_final: 0.7551 (m-70) REVERT: B 911 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6716 (mt-10) REVERT: B 928 HIS cc_start: 0.7114 (t70) cc_final: 0.6800 (t70) outliers start: 73 outliers final: 53 residues processed: 475 average time/residue: 0.2847 time to fit residues: 178.7908 Evaluate side-chains 503 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 439 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 82 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105112 restraints weight = 20215.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108488 restraints weight = 9366.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.110582 restraints weight = 5420.854| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10798 Z= 0.150 Angle : 0.577 14.279 14638 Z= 0.299 Chirality : 0.040 0.219 1772 Planarity : 0.004 0.048 1796 Dihedral : 5.906 58.401 1465 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 6.62 % Allowed : 23.08 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.23), residues: 1344 helix: 1.86 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.44 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.005 0.000 HIS B 889 PHE 0.022 0.001 PHE B 288 TYR 0.013 0.001 TYR A 313 ARG 0.011 0.000 ARG A 910 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 909) hydrogen bonds : angle 4.09952 ( 2718) covalent geometry : bond 0.00311 (10798) covalent geometry : angle 0.57722 (14638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 445 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7382 (mmtm) cc_final: 0.7160 (mmtm) REVERT: A 85 CYS cc_start: 0.8332 (m) cc_final: 0.7926 (m) REVERT: A 103 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7872 (p) REVERT: A 124 GLU cc_start: 0.7551 (tp30) cc_final: 0.6659 (tp30) REVERT: A 125 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 128 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7418 (ttp-170) REVERT: A 160 MET cc_start: 0.7765 (mmm) cc_final: 0.7368 (mmt) REVERT: A 186 MET cc_start: 0.6557 (mtp) cc_final: 0.6341 (mtp) REVERT: A 205 MET cc_start: 0.7593 (mmm) cc_final: 0.7137 (mpp) REVERT: A 217 LEU cc_start: 0.8328 (mt) cc_final: 0.8088 (mt) REVERT: A 218 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7487 (ttmt) REVERT: A 237 ASN cc_start: 0.7930 (t0) cc_final: 0.7698 (t0) REVERT: A 250 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7411 (mtmm) REVERT: A 292 HIS cc_start: 0.8204 (m-70) cc_final: 0.7633 (m-70) REVERT: A 319 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6589 (mt) REVERT: A 322 SER cc_start: 0.8114 (t) cc_final: 0.7743 (p) REVERT: A 335 ASN cc_start: 0.8666 (t0) cc_final: 0.8371 (t0) REVERT: A 337 GLU cc_start: 0.7288 (mp0) cc_final: 0.6674 (mp0) REVERT: A 346 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6695 (mt-10) REVERT: A 387 TYR cc_start: 0.7878 (m-10) cc_final: 0.7650 (m-10) REVERT: A 431 ARG cc_start: 0.8235 (mmt180) cc_final: 0.8017 (mmt180) REVERT: A 454 LYS cc_start: 0.8369 (mttm) cc_final: 0.8085 (mttm) REVERT: A 477 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8232 (tt) REVERT: A 479 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7549 (ttp80) REVERT: A 481 LEU cc_start: 0.8535 (mt) cc_final: 0.8263 (mt) REVERT: A 499 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7180 (ttp80) REVERT: A 506 ASN cc_start: 0.7980 (m-40) cc_final: 0.7539 (m-40) REVERT: A 512 LEU cc_start: 0.8543 (tp) cc_final: 0.8185 (tt) REVERT: A 578 MET cc_start: 0.8150 (ttm) cc_final: 0.7919 (ttm) REVERT: A 579 MET cc_start: 0.7951 (mmm) cc_final: 0.7389 (mmm) REVERT: A 596 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7769 (tmmt) REVERT: A 597 GLN cc_start: 0.7448 (mt0) cc_final: 0.7184 (mt0) REVERT: A 611 LEU cc_start: 0.8261 (tp) cc_final: 0.7973 (tp) REVERT: A 613 GLN cc_start: 0.7886 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 622 LYS cc_start: 0.7857 (tttp) cc_final: 0.7526 (tttp) REVERT: A 645 LYS cc_start: 0.8962 (tptp) cc_final: 0.8347 (tptp) REVERT: A 843 TYR cc_start: 0.8643 (t80) cc_final: 0.7936 (t80) REVERT: A 848 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 849 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 852 LYS cc_start: 0.8244 (mttp) cc_final: 0.8008 (tttp) REVERT: A 862 