Starting phenix.real_space_refine on Fri Jan 17 09:05:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqa_38571/01_2025/8xqa_38571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqa_38571/01_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_38571/01_2025/8xqa_38571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqa_38571/01_2025/8xqa_38571.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqa_38571/01_2025/8xqa_38571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqa_38571/01_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-5571/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: 6.45, 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: 2.61 Conformation dependent library (CDL) restraints added in 1.4 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: 0.90 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: 3.23 Time building geometry restraints manager: 3.01 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: 0.05 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: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.510 Find NCS groups from input model: 0.310 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- 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= 0.342 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 *********************** 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 : 1.147 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: 0.2999 time to fit residues: 205.6335 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 : 1.293 ------------------------------------------------------------------------------- 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 = 0.105407 restraints weight = 19566.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108705 restraints weight = 9139.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110751 restraints weight = 5311.962| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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= 0.172 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 *********************** 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 : 1.129 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: 0.7495 (mmtm) cc_final: 0.7238 (mmtm) REVERT: A 85 CYS cc_start: 0.8348 (m) cc_final: 0.8018 (m) REVERT: A 112 ILE cc_start: 0.8368 (mt) cc_final: 0.8037 (mm) REVERT: A 124 GLU cc_start: 0.7633 (tp30) cc_final: 0.6707 (tp30) REVERT: A 128 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7406 (ttp-170) REVERT: A 160 MET cc_start: 0.7768 (mmm) cc_final: 0.7382 (mmt) REVERT: A 168 ILE cc_start: 0.7706 (tt) cc_final: 0.7493 (tp) REVERT: A 186 MET cc_start: 0.6747 (mtp) cc_final: 0.6471 (mtp) REVERT: A 197 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 205 MET cc_start: 0.7623 (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: 0.7982 (mtmt) cc_final: 0.7643 (mtmt) REVERT: A 237 ASN cc_start: 0.7932 (t0) cc_final: 0.7722 (t0) REVERT: A 257 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7576 (pp) REVERT: A 292 HIS cc_start: 0.8279 (m-70) cc_final: 0.7742 (m-70) REVERT: A 335 ASN cc_start: 0.8676 (t0) cc_final: 0.8326 (t0) REVERT: A 401 MET cc_start: 0.7210 (mtm) cc_final: 0.6999 (mtm) REVERT: A 406 PHE cc_start: 0.7698 (m-80) cc_final: 0.7475 (m-80) REVERT: A 454 LYS cc_start: 0.8407 (mttm) cc_final: 0.8078 (mttm) REVERT: A 477 LEU cc_start: 0.8599 (tt) cc_final: 0.8209 (tt) REVERT: A 479 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7419 (ttp80) REVERT: A 481 LEU cc_start: 0.8547 (mt) cc_final: 0.8268 (mt) REVERT: A 486 ILE cc_start: 0.8473 (mt) cc_final: 0.8188 (tt) REVERT: A 499 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7121 (ttp80) REVERT: A 502 HIS cc_start: 0.7799 (t-90) cc_final: 0.7204 (t-90) REVERT: A 506 ASN cc_start: 0.7952 (m-40) cc_final: 0.7407 (m-40) REVERT: A 578 MET cc_start: 0.8181 (ttm) cc_final: 0.7900 (ttm) REVERT: A 579 MET cc_start: 0.7993 (mmm) cc_final: 0.7408 (mmm) REVERT: A 596 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7798 (tmmt) REVERT: A 597 GLN cc_start: 0.7508 (mt0) cc_final: 0.7265 (mt0) REVERT: A 613 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 622 LYS cc_start: 0.7953 (tttp) cc_final: 0.7702 (tttp) REVERT: A 645 LYS cc_start: 0.8939 (tptp) cc_final: 0.8325 (tptp) REVERT: A 843 TYR cc_start: 0.8601 (t80) cc_final: 0.7845 (t80) REVERT: A 848 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 852 LYS cc_start: 0.8184 (mttp) cc_final: 0.7948 (mttp) REVERT: A 862 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8380 (mmtm) REVERT: A 866 GLU cc_start: 0.7271 (tp30) cc_final: 0.7049 (tp30) REVERT: A 868 LYS cc_start: 0.8644 (mmmm) cc_final: 0.7860 (mmmm) REVERT: A 875 ARG cc_start: 0.7660 (tpt90) cc_final: 0.7180 (tpt90) REVERT: A 880 LYS cc_start: 0.8223 (tptp) cc_final: 0.7780 (tptp) REVERT: A 900 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7523 (tp40) REVERT: A 912 THR cc_start: 0.8422 (m) cc_final: 0.8217 (p) REVERT: A 925 MET cc_start: 0.7926 (mmm) cc_final: 0.7603 (mmm) REVERT: A 931 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 77 VAL cc_start: 0.8283 (t) cc_final: 0.7964 (m) REVERT: B 84 SER cc_start: 0.8066 (t) cc_final: 0.7668 (p) REVERT: B 109 LEU cc_start: 0.7936 (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: 0.7398 (tm-30) cc_final: 0.6956 (tm-30) REVERT: B 233 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 249 MET cc_start: 0.7535 (tmm) cc_final: 0.7067 (tmm) REVERT: B 278 TRP cc_start: 0.8373 (t-100) cc_final: 0.8042 (t-100) REVERT: B 300 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 337 GLU cc_start: 0.7688 (mp0) cc_final: 0.7404 (mp0) REVERT: B 351 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8076 (tpp-160) REVERT: B 384 ASP cc_start: 0.6992 (m-30) cc_final: 0.6741 (m-30) REVERT: B 390 ILE cc_start: 0.8500 (mm) cc_final: 0.8270 (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: 0.7213 (tp30) REVERT: B 499 ARG cc_start: 0.7557 (ptp90) cc_final: 0.7247 (ptp90) REVERT: B 500 ARG cc_start: 0.7797 (tpt90) cc_final: 0.7413 (tpt90) REVERT: B 512 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 517 PHE cc_start: 0.7546 (m-10) cc_final: 0.7288 (m-80) REVERT: B 527 THR cc_start: 0.8258 (p) cc_final: 0.7549 (p) REVERT: B 579 MET cc_start: 0.7820 (mmm) cc_final: 0.7442 (mmm) REVERT: B 581 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: B 586 MET cc_start: 0.7697 (tmm) cc_final: 0.6022 (tmm) REVERT: B 588 LYS cc_start: 0.8201 (ttpp) cc_final: 0.7788 (ttpp) REVERT: B 590 GLU cc_start: 0.7642 (mm-30) cc_final: 0.6754 (mm-30) REVERT: B 591 LYS cc_start: 0.8205 (mtmp) cc_final: 0.7953 (mtmp) REVERT: B 595 TRP cc_start: 0.7992 (m100) cc_final: 0.7720 (m100) REVERT: B 596 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8162 (mmmt) REVERT: B 613 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6981 (tm-30) REVERT: B 635 TRP cc_start: 0.5418 (m100) cc_final: 0.5192 (m100) REVERT: B 645 LYS cc_start: 0.8529 (tptp) cc_final: 0.7953 (tptp) REVERT: B 825 VAL cc_start: 0.8409 (t) cc_final: 0.8180 (p) REVERT: B 826 ASN cc_start: 0.7897 (t0) cc_final: 0.7552 (m110) REVERT: B 841 LYS cc_start: 0.8503 (ttmm) cc_final: 0.7985 (ttmm) REVERT: B 843 TYR cc_start: 0.8278 (t80) cc_final: 0.7614 (t80) REVERT: B 847 GLU cc_start: 0.7900 (tp30) cc_final: 0.7519 (tp30) REVERT: B 848 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 876 LEU cc_start: 0.8208 (mt) cc_final: 0.7974 (mt) REVERT: B 881 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6783 (mm-30) REVERT: B 889 HIS cc_start: 0.7997 (m90) cc_final: 0.7061 (m90) REVERT: B 907 ASN cc_start: 0.7616 (m-40) cc_final: 0.6513 (m-40) REVERT: B 908 HIS cc_start: 0.7859 (m-70) cc_final: 0.7266 (m-70) REVERT: B 911 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6664 (mp0) REVERT: B 913 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 915 GLU cc_start: 0.7677 (tt0) cc_final: 0.7272 (tt0) REVERT: B 928 HIS cc_start: 0.7123 (t70) cc_final: 0.6824 (t70) REVERT: B 938 MET cc_start: 0.7809 (tpp) cc_final: 0.7599 (tpp) outliers start: 66 outliers final: 34 residues processed: 495 average time/residue: 0.2956 time to fit residues: 193.9127 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 : 1.177 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 624 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104390 restraints weight = 19853.