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8363 (mmtm) REVERT: A 866 GLU cc_start: 0.7249 (tp30) cc_final: 0.6964 (tp30) REVERT: A 875 ARG cc_start: 0.7664 (tpt90) cc_final: 0.7391 (tpt90) REVERT: A 880 LYS cc_start: 0.8302 (tptp) cc_final: 0.7823 (tptp) REVERT: A 881 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6957 (tm-30) REVERT: A 923 ASP cc_start: 0.7777 (p0) cc_final: 0.7249 (p0) REVERT: A 931 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7489 (mm-30) REVERT: A 938 MET cc_start: 0.8504 (mmm) cc_final: 0.8276 (mmm) REVERT: B 81 ILE cc_start: 0.7928 (mt) cc_final: 0.7638 (mt) REVERT: B 84 SER cc_start: 0.8030 (t) cc_final: 0.7597 (p) REVERT: B 109 LEU cc_start: 0.7941 (mt) cc_final: 0.7690 (mt) REVERT: B 149 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7059 (tm-30) REVERT: B 188 LEU cc_start: 0.8085 (tp) cc_final: 0.7332 (tt) REVERT: B 199 MET cc_start: 0.7615 (mmm) cc_final: 0.6975 (tpt) REVERT: B 246 ASN cc_start: 0.8079 (m-40) cc_final: 0.7853 (m-40) REVERT: B 269 LEU cc_start: 0.8031 (tp) cc_final: 0.7713 (tp) REVERT: B 278 TRP cc_start: 0.8395 (t-100) cc_final: 0.8079 (t-100) REVERT: B 300 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6923 (mt-10) REVERT: B 320 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 337 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 351 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8278 (tpp-160) REVERT: B 361 ASN cc_start: 0.8199 (m-40) cc_final: 0.7716 (m110) REVERT: B 366 MET cc_start: 0.8147 (tpp) cc_final: 0.7854 (tpp) REVERT: B 387 TYR cc_start: 0.7895 (m-10) cc_final: 0.7428 (m-10) REVERT: B 420 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7463 (mtm-85) REVERT: B 443 GLU cc_start: 0.7726 (tp30) cc_final: 0.7421 (tm-30) REVERT: B 444 ASN cc_start: 0.8171 (t0) cc_final: 0.7921 (t0) REVERT: B 475 GLN cc_start: 0.7478 (tp40) cc_final: 0.7188 (tp40) REVERT: B 499 ARG cc_start: 0.7605 (ptp90) cc_final: 0.7267 (ptp90) REVERT: B 500 ARG cc_start: 0.7841 (tpt90) cc_final: 0.7480 (tpp80) REVERT: B 509 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 512 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 523 TRP cc_start: 0.7616 (m100) cc_final: 0.6930 (m100) REVERT: B 527 THR cc_start: 0.8071 (p) cc_final: 0.7442 (p) REVERT: B 531 GLU cc_start: 0.6318 (mm-30) cc_final: 0.5882 (mm-30) REVERT: B 579 MET cc_start: 0.7753 (mmm) cc_final: 0.7392 (mmm) REVERT: B 581 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5884 (pp20) REVERT: B 586 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6089 (tmm) REVERT: B 588 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7984 (ttpp) REVERT: B 590 GLU cc_start: 0.7703 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 595 TRP cc_start: 0.8045 (m100) cc_final: 0.7728 (m100) REVERT: B 596 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8298 (mmmt) REVERT: B 613 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7186 (tm-30) REVERT: B 645 LYS cc_start: 0.8508 (tptp) cc_final: 0.7995 (tptp) REVERT: B 825 VAL cc_start: 0.8484 (t) cc_final: 0.8254 (p) REVERT: B 826 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7550 (m110) REVERT: B 837 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7080 (m-80) REVERT: B 841 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8100 (ttmm) REVERT: B 847 GLU cc_start: 0.7742 (tp30) cc_final: 0.7472 (tp30) REVERT: B 848 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7817 (mt-10) REVERT: B 850 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 872 GLU cc_start: 0.7955 (tp30) cc_final: 0.7206 (tp30) REVERT: B 876 LEU cc_start: 0.8082 (mt) cc_final: 0.7567 (mt) REVERT: B 881 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7299 (mm-30) REVERT: B 885 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.7662 (pp) REVERT: B 904 THR cc_start: 0.7781 (p) cc_final: 0.7380 (t) REVERT: B 907 ASN cc_start: 0.7653 (m-40) cc_final: 0.6580 (m110) REVERT: B 908 HIS cc_start: 0.7924 (m-70) cc_final: 0.7549 (m-70) REVERT: B 911 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6716 (mt-10) REVERT: B 924 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7649 (pp20) REVERT: B 928 HIS cc_start: 0.7108 (t70) cc_final: 0.6804 (t70) REVERT: B 929 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7260 (mtpp) outliers start: 76 outliers final: 52 residues processed: 474 average time/residue: 0.2762 time to fit residues: 172.4596 Evaluate side-chains 509 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 444 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 54 optimal weight: 0.0060 chunk 93 optimal weight: 0.5980 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.111016 restraints weight = 19992.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114438 restraints weight = 9275.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116557 restraints weight = 5349.017| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10798 Z= 0.129 Angle : 0.583 14.827 14638 Z= 0.298 Chirality : 0.039 0.214 1772 Planarity : 0.004 0.044 1796 Dihedral : 5.879 56.204 1465 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 7.14 % Allowed : 22.74 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1344 helix: 1.97 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.58 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 635 HIS 0.002 0.000 HIS B 292 PHE 0.012 0.001 PHE A 455 TYR 0.013 0.001 TYR A 313 ARG 0.008 0.001 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 909) hydrogen bonds : angle 4.03440 ( 2718) covalent geometry : bond 0.00275 (10798) covalent geometry : angle 0.58304 (14638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 445 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.7366 (mmtm) cc_final: 0.7148 (mmtm) REVERT: A 85 CYS cc_start: 0.8305 (m) cc_final: 0.7900 (m) REVERT: A 112 ILE cc_start: 0.8398 (mt) cc_final: 0.8063 (mm) REVERT: A 124 GLU cc_start: 0.7506 (tp30) cc_final: 0.6600 (tp30) REVERT: A 125 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7020 (mt-10) REVERT: A 128 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: A 147 ILE cc_start: 0.8126 (mp) cc_final: 0.7713 (mt) REVERT: A 160 MET cc_start: 0.7727 (mmm) cc_final: 0.7335 (mmt) REVERT: A 186 MET cc_start: 0.6552 (mtp) cc_final: 0.6326 (mtp) REVERT: A 199 MET cc_start: 0.7881 (mmm) cc_final: 0.7647 (mmm) REVERT: A 205 MET cc_start: 0.7544 (mmm) cc_final: 0.7071 (mpp) REVERT: A 217 LEU cc_start: 0.8371 (mt) cc_final: 0.8120 (mt) REVERT: A 218 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7529 (ttmt) REVERT: A 237 ASN cc_start: 0.7889 (t0) cc_final: 0.7652 (t0) REVERT: A 250 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7336 (mtmm) REVERT: A 292 HIS cc_start: 0.8179 (m-70) cc_final: 0.7561 (m-70) REVERT: A 322 SER cc_start: 0.8091 (t) cc_final: 0.7719 (p) REVERT: A 335 ASN cc_start: 0.8647 (t0) cc_final: 0.8367 (t0) REVERT: A 337 GLU cc_start: 0.7272 (mp0) cc_final: 0.6612 (mp0) REVERT: A 387 TYR cc_start: 0.7842 (m-10) cc_final: 0.7605 (m-10) REVERT: A 398 ILE cc_start: 0.8492 (mm) cc_final: 0.8166 (tt) REVERT: A 431 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7939 (mmt180) REVERT: A 454 LYS cc_start: 0.8359 (mttm) cc_final: 0.8080 (mttm) REVERT: A 476 THR cc_start: 0.8329 (m) cc_final: 0.7712 (p) REVERT: A 477 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 479 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7558 (ttp80) REVERT: A 481 LEU cc_start: 0.8502 (mt) cc_final: 0.8247 (mt) REVERT: A 499 ARG cc_start: 0.7761 (ttp80) cc_final: 0.7160 (ttp80) REVERT: A 506 ASN cc_start: 0.7988 (m-40) cc_final: 0.7577 (m-40) REVERT: A 512 LEU cc_start: 0.8496 (tp) cc_final: 0.8125 (tt) REVERT: A 578 MET cc_start: 0.8033 (ttm) cc_final: 0.7821 (ttm) REVERT: A 579 MET cc_start: 0.7819 (mmm) cc_final: 0.7306 (mmm) REVERT: A 596 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7748 (tmmt) REVERT: A 597 GLN cc_start: 0.7457 (mt0) cc_final: 0.7194 (mt0) REVERT: A 611 LEU cc_start: 0.8260 (tp) cc_final: 0.7956 (tp) REVERT: A 613 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 622 LYS cc_start: 0.7862 (tttp) cc_final: 0.7476 (tttp) REVERT: A 645 LYS cc_start: 0.8939 (tptp) cc_final: 0.8317 (tptp) REVERT: A 837 TYR cc_start: 0.8244 (t80) cc_final: 0.7888 (t80) REVERT: A 843 TYR cc_start: 0.8637 (t80) cc_final: 0.8011 (t80) REVERT: A 848 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 852 LYS cc_start: 0.8212 (mttp) cc_final: 0.7989 (tttp) REVERT: A 862 LYS cc_start: 0.8530 (mmtm) cc_final: 