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107715 restraints weight = 9241.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109766 restraints weight = 5336.436| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10798 Z= 0.215 Angle : 0.598 14.788 14638 Z= 0.309 Chirality : 0.039 0.255 1772 Planarity : 0.004 0.048 1796 Dihedral : 7.245 66.696 1483 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.84 % Allowed : 19.34 % 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: 1.64 (0.23), residues: 1344 helix: 1.41 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.63 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 523 HIS 0.007 0.001 HIS B 889 PHE 0.020 0.001 PHE A 457 TYR 0.014 0.001 TYR A 392 ARG 0.005 0.000 ARG A 910 *********************** 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: 67 poor density : 456 time to evaluate : 1.269 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: 0.7493 (mmtm) cc_final: 0.7059 (mmtm) REVERT: A 85 CYS cc_start: 0.8364 (m) cc_final: 0.8034 (m) REVERT: A 112 ILE cc_start: 0.8407 (mt) cc_final: 0.8089 (mm) REVERT: A 124 GLU cc_start: 0.7666 (tp30) cc_final: 0.6782 (tp30) REVERT: A 125 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 128 ARG cc_start: 0.7663 (ttp-170) cc_final: 0.7427 (ttp-170) REVERT: A 160 MET cc_start: 0.7763 (mmm) cc_final: 0.7397 (mmt) REVERT: A 186 MET cc_start: 0.6602 (mtp) cc_final: 0.6364 (mtp) REVERT: A 199 MET cc_start: 0.7761 (mmm) cc_final: 0.7370 (mmm) REVERT: A 205 MET cc_start: 0.7618 (mmm) cc_final: 0.7363 (mmm) REVERT: A 217 LEU cc_start: 0.8392 (mt) cc_final: 0.8152 (mt) REVERT: A 237 ASN cc_start: 0.7946 (t0) cc_final: 0.7708 (t0) REVERT: A 257 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7614 (pp) REVERT: A 292 HIS cc_start: 0.8286 (m-70) cc_final: 0.7749 (m-70) REVERT: A 337 GLU cc_start: 0.7316 (mp0) cc_final: 0.6741 (mp0) REVERT: A 387 TYR cc_start: 0.7996 (m-10) cc_final: 0.7685 (m-10) REVERT: A 401 MET cc_start: 0.7171 (mtm) cc_final: 0.6968 (mtm) REVERT: A 454 LYS cc_start: 0.8418 (mttm) cc_final: 0.8156 (mttm) REVERT: A 477 LEU cc_start: 0.8612 (tt) cc_final: 0.8287 (tt) REVERT: A 479 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7506 (ttp80) REVERT: A 481 LEU cc_start: 0.8533 (mt) cc_final: 0.8269 (mt) REVERT: A 486 ILE cc_start: 0.8534 (mt) cc_final: 0.8243 (tt) REVERT: A 499 ARG cc_start: 0.7765 (ttp80) cc_final: 0.7154 (ttp80) REVERT: A 502 HIS cc_start: 0.7806 (t-90) cc_final: 0.7323 (t-90) REVERT: A 506 ASN cc_start: 0.7953 (m-40) cc_final: 0.7458 (m-40) REVERT: A 514 SER cc_start: 0.8260 (p) cc_final: 0.8006 (p) REVERT: A 578 MET cc_start: 0.8138 (ttm) cc_final: 0.7903 (ttm) REVERT: A 579 MET cc_start: 0.7901 (mmm) cc_final: 0.7294 (mmm) REVERT: A 585 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7942 (ttt180) REVERT: A 596 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7798 (tmmt) REVERT: A 597 GLN cc_start: 0.7511 (mt0) cc_final: 0.7265 (mt0) REVERT: A 611 LEU cc_start: 0.8295 (tp) cc_final: 0.8050 (tp) REVERT: A 613 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 616 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 622 LYS cc_start: 0.7995 (tttp) cc_final: 0.7680 (tttp) REVERT: A 645 LYS cc_start: 0.8972 (tptp) cc_final: 0.8719 (tptp) REVERT: A 843 TYR cc_start: 0.8612 (t80) cc_final: 0.7822 (t80) REVERT: A 848 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 849 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 862 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8408 (mmtm) REVERT: A 866 GLU cc_start: 0.7253 (tp30) cc_final: 0.7008 (tp30) REVERT: A 868 LYS cc_start: 0.8635 (mmmm) cc_final: 0.7839 (mmmm) REVERT: A 875 ARG cc_start: 0.7713 (tpt90) cc_final: 0.7199 (tpt90) REVERT: A 880 LYS cc_start: 0.8266 (tptp) cc_final: 0.7810 (tptp) REVERT: A 900 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7498 (tp40) REVERT: A 925 MET cc_start: 0.7891 (mmm) cc_final: 0.7578 (mmm) REVERT: A 940 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7656 (ttm-80) REVERT: B 81 ILE cc_start: 0.7942 (mt) cc_final: 0.7626 (mt) REVERT: B 84 SER cc_start: 0.8041 (t) cc_final: 0.7651 (p) REVERT: B 109 LEU cc_start: 0.7942 (mt) cc_final: 0.7672 (mt) REVERT: B 124 GLU cc_start: 0.7529 (tp30) cc_final: 0.7221 (tp30) REVERT: B 140 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7586 (mm110) REVERT: B 149 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 152 PHE cc_start: 0.8267 (t80) cc_final: 0.8048 (t80) REVERT: B 199 MET cc_start: 0.7638 (tpp) cc_final: 0.7148 (tpp) REVERT: B 278 TRP cc_start: 0.8382 (t-100) cc_final: 0.8073 (t-100) REVERT: B 284 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7844 (mmmm) REVERT: B 288 PHE cc_start: 0.7863 (t80) cc_final: 0.7588 (t80) REVERT: B 300 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 320 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6962 (mm-30) REVERT: B 337 GLU cc_start: 0.7694 (mp0) cc_final: 0.7421 (mp0) REVERT: B 361 ASN cc_start: 0.8163 (m-40) cc_final: 0.7950 (m-40) REVERT: B 384 ASP cc_start: 0.7043 (m-30) cc_final: 0.6823 (m-30) REVERT: B 387 TYR cc_start: 0.7799 (m-10) cc_final: 0.7390 (m-10) REVERT: B 390 ILE cc_start: 0.8494 (mm) cc_final: 0.8281 (mm) REVERT: B 399 ARG cc_start: 0.8559 (ttt90) cc_final: 0.8257 (tpt170) REVERT: B 420 ARG cc_start: 0.8035 (mtm180) cc_final: 0.7465 (mtm-85) REVERT: B 425 MET cc_start: 0.7621 (ttm) cc_final: 0.7417 (ttt) REVERT: B 438 LEU cc_start: 0.8162 (mt) cc_final: 0.7842 (mp) REVERT: B 443 GLU cc_start: 0.7690 (tp30) cc_final: 0.7328 (tm-30) REVERT: B 454 LYS cc_start: 0.7991 (mmtm) cc_final: 0.7791 (tppt) REVERT: B 475 GLN cc_start: 0.7493 (tp40) cc_final: 0.7189 (tp40) REVERT: B 499 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7241 (ptp90) REVERT: B 500 ARG cc_start: 0.7815 (tpt90) cc_final: 0.7472 (tpp80) REVERT: B 512 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 527 THR cc_start: 0.8086 (p) cc_final: 0.7537 (p) REVERT: B 531 GLU cc_start: 0.6400 (mm-30) cc_final: 0.6079 (mm-30) REVERT: B 579 MET cc_start: 0.7797 (mmm) cc_final: 0.7424 (mmm) REVERT: B 581 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6026 (pp20) REVERT: B 586 MET cc_start: 0.7693 (tmm) cc_final: 0.6065 (tmm) REVERT: B 588 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7840 (ttpp) REVERT: B 590 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6743 (mm-30) REVERT: B 591 LYS cc_start: 0.8159 (mtmp) cc_final: 0.7926 (mtmp) REVERT: B 595 TRP cc_start: 0.7995 (m100) cc_final: 0.7709 (m100) REVERT: B 596 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8230 (mmmt) REVERT: B 613 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6992 (tm-30) REVERT: B 645 LYS cc_start: 0.8524 (tptp) cc_final: 0.8012 (tptp) REVERT: B 825 VAL cc_start: 0.8445 (t) cc_final: 0.8213 (p) REVERT: B 826 ASN cc_start: 0.7903 (t0) cc_final: 0.7512 (m110) REVERT: B 841 LYS cc_start: 0.8458 (ttmm) cc_final: 0.8132 (ttmm) REVERT: B 843 TYR cc_start: 0.8261 (t80) cc_final: 0.7774 (t80) REVERT: B 847 GLU cc_start: 0.7898 (tp30) cc_final: 0.7531 (tp30) REVERT: B 848 