0.8287 (mmtm) REVERT: A 866 GLU cc_start: 0.7040 (tp30) cc_final: 0.6832 (tp30) REVERT: A 867 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9015 (mm) REVERT: A 868 LYS cc_start: 0.8545 (mmmm) cc_final: 0.7727 (mmmm) REVERT: A 880 LYS cc_start: 0.8262 (tptp) cc_final: 0.7775 (tptp) REVERT: A 881 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6963 (tm-30) REVERT: A 923 ASP cc_start: 0.7697 (p0) cc_final: 0.7329 (p0) REVERT: A 931 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 938 MET cc_start: 0.8535 (mmm) cc_final: 0.8299 (mmm) REVERT: A 940 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7681 (tpp80) REVERT: B 81 ILE cc_start: 0.7915 (mt) cc_final: 0.7632 (mt) REVERT: B 84 SER cc_start: 0.8006 (t) cc_final: 0.7588 (p) REVERT: B 149 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7052 (tm-30) REVERT: B 199 MET cc_start: 0.7570 (mmm) cc_final: 0.6957 (tpt) REVERT: B 246 ASN cc_start: 0.8048 (m-40) cc_final: 0.7765 (m-40) REVERT: B 249 MET cc_start: 0.7435 (ttp) cc_final: 0.7056 (tmm) REVERT: B 269 LEU cc_start: 0.7964 (tp) cc_final: 0.7687 (tp) REVERT: B 278 TRP cc_start: 0.8378 (t-100) cc_final: 0.8058 (t-100) REVERT: B 300 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6927 (mt-10) REVERT: B 337 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 351 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8056 (tpp-160) REVERT: B 366 MET cc_start: 0.8142 (tpp) cc_final: 0.7505 (tpp) REVERT: B 384 ASP cc_start: 0.7227 (m-30) cc_final: 0.6894 (m-30) REVERT: B 387 TYR cc_start: 0.7844 (m-10) cc_final: 0.7441 (m-10) REVERT: B 420 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7523 (mtm-85) REVERT: B 443 GLU cc_start: 0.7713 (tp30) cc_final: 0.7094 (tp30) REVERT: B 475 GLN cc_start: 0.7467 (tp40) cc_final: 0.7197 (tp40) REVERT: B 499 ARG cc_start: 0.7540 (ptp90) cc_final: 0.7199 (ptp90) REVERT: B 500 ARG cc_start: 0.7783 (tpt90) cc_final: 0.7410 (tpp80) REVERT: B 509 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8219 (mm) REVERT: B 512 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8187 (tp) REVERT: B 517 PHE cc_start: 0.7520 (m-10) cc_final: 0.7213 (m-80) REVERT: B 523 TRP cc_start: 0.7632 (m100) cc_final: 0.6944 (m100) REVERT: B 527 THR cc_start: 0.8039 (p) cc_final: 0.7338 (p) REVERT: B 531 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5976 (mm-30) REVERT: B 579 MET cc_start: 0.7706 (mmm) cc_final: 0.7409 (mmm) REVERT: B 581 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5839 (pp20) REVERT: B 586 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.6259 (tmm) REVERT: B 588 LYS cc_start: 0.8276 (ttpp) cc_final: 0.7959 (ttpp) REVERT: B 590 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 595 TRP cc_start: 0.8018 (m100) cc_final: 0.7703 (m100) REVERT: B 596 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8282 (mmmt) REVERT: B 600 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6300 (m-70) REVERT: B 613 GLN cc_start: 0.7561 (tm-30) cc_final: 0.7110 (tm-30) REVERT: B 645 LYS cc_start: 0.8455 (tptp) cc_final: 0.7968 (tptp) REVERT: B 825 VAL cc_start: 0.8490 (t) cc_final: 0.8254 (p) REVERT: B 826 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7610 (m110) REVERT: B 837 TYR cc_start: 0.8397 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: B 841 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8233 (ttmm) REVERT: B 847 GLU cc_start: 0.7694 (tp30) cc_final: 0.7462 (tp30) REVERT: B 848 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 850 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 872 GLU cc_start: 0.7918 (tp30) cc_final: 0.7564 (tp30) REVERT: B 881 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7186 (mm-30) REVERT: B 903 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6395 (mtm180) REVERT: B 904 THR cc_start: 0.7783 (p) cc_final: 0.7363 (t) REVERT: B 907 ASN cc_start: 0.7637 (m-40) cc_final: 0.6583 (m110) REVERT: B 908 HIS cc_start: 0.7929 (m-70) cc_final: 0.7540 (m-70) REVERT: B 911 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6688 (mt-10) REVERT: B 916 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 928 HIS cc_start: 0.7129 (t70) cc_final: 0.6798 (t70) REVERT: B 929 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7184 (mtpp) REVERT: B 941 LEU cc_start: 0.8619 (tt) cc_final: 0.8408 (tp) outliers start: 82 outliers final: 53 residues processed: 471 average time/residue: 0.2833 time to fit residues: 176.2518 Evaluate side-chains 509 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 441 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107112 restraints weight = 20190.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110486 restraints weight = 9435.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112599 restraints weight = 5444.225| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10798 Z= 0.193 Angle : 0.628 14.834 14638 Z= 0.325 Chirality : 0.041 0.249 1772 Planarity : 0.005 0.119 1796 Dihedral : 5.971 59.660 1465 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.36 % Allowed : 23.87 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.23), residues: 1344 helix: 1.85 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.51 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 635 HIS 0.006 0.001 HIS A 157 PHE 0.027 0.001 PHE B 288 TYR 0.016 0.001 TYR B 837 ARG 0.009 0.001 ARG A 609 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 909) hydrogen bonds : angle 4.16608 ( 2718) covalent geometry : bond 0.00399 (10798) covalent geometry : angle 0.62819 (14638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 445 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8372 (m) cc_final: 0.8044 (m) REVERT: A 103 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 124 GLU cc_start: 0.7541 (tp30) cc_final: 0.6633 (tp30) REVERT: A 125 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 147 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7813 (mt) REVERT: A 160 MET cc_start: 0.7662 (mmm) cc_final: 0.7295 (mmt) REVERT: A 186 MET cc_start: 0.6603 (mtp) cc_final: 0.6400 (mtp) REVERT: A 194 ASN cc_start: 0.8502 (p0) cc_final: 0.8241 (p0) REVERT: A 197 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7148 (mt-10) REVERT: A 205 MET cc_start: 0.7581 (mmm) cc_final: 0.7124 (mpp) REVERT: A 217 LEU cc_start: 0.8379 (mt) cc_final: 0.8139 (mt) REVERT: A 218 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7511 (ttmt) REVERT: A 237 ASN cc_start: 0.7945 (t0) cc_final: 0.7707 (t0) REVERT: A 250 LYS cc_start: 0.8187 (mtmm) cc_final: 0.7408 (mtmm) REVERT: A 292 HIS cc_start: 0.8255 (m-70) cc_final: 0.7684 (m-70) REVERT: A 319 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6687 (mt) REVERT: A 322 SER cc_start: 0.8134 (t) cc_final: 0.7744 (p) REVERT: A 335 ASN cc_start: 0.8630 (t0) cc_final: 0.8355 (t0) REVERT: A 337 GLU cc_start: 0.7270 (mp0) cc_final: 0.6679 (mp0) REVERT: A 346 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 387 TYR cc_start: 0.7889 (m-10) cc_final: 0.7663 (m-10) REVERT: A 401 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6636 (mtm) REVERT: A 431 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8081 (mmt180) REVERT: A 454 LYS cc_start: 0.8378 (mttm) cc_final: 0.8128 (mttm) REVERT: A 477 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (tt) REVERT: A 479 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7573 (ttp80) REVERT: A 481 LEU cc_start: 0.8587 (mt) cc_final: 0.8301 (mt) REVERT: A 499 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7150 (ttp80) REVERT: A 506 ASN cc_start: 0.7996 (m-40) cc_final: 0.7609 (m-40) REVERT: A 512 LEU cc_start: 0.8549 (tp) cc_final: 0.8176 (tt) REVERT: A 579 MET cc_start: 0.7827 (mmm) cc_final: 0.7321 (mmm) REVERT: A 596 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7776 (tmmt) REVERT: A 597 GLN cc_start: 0.7475 (mt0) cc_final: 0.7217 (mt0) REVERT: A 613 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 645 LYS cc_start: 0.8939 (tptp) cc_final: 0.8326 (tptp) REVERT: A 843 TYR cc_start: 0.8650 (t80) cc_final: 0.7952 (t80) REVERT: A 848 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 849 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 852 LYS cc_start: 0.8269 (mttp) cc_final: 0.8025 (tttp) REVERT: A 862 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8315 (mmtm) REVERT: A 866 GLU cc_start: 0.7087 (tp30) cc_final: 0.6886 (tp30) REVERT: A 867 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9033 (mm) REVERT: A 868 LYS cc_start: 0.8615 (mmmm) cc_final: 0.7792 (mmmm) REVERT: A 875 ARG cc_start: 0.7711 (tpt90) cc_final: 0.7324 (tpt170) REVERT: A 880 LYS cc_start: 0.8280 (tptp) cc_final: 0.7824 (tptp) REVERT: A 881 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6994 (tm-30) REVERT: A 923 ASP cc_start: 0.7672 (p0) cc_final: 0.7375 (p0) REVERT: A 931 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 938 MET cc_start: 0.8547 (mmm) cc_final: 0.8272 (mmm) REVERT: A 940 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7721 (tpp80) REVERT: B 109 LEU cc_start: 0.7928 (mt) cc_final: 0.7689 (mt) REVERT: B 120 VAL cc_start: 0.8532 (t) cc_final: 0.8149 (p) REVERT: B 128 ARG cc_start: 0.7858 (ttp-170) cc_final: 0.7632 (ttp-110) REVERT: B 149 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7081 (tm-30) REVERT: B 188 LEU cc_start: 0.8076 (tp) cc_final: 0.7406 (tt) REVERT: B 199 MET cc_start: 0.7679 (mmm) cc_final: 0.7031 (tpt) REVERT: B 246 ASN cc_start: 0.8098 (m-40) cc_final: 0.7806 (m-40) REVERT: B 249 MET cc_start: 0.7492 (ttp) cc_final: 0.7291 (ttp) REVERT: B 269 LEU cc_start: 0.8013 (tp) cc_final: 0.7730 (tp) REVERT: B 278 TRP cc_start: 0.8423 (t-100) cc_final: 0.8139 (t-100) REVERT: B 300 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6957 (mt-10) REVERT: B 337 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: B 351 ARG cc_start: 0.8503 (ttm-80) cc_final: 0.8059 (tpp-160) REVERT: B 387 TYR cc_start: 0.7910 (m-10) cc_final: 0.7451 (m-10) REVERT: B 420 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7495 (mtm-85) REVERT: B 443 GLU cc_start: 0.7722 (tp30) cc_final: 0.7102 (tp30) REVERT: B 475 GLN cc_start: 0.7472 (tp40) cc_final: 0.7206 (tp40) REVERT: B 499 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7272 (ptp90) REVERT: B 500 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7471 (tpt90) REVERT: B 512 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8149 (tp) REVERT: B 523 TRP cc_start: 0.7694 (m100) cc_final: 0.7011 (m100) REVERT: B 527 THR cc_start: 0.8116 (p) cc_final: 0.7322 (p) REVERT: B 531 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5920 (mm-30) REVERT: B 579 MET cc_start: 0.7668 (mmm) cc_final: 0.7404 (mmm) REVERT: B 586 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6272 (tmm) REVERT: B 588 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7953 (ttpp) REVERT: B 590 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7106 (mm-30) REVERT: B 595 TRP cc_start: 0.7987 (m100) cc_final: 0.7660 (m100) REVERT: B 596 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8286 (mmmt) REVERT: B 600 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6272 (m-70) REVERT: B 613 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7175 (tm-30) REVERT: B 645 LYS cc_start: 0.8438 (tptp) cc_final: 0.7960 (tptp) REVERT: B 825 VAL cc_start: 0.8492 (t) cc_final: 0.8262 (p) REVERT: B 826 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7586 (m110) REVERT: B 837 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6903 (m-80) REVERT: B 847 GLU cc_start: 0.7710 (tp30) cc_final: 0.7451 (tp30) REVERT: B 848 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7631 (mt-10) REVERT: B 881 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7092 (mm-30) REVERT: B 903 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6253 (mtp-110) REVERT: B 904 THR cc_start: 0.7836 (p) cc_final: 0.7432 (t) REVERT: B 907 ASN cc_start: 0.7657 (m-40) cc_final: 0.7057 (m110) REVERT: B 911 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6858 (mt-10) REVERT: B 928 HIS cc_start: 0.7172 (t70) cc_final: 0.6825 (t70) REVERT: B 929 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7321 (mtpp) outliers start: 73 outliers final: 52 residues processed: 470 average time/residue: 0.2831 time to fit residues: 175.3130 Evaluate side-chains 506 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 439 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 421 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.128000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109494 restraints weight = 19961.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112898 restraints weight = 9299.