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7824 (mt-10) REVERT: B 850 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 872 GLU cc_start: 0.8163 (tp30) cc_final: 0.7026 (tp30) REVERT: B 876 LEU cc_start: 0.8261 (mt) cc_final: 0.7653 (mt) REVERT: B 881 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6783 (mm-30) REVERT: B 907 ASN cc_start: 0.7665 (m-40) cc_final: 0.6588 (m-40) REVERT: B 908 HIS cc_start: 0.7918 (m-70) cc_final: 0.7486 (m-70) REVERT: B 911 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6693 (mt-10) REVERT: B 915 GLU cc_start: 0.7628 (tt0) cc_final: 0.7223 (tt0) REVERT: B 924 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7687 (pp20) REVERT: B 928 HIS cc_start: 0.7142 (t70) cc_final: 0.6840 (t70) outliers start: 67 outliers final: 45 residues processed: 483 average time/residue: 0.2867 time to fit residues: 181.9411 Evaluate side-chains 502 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 451 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 928 HIS 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 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 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 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 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: 0.5980 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 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 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 = 0.3701 r_free = 0.3701 target = 0.123899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105027 restraints weight = 19948.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108351 restraints weight = 9205.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110422 restraints weight = 5322.680| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10798 Z= 0.202 Angle : 0.564 13.926 14638 Z= 0.295 Chirality : 0.039 0.217 1772 Planarity : 0.004 0.048 1796 Dihedral : 6.807 59.923 1480 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.79 % Allowed : 19.77 % Favored : 73.43 % 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: 2.03 (0.23), residues: 1344 helix: 1.67 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.46 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 523 HIS 0.003 0.000 HIS A 614 PHE 0.018 0.001 PHE A 245 TYR 0.017 0.001 TYR A 392 ARG 0.006 0.000 ARG B 875 *********************** 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 : 1.194 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: A 76 LYS cc_start: 0.7423 (mmtm) cc_final: 0.7152 (mmtm) REVERT: A 85 CYS cc_start: 0.8339 (m) cc_final: 0.8021 (m) REVERT: A 112 ILE cc_start: 0.8411 (mt) cc_final: 0.8067 (mm) REVERT: A 124 GLU cc_start: 0.7654 (tp30) cc_final: 0.6796 (tp30) REVERT: A 125 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 128 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7469 (ttp-170) REVERT: A 160 MET cc_start: 0.7734 (mmm) cc_final: 0.7345 (mmt) REVERT: A 186 MET cc_start: 0.6572 (mtp) cc_final: 0.6371 (mtp) REVERT: A 199 MET cc_start: 0.7606 (mmm) cc_final: 0.7188 (mmm) REVERT: A 205 MET cc_start: 0.7621 (mmm) cc_final: 0.7253 (mmm) REVERT: A 217 LEU cc_start: 0.8336 (mt) cc_final: 0.8087 (mt) REVERT: A 218 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7554 (ttmt) REVERT: A 237 ASN cc_start: 0.7946 (t0) cc_final: 0.7718 (t0) REVERT: A 292 HIS cc_start: 0.8213 (m-70) cc_final: 0.7625 (m-70) REVERT: A 319 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6563 (mt) REVERT: A 335 ASN cc_start: 0.8665 (t0) cc_final: 0.8396 (t0) REVERT: A 337 GLU cc_start: 0.7292 (mp0) cc_final: 0.6701 (mp0) REVERT: A 387 TYR cc_start: 0.7970 (m-10) cc_final: 0.7591 (m-10) REVERT: A 431 ARG cc_start: 0.8287 (mmt180) cc_final: 0.8070 (mmt180) REVERT: A 454 LYS cc_start: 0.8432 (mttm) cc_final: 0.8123 (mttm) REVERT: A 477 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 479 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7533 (ttp80) REVERT: A 481 LEU cc_start: 0.8520 (mt) cc_final: 0.8246 (mt) REVERT: A 486 ILE cc_start: 0.8546 (mt) cc_final: 0.8284 (tt) REVERT: A 499 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7182 (ttp80) REVERT: A 502 HIS cc_start: 0.7868 (t-90) cc_final: 0.7393 (t-90) REVERT: A 506 ASN cc_start: 0.7968 (m-40) cc_final: 0.7478 (m-40) REVERT: A 514 SER cc_start: 0.8293 (p) cc_final: 0.8054 (p) REVERT: A 578 MET cc_start: 0.8199 (ttm) cc_final: 0.7958 (ttm) REVERT: A 579 MET cc_start: 0.7979 (mmm) cc_final: 0.7396 (mmm) REVERT: A 596 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7795 (tmmt) REVERT: A 597 GLN cc_start: 0.7481 (mt0) cc_final: 0.7241 (mt0) REVERT: A 611 LEU cc_start: 0.8260 (tp) cc_final: 0.7998 (tp) REVERT: A 613 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 645 LYS cc_start: 0.8994 (tptp) cc_final: 0.8354 (tptp) REVERT: A 826 ASN cc_start: 0.7458 (t0) cc_final: 0.7124 (t0) REVERT: A 843 TYR cc_start: 0.8630 (t80) cc_final: 0.7912 (t80) REVERT: A 848 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 849 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 862 LYS cc_start: 0.8658 (mmtm) cc_final: 0.8388 (mmtm) REVERT: A 866 GLU cc_start: 0.7283 (tp30) cc_final: 0.7041 (tp30) REVERT: A 868 LYS cc_start: 0.8597 (mmmm) cc_final: 0.7800 (mmmm) REVERT: A 875 ARG cc_start: 0.7731 (tpt90) cc_final: 0.7487 (tpt90) REVERT: A 880 LYS cc_start: 0.8266 (tptp) cc_final: 0.7846 (tptp) REVERT: A 881 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6913 (tm-30) REVERT: A 900 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7553 (tp40) REVERT: A 925 MET cc_start: 0.7986 (mmm) cc_final: 0.7732 (mmm) REVERT: A 931 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7459 (mm-30) REVERT: A 938 MET cc_start: 0.8515 (mmm) cc_final: 0.8203 (mmm) REVERT: A 940 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7477 (ttm-80) REVERT: B 81 ILE cc_start: 0.7948 (mt) cc_final: 0.7626 (mt) REVERT: B 84 SER cc_start: 0.8041 (t) cc_final: 0.7617 (p) REVERT: B 109 LEU cc_start: 0.7919 (mt) cc_final: 0.7591 (mt) REVERT: B 124 GLU cc_start: 0.7528 (tp30) cc_final: 0.7153 (tp30) REVERT: B 149 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 152 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7933 (t80) REVERT: B 193 TRP cc_start: 0.8264 (m-10) cc_final: 0.8054 (m-10) REVERT: B 199 MET cc_start: 0.7529 (tpp) cc_final: 0.7234 (tpp) REVERT: B 226 LEU cc_start: 0.8209 (tt) cc_final: 0.7983 (tp) REVERT: B 233 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7043 (tm-30) REVERT: B 246 ASN cc_start: 0.8129 (m-40) cc_final: 0.7905 (m-40) REVERT: B 269 LEU cc_start: 0.8001 (tp) cc_final: 0.7680 (tp) REVERT: B 278 TRP cc_start: 0.8390 (t-100) cc_final: 0.8081 (t-100) REVERT: B 300 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6846 (mt-10) REVERT: B 335 ASN cc_start: 0.8250 (t0) cc_final: 0.7962 (t0) REVERT: B 337 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 351 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8109 (tpp-160) REVERT: B 387 TYR cc_start: 0.7857 (m-10) cc_final: 0.7439 (m-10) REVERT: B 390 ILE cc_start: 0.8522 (mm) cc_final: 0.8302 (mm) REVERT: B 399 ARG cc_start: 0.8574 (ttt90) cc_final: 0.8221 (tpt170) REVERT: B 420 ARG cc_start: 0.8050 (mtm180) cc_final: 0.7495 (mtm-85) REVERT: B 443 GLU cc_start: 0.7731 (tp30) cc_final: 0.7164 (tp30) REVERT: B 475 GLN cc_start: 0.7466 (tp40) cc_final: 0.7183 (tp40) REVERT: B 499 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7279 (ptp90) REVERT: B 500 ARG cc_start: 0.7842 (tpt90) cc_final: 0.7486 (tpp80) REVERT: B 527 THR cc_start: 0.8187 (p) cc_final: 0.7480 (p) REVERT: B 531 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6222 (mm-30) REVERT: B 579 MET cc_start: 0.7784 (mmm) cc_final: 0.7322 (mmm) REVERT: B 581 