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115044 restraints weight = 5361.287| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10798 Z= 0.135 Angle : 0.620 14.608 14638 Z= 0.314 Chirality : 0.040 0.241 1772 Planarity : 0.004 0.042 1796 Dihedral : 5.890 56.811 1465 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.40 % Allowed : 25.00 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.23), residues: 1344 helix: 1.97 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.67 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 635 HIS 0.003 0.000 HIS A 157 PHE 0.011 0.001 PHE A 455 TYR 0.013 0.001 TYR A 313 ARG 0.007 0.001 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 909) hydrogen bonds : angle 4.08423 ( 2718) covalent geometry : bond 0.00287 (10798) covalent geometry : angle 0.61970 (14638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 442 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8300 (m) cc_final: 0.7928 (m) REVERT: A 124 GLU cc_start: 0.7471 (tp30) cc_final: 0.6544 (tp30) REVERT: A 125 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 160 MET cc_start: 0.7616 (mmm) cc_final: 0.7275 (mmt) REVERT: A 186 MET cc_start: 0.6578 (mtp) cc_final: 0.6356 (mtp) REVERT: A 199 MET cc_start: 0.7831 (mmm) cc_final: 0.7537 (mmm) REVERT: A 205 MET cc_start: 0.7578 (mmm) cc_final: 0.7089 (mpp) REVERT: A 217 LEU cc_start: 0.8366 (mt) cc_final: 0.8108 (mt) REVERT: A 218 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7509 (ttmt) REVERT: A 237 ASN cc_start: 0.7890 (t0) cc_final: 0.7660 (t0) REVERT: A 292 HIS cc_start: 0.8223 (m-70) cc_final: 0.7647 (m-70) REVERT: A 319 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6556 (mt) REVERT: A 322 SER cc_start: 0.8072 (t) cc_final: 0.7712 (p) REVERT: A 335 ASN cc_start: 0.8607 (t0) cc_final: 0.8344 (t0) REVERT: A 337 GLU cc_start: 0.7247 (mp0) cc_final: 0.6603 (mp0) REVERT: A 387 TYR cc_start: 0.7850 (m-10) cc_final: 0.7619 (m-10) REVERT: A 401 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6574 (mtm) REVERT: A 431 ARG cc_start: 0.8163 (mmt180) cc_final: 0.7931 (mmt180) REVERT: A 454 LYS cc_start: 0.8351 (mttm) cc_final: 0.8140 (mttm) REVERT: A 477 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8215 (tt) REVERT: A 479 ARG cc_start: 0.7853 (ttp80) cc_final: 0.7564 (ttp80) REVERT: A 481 LEU cc_start: 0.8529 (mt) cc_final: 0.8251 (mt) REVERT: A 499 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7159 (ttp80) REVERT: A 506 ASN cc_start: 0.7987 (m-40) cc_final: 0.7577 (m-40) REVERT: A 512 LEU cc_start: 0.8475 (tp) cc_final: 0.8126 (tt) REVERT: A 579 MET cc_start: 0.7790 (mmm) cc_final: 0.7298 (mmm) REVERT: A 596 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7740 (tmmt) REVERT: A 597 GLN cc_start: 0.7511 (mt0) cc_final: 0.7304 (mt0) REVERT: A 613 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 616 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 645 LYS cc_start: 0.8920 (tptp) cc_final: 0.8297 (tptp) REVERT: A 837 TYR cc_start: 0.8248 (t80) cc_final: 0.7936 (t80) REVERT: A 843 TYR cc_start: 0.8613 (t80) cc_final: 0.8037 (t80) REVERT: A 848 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7506 (mt-10) REVERT: A 849 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 852 LYS cc_start: 0.8192 (mttp) cc_final: 0.7944 (tttp) REVERT: A 862 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8261 (mmtm) REVERT: A 866 GLU cc_start: 0.7159 (tp30) cc_final: 0.6929 (tp30) REVERT: A 867 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8999 (mm) REVERT: A 868 LYS cc_start: 0.8571 (mmmm) cc_final: 0.7744 (mmmm) REVERT: A 875 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7263 (tpt170) REVERT: A 880 LYS cc_start: 0.8248 (tptp) cc_final: 0.7767 (tptp) REVERT: A 881 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6956 (tm-30) REVERT: A 923 ASP cc_start: 0.7654 (p0) cc_final: 0.7370 (p0) REVERT: A 931 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 938 MET cc_start: 0.8558 (mmm) cc_final: 0.8326 (mmm) REVERT: A 940 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7685 (tpp80) REVERT: B 84 SER cc_start: 0.7983 (t) cc_final: 0.7534 (p) REVERT: B 149 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 199 MET cc_start: 0.7607 (mmm) cc_final: 0.6967 (tpt) REVERT: B 246 ASN cc_start: 0.8043 (m-40) cc_final: 0.7744 (m-40) REVERT: B 269 LEU cc_start: 0.7979 (tp) cc_final: 0.7682 (tp) REVERT: B 278 TRP cc_start: 0.8376 (t-100) cc_final: 0.8076 (t-100) REVERT: B 300 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: B 337 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: B 351 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8051 (tpp-160) REVERT: B 361 ASN cc_start: 0.8173 (m-40) cc_final: 0.7655 (m110) REVERT: B 366 MET cc_start: 0.8106 (tpp) cc_final: 0.7859 (tpp) REVERT: B 384 ASP cc_start: 0.7166 (m-30) cc_final: 0.6878 (m-30) REVERT: B 387 TYR cc_start: 0.7867 (m-10) cc_final: 0.7481 (m-10) REVERT: B 420 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7608 (mtm-85) REVERT: B 443 GLU cc_start: 0.7700 (tp30) cc_final: 0.7058 (tp30) REVERT: B 475 GLN cc_start: 0.7508 (tp40) cc_final: 0.7218 (tp40) REVERT: B 499 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7210 (ptp90) REVERT: B 500 ARG cc_start: 0.7772 (tpt90) cc_final: 0.7407 (tpp80) REVERT: B 509 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8318 (mm) REVERT: B 512 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8098 (tp) REVERT: B 523 TRP cc_start: 0.7622 (m100) cc_final: 0.6973 (m100) REVERT: B 527 THR cc_start: 0.8011 (p) cc_final: 0.7229 (p) REVERT: B 531 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5957 (mm-30) REVERT: B 579 MET cc_start: 0.7669 (mmm) cc_final: 0.7412 (mmm) REVERT: B 586 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.6243 (tmm) REVERT: B 588 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7933 (ttpp) REVERT: B 590 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 595 TRP cc_start: 0.7980 (m100) cc_final: 0.7654 (m100) REVERT: B 596 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8265 (mmmt) REVERT: B 600 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6229 (m-70) REVERT: B 613 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 645 LYS cc_start: 0.8416 (tptp) cc_final: 0.7924 (tptp) REVERT: B 825 VAL cc_start: 0.8472 (t) cc_final: 0.8247 (p) REVERT: B 826 ASN cc_start: 0.7868 (t0) cc_final: 0.7564 (m110) REVERT: B 837 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: B 841 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8186 (ttmm) REVERT: B 847 GLU cc_start: 0.7636 (tp30) cc_final: 0.7378 (tp30) REVERT: B 848 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 881 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7016 (mm-30) REVERT: B 903 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6110 (mtp-110) REVERT: B 907 ASN cc_start: 0.7646 (m-40) cc_final: 0.7008 (m110) REVERT: B 911 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6778 (mt-10) REVERT: B 916 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 928 HIS cc_start: 0.7145 (t70) cc_final: 0.6791 (t70) REVERT: B 929 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7229 (mtpp) REVERT: B 941 LEU cc_start: 0.8690 (tp) cc_final: 0.8484 (tt) outliers start: 62 outliers final: 46 residues processed: 464 average time/residue: 0.2848 time to fit residues: 174.8084 Evaluate side-chains 499 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 439 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106220 restraints weight = 19905.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109609 restraints weight = 9262.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111695 restraints weight = 5360.927| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 10798 Z= 0.178 Angle : 0.883 59.199 14638 Z= 0.507 Chirality : 0.040 0.236 1772 Planarity : 0.004 0.047 1796 Dihedral : 5.920 56.799 1465 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.23 % Allowed : 25.61 % Favored : 69.16 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.23), residues: 1344 helix: 1.95 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.68 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 635 HIS 0.003 0.001 HIS B 292 PHE 0.013 0.001 PHE A 457 TYR 0.012 0.001 TYR A 313 ARG 0.008 0.001 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 909) hydrogen bonds : angle 4.10120 ( 2718) covalent geometry : bond 0.00358 (10798) covalent geometry : angle 0.88272 (14638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4520.85 seconds wall clock time: 78 minutes 44.80 seconds (4724.80 seconds total)