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5986 (pp20) REVERT: B 586 MET cc_start: 0.7708 (tmm) cc_final: 0.6042 (tmm) REVERT: B 588 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7863 (ttpp) REVERT: B 590 GLU cc_start: 0.7678 (mm-30) cc_final: 0.6686 (mm-30) REVERT: B 591 LYS cc_start: 0.8088 (mtmp) cc_final: 0.7867 (mtmp) REVERT: B 595 TRP cc_start: 0.7981 (m100) cc_final: 0.7670 (m100) REVERT: B 596 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8223 (mmmt) REVERT: B 613 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 645 LYS cc_start: 0.8565 (tptp) cc_final: 0.8033 (tptp) REVERT: B 825 VAL cc_start: 0.8487 (t) cc_final: 0.8248 (p) REVERT: B 826 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7522 (m110) REVERT: B 841 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8196 (ttmm) REVERT: B 843 TYR cc_start: 0.8166 (t80) cc_final: 0.7826 (t80) REVERT: B 847 GLU cc_start: 0.7852 (tp30) cc_final: 0.7583 (tp30) REVERT: B 848 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 850 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7997 (p) REVERT: B 872 GLU cc_start: 0.8005 (tp30) cc_final: 0.7537 (tp30) REVERT: B 876 LEU cc_start: 0.8110 (mt) cc_final: 0.7808 (mt) REVERT: B 880 LYS cc_start: 0.8022 (tmmt) cc_final: 0.7803 (tmmt) REVERT: B 881 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 907 ASN cc_start: 0.7659 (m-40) cc_final: 0.6607 (m-40) REVERT: B 908 HIS cc_start: 0.7941 (m-70) cc_final: 0.7522 (m-70) REVERT: B 911 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6698 (mt-10) REVERT: B 925 MET cc_start: 0.7339 (tmm) cc_final: 0.6998 (tmm) REVERT: B 928 HIS cc_start: 0.7130 (t70) cc_final: 0.6851 (t70) REVERT: B 929 LYS cc_start: 0.7776 (mtpp) cc_final: 0.7232 (mtpp) outliers start: 78 outliers final: 46 residues processed: 478 average time/residue: 0.2921 time to fit residues: 184.4365 Evaluate side-chains 503 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 448 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 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 477 LEU Chi-restraints excluded: chain A residue 490 LYS 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 896 VAL 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 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 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 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 509 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 850 VAL 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: 0.0770 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105236 restraints weight = 19830.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108520 restraints weight = 9218.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110589 restraints weight = 5359.542| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10798 Z= 0.197 Angle : 0.579 15.331 14638 Z= 0.298 Chirality : 0.039 0.215 1772 Planarity : 0.004 0.046 1796 Dihedral : 6.235 58.713 1468 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.45 % Allowed : 21.08 % Favored : 72.47 % 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: 2.16 (0.23), residues: 1344 helix: 1.76 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.47 (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 889 PHE 0.020 0.001 PHE B 288 TYR 0.018 0.001 TYR A 392 ARG 0.011 0.000 ARG A 910 *********************** 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 531 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 457 time to evaluate : 1.129 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: 0.7415 (mmtm) cc_final: 0.7136 (mmtm) REVERT: A 85 CYS cc_start: 0.8347 (m) cc_final: 0.8020 (m) REVERT: A 112 ILE cc_start: 0.8421 (mt) cc_final: 0.8072 (mm) REVERT: A 124 GLU cc_start: 0.7594 (tp30) cc_final: 0.6888 (tp30) REVERT: A 125 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 128 ARG cc_start: 0.7677 (ttp-170) cc_final: 0.7463 (ttp-170) REVERT: A 160 MET cc_start: 0.7718 (mmm) cc_final: 0.7335 (mmt) REVERT: A 205 MET cc_start: 0.7593 (mmm) cc_final: 0.7250 (mmm) REVERT: A 217 LEU cc_start: 0.8337 (mt) cc_final: 0.8094 (mt) REVERT: A 218 LYS cc_start: 0.7822 (mtmt) cc_final: 0.7575 (ttmt) REVERT: A 237 ASN cc_start: 0.7940 (t0) cc_final: 0.7719 (t0) REVERT: A 250 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7447 (mtmm) REVERT: A 292 HIS cc_start: 0.8201 (m-70) cc_final: 0.7615 (m-70) REVERT: A 319 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6586 (mt) REVERT: A 335 ASN cc_start: 0.8664 (t0) cc_final: 0.8386 (t0) REVERT: A 337 GLU cc_start: 0.7289 (mp0) cc_final: 0.6696 (mp0) REVERT: A 387 TYR cc_start: 0.7945 (m-10) cc_final: 0.7611 (m-10) REVERT: A 431 ARG cc_start: 0.8250 (mmt180) cc_final: 0.8014 (mmt180) REVERT: A 454 LYS cc_start: 0.8421 (mttm) cc_final: 0.8111 (mttm) REVERT: A 477 LEU cc_start: 0.8564 (tt) cc_final: 0.8247 (tt) REVERT: A 479 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7547 (ttp80) REVERT: A 481 LEU cc_start: 0.8501 (mt) cc_final: 0.8225 (mt) REVERT: A 499 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7142 (ttp80) REVERT: A 502 HIS cc_start: 0.7872 (t-90) cc_final: 0.7386 (t-90) REVERT: A 506 ASN cc_start: 0.7967 (m-40) cc_final: 0.7475 (m-40) REVERT: A 514 SER cc_start: 0.8318 (p) cc_final: 0.8070 (p) REVERT: A 578 MET cc_start: 0.8239 (ttm) cc_final: 0.7989 (ttm) REVERT: A 579 MET cc_start: 0.7970 (mmm) cc_final: 0.7406 (mmm) REVERT: A 596 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7768 (tmmt) REVERT: A 597 GLN cc_start: 0.7455 (mt0) cc_final: 0.7203 (mt0) REVERT: A 602 MET cc_start: 0.6558 (tpp) cc_final: 0.6350 (tpp) REVERT: A 611 LEU cc_start: 0.8244 (tp) cc_final: 0.7957 (tp) REVERT: A 613 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 645 LYS cc_start: 0.8989 (tptp) cc_final: 0.8360 (tptp) REVERT: A 826 ASN cc_start: 0.7446 (t0) cc_final: 0.7057 (t0) REVERT: A 843 TYR cc_start: 0.8636 (t80) cc_final: 0.7963 (t80) REVERT: A 848 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7590 (mt-10) REVERT: A 849 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 852 LYS cc_start: 0.8309 (mttp) cc_final: 0.8043 (tttp) REVERT: A 862 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8386 (mmtm) REVERT: A 866 GLU cc_start: 0.7277 (tp30) cc_final: 0.6999 (tp30) REVERT: A 868 LYS cc_start: 0.8587 (mmmm) cc_final: 0.7812 (mmmm) REVERT: A 875 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7365 (tpt90) REVERT: A 880 LYS cc_start: 0.8270 (tptp) cc_final: 0.7825 (tptp) REVERT: A 881 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6904 (tm-30) REVERT: A 900 GLN cc_start: 0.8149 (tm130) cc_final: 0.7924 (tp40) REVERT: A 925 MET cc_start: 0.8029 (mmm) cc_final: 0.7763 (mmm) REVERT: A 931 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 938 MET cc_start: 0.8502 (mmm) cc_final: 0.8265 (mmm) REVERT: B 81 ILE cc_start: 0.7932 (mt) cc_final: 0.7642 (mt) REVERT: B 84 SER cc_start: 0.8045 (t) cc_final: 0.7616 (p) REVERT: B 109 LEU cc_start: 0.7938 (mt) cc_final: 0.7620 (mt) REVERT: B 124 GLU cc_start: 0.7533 (tp30) cc_final: 0.7180 (tp30) REVERT: B 149 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 152 PHE cc_start: 0.8267 (t80) cc_final: 0.7909 (t80) REVERT: B 188 LEU cc_start: 0.8141 (tp) cc_final: 0.7426 (tt) REVERT: B 246 ASN cc_start: 0.8099 (m-40) cc_final: 0.7895 (m-40) REVERT: B 269 LEU cc_start: 0.7980 (tp) cc_final: 0.7675 (tp) REVERT: B 278 TRP cc_start: 0.8390 (t-100) cc_final: 0.8085 (t-100) REVERT: B 300 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 337 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: B 351 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8071 (tpp-160) REVERT: B 384 ASP cc_start: 0.7030 (m-30) cc_final: 0.6680 (m-30) REVERT: B 387 TYR cc_start: 0.7855 (m-10) cc_final: 0.7388 (m-10) REVERT: B 399 ARG cc_start: 0.8568 (ttt90) cc_final: 0.8183 (tpt170) REVERT: B 420 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7450 (mtm-85) REVERT: B 443 GLU cc_start: 0.7731 (tp30) cc_final: 0.7156 (tp30) REVERT: B 475 GLN cc_start: 0.7473 (tp40) cc_final: 0.7180 (tp40) REVERT: B 499 ARG cc_start: 0.7585 (ptp90) cc_final: 0.7275 (ptp90) REVERT: B 500 ARG cc_start: 0.7836 (tpt90) cc_final: 0.7476 (tpp80) REVERT: B 512 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 527 THR cc_start: 0.8193 (p) cc_final: 0.7455 (p) REVERT: B 579 MET cc_start: 0.7764 (mmm) cc_final: 0.7316 (mmm) REVERT: B 581 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5999 (pp20) REVERT: B 586 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.5933 (tmm) REVERT: B 588 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7890 (ttpp) REVERT: B 590 GLU cc_start: 0.7679 (mm-30) cc_final: 0.6675 (mm-30) REVERT: B 595 TRP cc_start: 0.7998 (m100) cc_final: 0.7682 (m100) REVERT: B 613 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7027 (tm-30) REVERT: B 645 LYS cc_start: 0.8571 (tptp) cc_final: 0.8039 (tptp) REVERT: B 825 VAL cc_start: 0.8503 (t) cc_final: 0.8267 (p) REVERT: B 826 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7527 (m110) REVERT: B 841 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8177 (ttmm) REVERT: B 843 TYR cc_start: 0.8091 (t80) cc_final: 0.7838 (t80) REVERT: B 847 GLU cc_start: 0.7835 (tp30) cc_final: 0.7568 (tp30) REVERT: B 848 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 850 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 872 GLU cc_start: 0.7951 (tp30) cc_final: 0.7574 (tp30) REVERT: B 876 LEU cc_start: 0.8104 (mt) cc_final: 0.7822 (mt) REVERT: B 880 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (tmmt) REVERT: B 881 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 907 ASN cc_start: 0.7651 (m-40) cc_final: 0.6617 (m-40) REVERT: B 908 HIS cc_start: 0.7944 (m-70) cc_final: 0.7536 (m-70) REVERT: B 911 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6715 (mt-10) REVERT: B 925 MET cc_start: 0.7307 (tmm) cc_final: 0.7040 (tmm) REVERT: B 928 HIS cc_start: 0.7129 (t70) cc_final: 0.6833 (t70) REVERT: B 929 LYS cc_start: 0.7791 (mtpp) cc_final: 0.7232 (mtpp) outliers start: 74 outliers final: 48 residues processed: 483 average time/residue: 0.2938 time to fit residues: 187.1838 Evaluate side-chains 508 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 451 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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 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 896 VAL Chi-restraints excluded: chain A residue 915 GLU 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 393 LEU Chi-restraints excluded: chain B residue 405 LEU 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 850 VAL Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 886 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.123789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104621 restraints weight = 19992.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.107953 restraints weight = 9283.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110023 restraints weight = 5406.059| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2407 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= 0.214 Angle : 0.604 15.899 14638 Z= 0.311 Chirality : 0.040 0.196 1772 Planarity : 0.004 0.051 1796 Dihedral : 5.988 59.380 1465 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.62 % Allowed : 21.95 % 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: 2.13 (0.23), residues: 1344 helix: 1.74 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.45 (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 889 PHE 0.031 0.001 PHE B 625 TYR 0.014 0.001 TYR A 313 ARG 0.008 0.001 ARG A 491 *********************** 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 530 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 454 time to evaluate : 1.253 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: A 76 LYS cc_start: 0.7411 (mmtm) cc_final: 0.7150 (mmtm) REVERT: A 85 CYS cc_start: 0.8355 (m) cc_final: 0.8024 (m) REVERT: A 112 ILE cc_start: 0.8431 (mt) cc_final: 0.8084 (mm) REVERT: A 124 GLU cc_start: 0.7568 (tp30) cc_final: 0.6988 (tp30) REVERT: A 125 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 160 MET cc_start: 0.7744 (mmm) cc_final: 0.7353 (mmt) REVERT: A 199 MET cc_start: 0.7829 (mmm) cc_final: 0.7524 (mmm) REVERT: A 205 MET cc_start: 0.7589 (mmm) cc_final: 0.7249 (mmm) REVERT: A 217 LEU cc_start: 0.8363 (mt) cc_final: 0.8103 (mt) REVERT: A 218 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7617 (ttmt) REVERT: A 237 ASN cc_start: 0.7938 (t0) cc_final: 0.7720 (t0) REVERT: A 250 LYS cc_start: 0.8181 (mtmm) cc_final: 0.7469 (mtmm) REVERT: A 292 HIS cc_start: 0.8207 (m-70) cc_final: 0.7660 (m-70) REVERT: A 319 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6578 (mt) REVERT: A 335 ASN cc_start: 0.8666 (t0) cc_final: 0.8404 (t0) REVERT: A 337 GLU cc_start: 0.7300 (mp0) cc_final: 0.6704 (mp0) REVERT: A 387 TYR cc_start: 0.7948 (m-10) cc_final: 0.7566 (m-10) REVERT: A 431 ARG cc_start: 0.8270 (mmt180) cc_final: 0.8041 (mmt180) REVERT: A 454 LYS cc_start: 0.8379 (mttm) cc_final: 0.8089 (mttm) REVERT: A 477 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 479 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7566 (ttp80) REVERT: A 481 LEU cc_start: 0.8550 (mt) cc_final: 0.8275 (mt) REVERT: A 499 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7123 (ttp80) REVERT: A 502 HIS cc_start: 0.7877 (t-90) cc_final: 0.7373 (t-90) REVERT: A 506 ASN cc_start: 0.7972 (m-40) cc_final: 0.7466 (m-40) REVERT: A 578 MET cc_start: 0.8195 (ttm) cc_final: 0.7958 (ttm) REVERT: A 579 MET cc_start: 0.7997 (mmm) cc_final: 0.7423 (mmm) REVERT: A 596 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7773 (tmmt) REVERT: A 597 GLN cc_start: 0.7465 (mt0) cc_final: 0.7189 (mt0) REVERT: A 602 MET cc_start: 0.6531 (tpp) cc_final: 0.6280 (tpp) REVERT: A 611 LEU cc_start: 0.8262 (tp) cc_final: 0.7970 (tp) REVERT: A 613 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 645 LYS cc_start: 0.8971 (tptp) cc_final: 0.8339 (tptp) REVERT: A 826 ASN cc_start: 0.7500 (t0) cc_final: 0.7152 (t0) REVERT: A 843 TYR cc_start: 0.8639 (t80) cc_final: 0.7941 (t80) REVERT: A 848 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 849 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 852 LYS cc_start: 0.8291 (mttp) cc_final: 0.8026 (tttp) REVERT: A 862 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8400 (mmtm) REVERT: A 866 GLU cc_start: 0.7294 (tp30) cc_final: 0.7030 (tp30) REVERT: A 868 LYS cc_start: 0.8594 (mmmm) cc_final: 0.7798 (mmmm) REVERT: A 875 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7422 (tpt90) REVERT: A 880 LYS cc_start: 0.8293 (tptp) cc_final: 0.7835 (tptp) REVERT: A 881 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6933 (tm-30) REVERT: A 900 GLN cc_start: 0.8174 (tm130) cc_final: 0.7913 (tp40) REVERT: A 910 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7737 (ttm-80) REVERT: A 931 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 938 MET cc_start: 0.8521 (mmm) cc_final: 0.8239 (mmm) REVERT: B 81 ILE cc_start: 0.7953 (mt) cc_final: 0.7646 (mt) REVERT: B 84 SER cc_start: 0.8032 (t) cc_final: 0.7610 (p) REVERT: B 109 LEU cc_start: 0.7955 (mt) cc_final: 0.7643 (mt) REVERT: B 120 VAL cc_start: 0.8513 (t) cc_final: 0.8123 (p) REVERT: B 149 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7050 (tm-30) REVERT: B 188 LEU cc_start: 0.8128 (tp) cc_final: 0.7264 (tt) REVERT: B 199 MET cc_start: 0.7719 (mmm) cc_final: 0.7068 (tpt) REVERT: B 246 ASN cc_start: 0.8116 (m-40) cc_final: 0.7873 (m-40) REVERT: B 269 LEU cc_start: 0.7982 (tp) cc_final: 0.7685 (tp) REVERT: B 278 TRP cc_start: 0.8401 (t-100) cc_final: 0.8115 (t-100) REVERT: B 300 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6965 (mt-10) REVERT: B 337 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: B 351 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8075 (tpp-160) REVERT: B 384 ASP cc_start: 0.7091 (m-30) cc_final: 0.6885 (m-30) REVERT: B 387 TYR cc_start: 0.7849 (m-10) cc_final: 0.7378 (m-10) REVERT: B 420 ARG cc_start: 0.8083 (mtm180) cc_final: 0.7505 (mtm-85) REVERT: B 425 MET cc_start: 0.7636 (ttm) cc_final: 0.7400 (ttt) REVERT: B 443 GLU cc_start: 0.7736 (tp30) cc_final: 0.7139 (tp30) REVERT: B 475 GLN cc_start: 0.7470 (tp40) cc_final: 0.7187 (tp40) REVERT: B 499 ARG cc_start: 0.7616 (ptp90) cc_final: 0.7290 (ptp90) REVERT: B 500 ARG cc_start: 0.7857 (tpt90) cc_final: 0.7504 (tpp80) REVERT: B 512 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8231 (tp) REVERT: B 523 TRP cc_start: 0.7604 (m100) cc_final: 0.7031 (m100) REVERT: B 527 THR cc_start: 0.8041 (p) cc_final: 0.7546 (p) REVERT: B 531 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6021 (mm-30) REVERT: B 579 MET cc_start: 0.7765 (mmm) cc_final: 0.7378 (mmm) REVERT: B 581 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5897 (pp20) REVERT: B 586 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6235 (tmm) REVERT: B 588 LYS cc_start: 0.8212 (ttpp) cc_final: 0.7945 (ttpp) REVERT: B 590 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6858 (mm-30) REVERT: B 595 TRP cc_start: 0.8031 (m100) cc_final: 0.7709 (m100) REVERT: B 613 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 645 LYS cc_start: 0.8558 (tptp) cc_final: 0.8010 (tptp) REVERT: B 825 VAL cc_start: 0.8508 (t) cc_final: 0.8266 (p) REVERT: B 826 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7532 (m110) REVERT: B 841 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8146 (ttmm) REVERT: B 847 GLU cc_start: 0.7784 (tp30) cc_final: 0.7510 (tp30) REVERT: B 848 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 850 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 872 GLU cc_start: 0.7941 (tp30) cc_final: 0.7557 (tp30) REVERT: B 876 LEU cc_start: 0.8101 (mt) cc_final: 0.7831 (mt) REVERT: B 880 LYS cc_start: 0.8070 (tmmt) cc_final: 0.7689 (tmmt) REVERT: B 881 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7253 (mm-30) REVERT: B 903 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6210 (mtp-110) REVERT: B 907 ASN cc_start: 0.7669 (m-40) cc_final: 0.6413 (m110) REVERT: B 908 HIS cc_start: 0.7938 (m-70) cc_final: 0.7506 (m-70) REVERT: B 911 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6657 (mp0) REVERT: B 925 MET cc_start: 0.7352 (tmm) cc_final: 0.7099 (tmm) REVERT: B 928 HIS cc_start: 0.7136 (t70) cc_final: 0.6848 (t70) REVERT: B 929 LYS cc_start: 0.7785 (mtpp) cc_final: 0.7279 (mtpp) outliers start: 76 outliers final: 55 residues processed: 482 average time/residue: 0.3081 time to fit residues: 197.5416 Evaluate side-chains 512 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 447 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 894 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 GLU 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 389 ILE 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 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 626 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 361 ASN B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105580 restraints weight = 20184.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108986 restraints weight = 9372.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111056 restraints weight = 5421.072| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10798 Z= 0.183 Angle : 0.592 15.802 14638 Z= 0.303 Chirality : 0.039 0.194 1772 Planarity : 0.004 0.047 1796 Dihedral : 5.928 57.515 1465 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.36 % Allowed : 23.61 % Favored : 70.03 % 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: 1.86 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.57 (0.46), residues: 194 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 0.024 0.001 PHE B 625 TYR 0.013 0.001 TYR A 313 ARG 0.006 0.000 ARG A 351 *********************** 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 516 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 443 time to evaluate : 1.145 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: A 85 CYS cc_start: 0.8320 (m) cc_final: 0.7903 (m) REVERT: A 103 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 124 GLU cc_start: 0.7565 (tp30) cc_final: 0.6715 (tp30) REVERT: A 125 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 160 MET cc_start: 0.7751 (mmm) cc_final: 0.7362 (mmt) REVERT: A 199 MET cc_start: 0.7769 (mmm) cc_final: 0.7418 (mmm) REVERT: A 205 MET cc_start: 0.7593 (mmm) cc_final: 0.7153 (mpp) REVERT: A 217 LEU cc_start: 0.8375 (mt) cc_final: 0.8124 (mt) REVERT: A 218 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7574 (ttmt) REVERT: A 237 ASN cc_start: 0.7929 (t0) cc_final: 0.7702 (t0) REVERT: A 250 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7371 (mtmm) REVERT: A 292 HIS cc_start: 0.8183 (m-70) cc_final: 0.7607 (m-70) REVERT: A 319 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6582 (mt) REVERT: A 322 SER cc_start: 0.8103 (t) cc_final: 0.7739 (p) REVERT: A 335 ASN cc_start: 0.8644 (t0) cc_final: 0.8344 (t0) REVERT: A 337 GLU cc_start: 0.7281 (mp0) cc_final: 0.6616 (mp0) REVERT: A 346 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6622 (mt-10) REVERT: A 387 TYR cc_start: 0.7873 (m-10) cc_final: 0.7641 (m-10) REVERT: A 431 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7992 (mmt180) REVERT: A 454 LYS cc_start: 0.8359 (mttm) cc_final: 0.8080 (mttm) REVERT: A 477 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 479 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7537 (ttp80) REVERT: A 481 LEU cc_start: 0.8519 (mt) cc_final: 0.8251 (mt) REVERT: A 491 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7600 (ttm110) REVERT: A 499 ARG cc_start: 0.7802 (ttp80) cc_final: 0.7160 (ttp80) REVERT: A 502 HIS cc_start: 0.7836 (t-90) cc_final: 0.7320 (t-90) REVERT: A 506 ASN cc_start: 0.7967 (m-40) cc_final: 0.7531 (m-40) REVERT: A 512 LEU cc_start: 0.8531 (tp) cc_final: 0.8163 (tt) REVERT: A 534 ASP cc_start: 0.8082 (t0) cc_final: 0.7812 (t70) REVERT: A 578 MET cc_start: 0.8140 (ttm) cc_final: 0.7903 (ttm) REVERT: A 579 MET cc_start: 0.7949 (mmm) cc_final: 0.7396 (mmm) REVERT: A 596 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7767 (tmmt) REVERT: A 597 GLN cc_start: 0.7446 (mt0) cc_final: 0.7173 (mt0) REVERT: A 602 MET cc_start: 0.6498 (tpp) cc_final: 0.6238 (tpp) REVERT: A 611 LEU cc_start: 0.8262 (tp) cc_final: 0.7971 (tp) REVERT: A 613 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7627 (tm-30) REVERT: A 622 LYS cc_start: 0.7913 (tttp) cc_final: 0.7531 (tttp) REVERT: A 645 LYS cc_start: 0.8957 (tptp) cc_final: 0.8338 (tptp) REVERT: A 843 TYR cc_start: 0.8635 (t80) cc_final: 0.7925 (t80) REVERT: A 848 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 849 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 852 LYS cc_start: 0.8222 (mttp) cc_final: 0.7990 (tttp) REVERT: A 862 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8412 (mmtm) REVERT: A 866 GLU cc_start: 0.7240 (tp30) cc_final: 0.6972 (tp30) REVERT: A 868 LYS cc_start: 0.8575 (mmmm) cc_final: 0.7763 (mmmm) REVERT: A 875 ARG cc_start: 0.7667 (tpt90) cc_final: 0.7424 (tpt90) REVERT: A 880 LYS cc_start: 0.8290 (tptp) cc_final: 0.7816 (tptp) REVERT: A 881 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6967 (tm-30) REVERT: A 900 GLN cc_start: 0.8206 (tm130) cc_final: 0.7917 (tp40) REVERT: A 910 ARG cc_start: 0.8061 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: A 923 ASP cc_start: 0.7710 (p0) cc_final: 0.7338 (p0) REVERT: A 931 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 938 MET cc_start: 0.8536 (mmm) cc_final: 0.8262 (mmm) REVERT: B 109 LEU cc_start: 0.7926 (mt) cc_final: 0.7646 (mt) REVERT: B 149 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7051 (tm-30) REVERT: B 199 MET cc_start: 0.7632 (mmm) cc_final: 0.6862 (tpp) REVERT: B 246 ASN cc_start: 0.8073 (m-40) cc_final: 0.7755 (m-40) REVERT: B 269 LEU cc_start: 0.7965 (tp) cc_final: 0.7685 (tp) REVERT: B 278 TRP cc_start: 0.8392 (t-100) cc_final: 0.8082 (t-100) REVERT: B 300 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: B 337 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 351 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8048 (tpp-160) REVERT: B 361 ASN cc_start: 0.8135 (m-40) cc_final: 0.7789 (m110) REVERT: B 366 MET cc_start: 0.8109 (tpp) cc_final: 0.7659 (tpp) REVERT: B 387 TYR cc_start: 0.7835 (m-10) cc_final: 0.7443 (m-10) REVERT: B 420 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7596 (mtm-85) REVERT: B 443 GLU cc_start: 0.7734 (tp30) cc_final: 0.7106 (tp30) REVERT: B 475 GLN cc_start: 0.7467 (tp40) cc_final: 0.7169 (tp40) REVERT: B 499 ARG cc_start: 0.7605 (ptp90) cc_final: 0.7281 (ptp90) REVERT: B 500 ARG cc_start: 0.7827 (tpt90) cc_final: 0.7465 (tpp80) REVERT: B 512 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 523 TRP cc_start: 0.7625 (m100) cc_final: 0.7003 (m100) REVERT: B 527 THR cc_start: 0.8037 (p) cc_final: 0.7378 (p) REVERT: B 531 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5857 (mm-30) REVERT: B 579 MET cc_start: 0.7765 (mmm) cc_final: 0.7392 (mmm) REVERT: B 581 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5876 (pp20) REVERT: B 586 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.6198 (tmm) REVERT: B 588 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7915 (ttpp) REVERT: B 590 GLU cc_start: 0.7731 (mm-30) cc_final: 0.6822 (mm-30) REVERT: B 595 TRP cc_start: 0.8026 (m100) cc_final: 0.7702 (m100) REVERT: B 596 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8283 (mmmt) REVERT: B 613 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 645 LYS cc_start: 0.8491 (tptp) cc_final: 0.7987 (tptp) REVERT: B 825 VAL cc_start: 0.8483 (t) cc_final: 0.8249 (p) REVERT: B 826 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7562 (m110) REVERT: B 841 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8128 (ttmm) REVERT: B 847 GLU cc_start: 0.7743 (tp30) cc_final: 0.7494 (tp30) REVERT: B 848 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 850 VAL cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (p) REVERT: B 872 GLU cc_start: 0.7916 (tp30) cc_final: 0.7505 (tp30) REVERT: B 876 LEU cc_start: 0.8079 (mt) cc_final: 0.7833 (mt) REVERT: B 880 LYS cc_start: 0.8061 (tmmt) cc_final: 0.7672 (tmmt) REVERT: B 881 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7298 (mm-30) REVERT: B 903 ARG cc_start: 0.7151 (mtm180) cc_final: 0.6465 (mtm180) REVERT: B 907 ASN cc_start: 0.7669 (m-40) cc_final: 0.6472 (m-40) REVERT: B 908 HIS cc_start: 0.7918 (m-70) cc_final: 0.7478 (m-70) REVERT: B 911 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6630 (mp0) REVERT: B 925 MET cc_start: 0.7330 (tmm) cc_final: 0.7054 (tmm) REVERT: B 928 HIS cc_start: 0.7156 (t70) cc_final: 0.6828 (t70) REVERT: B 929 LYS cc_start: 0.7750 (mtpp) cc_final: 0.7268 (mtpp) outliers start: 73 outliers final: 52 residues processed: 471 average time/residue: 0.3004 time to fit residues: 187.0821 Evaluate side-chains 497 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 434 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 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 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 894 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 915 GLU 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 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 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 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU 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 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 74 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 111 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.0050 chunk 93 optimal weight: 0.7980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107080 restraints weight = 19941.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110474 restraints weight = 9327.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112563 restraints weight = 5428.493| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10798 Z= 0.164 Angle : 0.583 15.761 14638 Z= 0.299 Chirality : 0.039 0.214 1772 Planarity : 0.004 0.043 1796 Dihedral : 5.907 55.318 1465 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.10 % Allowed : 24.13 % 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: 2.37 (0.23), residues: 1344 helix: 1.91 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.50 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 635 HIS 0.002 0.000 HIS B 292 PHE 0.021 0.001 PHE B 625 TYR 0.012 0.001 TYR A 313 ARG 0.007 0.001 ARG A 351 *********************** 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 512 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 442 time to evaluate : 1.315 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: 0.8288 (m) cc_final: 0.7893 (m) REVERT: A 103 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 124 GLU cc_start: 0.7491 (tp30) cc_final: 0.6635 (tp30) REVERT: A 160 MET cc_start: 0.7738 (mmm) cc_final: 0.7341 (mmt) REVERT: A 199 MET cc_start: 0.7706 (mmm) cc_final: 0.7345 (mmm) REVERT: A 205 MET cc_start: 0.7540 (mmm) cc_final: 0.7094 (mpp) REVERT: A 217 LEU cc_start: 0.8373 (mt) cc_final: 0.8106 (mt) REVERT: A 218 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7595 (ttmt) REVERT: A 237 ASN cc_start: 0.7885 (t0) cc_final: 0.7672 (t0) REVERT: A 292 HIS cc_start: 0.8180 (m-70) cc_final: 0.7547 (m-70) REVERT: A 322 SER cc_start: 0.8075 (t) cc_final: 0.7707 (p) REVERT: A 335 ASN cc_start: 0.8640 (t0) cc_final: 0.8369 (t0) REVERT: A 337 GLU cc_start: 0.7270 (mp0) cc_final: 0.6602 (mp0) REVERT: A 387 TYR cc_start: 0.7837 (m-10) cc_final: 0.7552 (m-10) REVERT: A 401 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6698 (mtm) REVERT: A 431 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7893 (mmt180) REVERT: A 454 LYS cc_start: 0.8377 (mttm) cc_final: 0.8169 (mttm) REVERT: A 476 THR cc_start: 0.8325 (m) cc_final: 0.7723 (p) REVERT: A 477 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 479 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7564 (ttp80) REVERT: A 481 LEU cc_start: 0.8487 (mt) cc_final: 0.8222 (mt) REVERT: A 491 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7596 (ttm110) REVERT: A 499 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7168 (ttp80) REVERT: A 506 ASN cc_start: 0.7971 (m-40) cc_final: 0.7620 (m-40) REVERT: A 512 LEU cc_start: 0.8479 (tp) cc_final: 0.8135 (tt) REVERT: A 578 MET cc_start: 0.8185 (ttm) cc_final: 0.7929 (ttm) REVERT: A 579 MET cc_start: 0.7965 (mmm) cc_final: 0.7393 (mmm) REVERT: A 596 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7742 (tmmt) REVERT: A 597 GLN cc_start: 0.7431 (mt0) cc_final: 0.7177 (mt0) REVERT: A 602 MET cc_start: 0.6538 (tpp) cc_final: 0.6287 (tpp) REVERT: A 611 LEU cc_start: 0.8278 (tp) cc_final: 0.7964 (tp) REVERT: A 613 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7585 (tm-30) REVERT: A 622 LYS cc_start: 0.7897 (tttp) cc_final: 0.7501 (tttp) REVERT: A 645 LYS cc_start: 0.8950 (tptp) cc_final: 0.8349 (tptp) REVERT: A 837 TYR cc_start: 0.8252 (t80) cc_final: 0.7902 (t80) REVERT: A 843 TYR cc_start: 0.8624 (t80) cc_final: 0.8036 (t80) REVERT: A 848 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 852 LYS cc_start: 0.8216 (mttp) cc_final: 0.7984 (tttp) REVERT: A 862 LYS cc_start: 0.8601 (mmtm) cc_final: 0.8339 (mmtm) REVERT: A 866 GLU cc_start: 0.7235 (tp30) cc_final: 0.6972 (tp30) REVERT: A 880 LYS cc_start: 0.8282 (tptp) cc_final: 0.7777 (tptp) REVERT: A 881 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6977 (tm-30) REVERT: A 900 GLN cc_start: 0.8189 (tm130) cc_final: 0.7893 (tp40) REVERT: A 910 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7756 (ttm-80) REVERT: A 923 ASP cc_start: 0.7655 (p0) cc_final: 0.7351 (p0) REVERT: A 931 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 938 MET cc_start: 0.8548 (mmm) cc_final: 0.8281 (mmm) REVERT: B 84 SER cc_start: 0.7983 (t) cc_final: 0.7532 (p) REVERT: B 109 LEU cc_start: 0.7919 (mt) cc_final: 0.7669 (mt) REVERT: B 149 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7033 (tm-30) REVERT: B 199 MET cc_start: 0.7585 (mmm) cc_final: 0.6942 (tpt) REVERT: B 246 ASN cc_start: 0.8061 (m-40) cc_final: 0.7741 (m-40) REVERT: B 269 LEU cc_start: 0.7906 (tp) cc_final: 0.7625 (tp) REVERT: B 278 TRP cc_start: 0.8367 (t-100) cc_final: 0.8067 (t-100) REVERT: B 300 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6936 (mt-10) REVERT: B 337 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 351 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8049 (tpp-160) REVERT: B 366 MET cc_start: 0.8081 (tpp) cc_final: 0.7634 (tpp) REVERT: B 384 ASP cc_start: 0.7276 (m-30) cc_final: 0.6901 (m-30) REVERT: B 387 TYR cc_start: 0.7797 (m-10) cc_final: 0.7386 (m-10) REVERT: B 420 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7517 (mtm-85) REVERT: B 443 GLU cc_start: 0.7706 (tp30) cc_final: 0.7038 (tp30) REVERT: B 475 GLN cc_start: 0.7497 (tp40) cc_final: 0.7183 (tp40) REVERT: B 499 ARG cc_start: 0.7576 (ptp90) cc_final: 0.7230 (ptp90) REVERT: B 500 ARG cc_start: 0.7822 (tpt90) cc_final: 0.7436 (tpp80) REVERT: B 512 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8215 (tp) REVERT: B 517 PHE cc_start: 0.7539 (m-10) cc_final: 0.7225 (m-80) REVERT: B 523 TRP cc_start: 0.7629 (m100) cc_final: 0.7085 (m100) REVERT: B 527 THR cc_start: 0.7993 (p) cc_final: 0.7275 (p) REVERT: B 531 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5929 (mm-30) REVERT: B 579 MET cc_start: 0.7755 (mmm) cc_final: 0.7412 (mmm) REVERT: B 581 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5837 (pp20) REVERT: B 586 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6162 (tmm) REVERT: B 588 LYS cc_start: 0.8196 (ttpp) cc_final: 0.7904 (ttpp) REVERT: B 590 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6778 (mm-30) REVERT: B 595 TRP cc_start: 0.8011 (m100) cc_final: 0.7669 (m100) REVERT: B 596 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8254 (mmmt) REVERT: B 600 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6308 (m-70) REVERT: B 613 GLN cc_start: 0.7491 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 645 LYS cc_start: 0.8474 (tptp) cc_final: 0.7965 (tptp) REVERT: B 825 VAL cc_start: 0.8506 (t) cc_final: 0.8291 (p) REVERT: B 826 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7611 (m110) REVERT: B 847 GLU cc_start: 0.7661 (tp30) cc_final: 0.7438 (tp30) REVERT: B 848 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 850 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7893 (p) REVERT: B 872 GLU cc_start: 0.7842 (tp30) cc_final: 0.7441 (tp30) REVERT: B 876 LEU cc_start: 0.8068 (mt) cc_final: 0.7854 (mt) REVERT: B 880 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7489 (tmmt) REVERT: B 903 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6155 (mtm180) REVERT: B 907 ASN cc_start: 0.7686 (m-40) cc_final: 0.6362 (m110) REVERT: B 911 GLU cc_start: 0.7435 (mt-10) cc_final: 0.6603 (mp0) REVERT: B 925 MET cc_start: 0.7425 (tmm) cc_final: 0.7151 (tmm) REVERT: B 928 HIS cc_start: 0.7133 (t70) cc_final: 0.6791 (t70) REVERT: B 929 LYS cc_start: 0.7579 (mtpp) cc_final: 0.7104 (mtpp) REVERT: B 941 LEU cc_start: 0.8690 (tp) cc_final: 0.8487 (tt) outliers start: 70 outliers final: 49 residues processed: 468 average time/residue: 0.2908 time to fit residues: 179.4549 Evaluate side-chains 502 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 439 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 889 HIS Chi-restraints excluded: chain A residue 894 VAL 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 300 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 498 VAL 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 626 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 875 ARG Chi-restraints excluded: chain B residue 880 LYS Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 101 optimal weight: 0.0050 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.129028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110350 restraints weight = 20183.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113806 restraints weight = 9389.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115795 restraints weight = 5398.690| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10798 Z= 0.176 Angle : 0.609 16.381 14638 Z= 0.313 Chirality : 0.039 0.216 1772 Planarity : 0.005 0.122 1796 Dihedral : 5.811 55.508 1464 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.84 % Allowed : 24.74 % Favored : 69.43 % 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: 2.40 (0.23), residues: 1344 helix: 1.96 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.59 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 643 HIS 0.005 0.000 HIS A 157 PHE 0.023 0.001 PHE B 288 TYR 0.014 0.001 TYR B 843 ARG 0.009 0.001 ARG A 609 *********************** 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 510 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 443 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8270 (m) cc_final: 0.7898 (m) REVERT: A 124 GLU cc_start: 0.7463 (tp30) cc_final: 0.6627 (tp30) REVERT: A 160 MET cc_start: 0.7638 (mmm) cc_final: 0.7237 (mmt) REVERT: A 205 MET cc_start: 0.7545 (mmm) cc_final: 0.7076 (mpp) REVERT: A 217 LEU cc_start: 0.8373 (mt) cc_final: 0.8118 (mt) REVERT: A 218 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7631 (ttmt) REVERT: A 237 ASN cc_start: 0.7892 (t0) cc_final: 0.7668 (t0) REVERT: A 292 HIS cc_start: 0.8206 (m-70) cc_final: 0.7604 (m-70) REVERT: A 322 SER cc_start: 0.8062 (t) cc_final: 0.7703 (p) REVERT: A 335 ASN cc_start: 0.8598 (t0) cc_final: 0.8361 (t0) REVERT: A 337 GLU cc_start: 0.7306 (mp0) cc_final: 0.6693 (mp0) REVERT: A 387 TYR cc_start: 0.7926 (m-10) cc_final: 0.7571 (m-10) REVERT: A 431 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7897 (mmt180) REVERT: A 454 LYS cc_start: 0.8381 (mttm) cc_final: 0.8091 (mtpp) REVERT: A 476 THR cc_start: 0.8314 (m) cc_final: 0.7667 (p) REVERT: A 477 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8172 (tt) REVERT: A 479 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7579 (ttp80) REVERT: A 481 LEU cc_start: 0.8513 (mt) cc_final: 0.8255 (mt) REVERT: A 499 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7263 (ttp80) REVERT: A 506 ASN cc_start: 0.7981 (m-40) cc_final: 0.7610 (m-40) REVERT: A 512 LEU cc_start: 0.8448 (tp) cc_final: 0.8115 (tt) REVERT: A 534 ASP cc_start: 0.7992 (t0) cc_final: 0.7778 (t70) REVERT: A 578 MET cc_start: 0.8085 (ttm) cc_final: 0.7855 (ttm) REVERT: A 579 MET cc_start: 0.7843 (mmm) cc_final: 0.7324 (mmm) REVERT: A 586 MET cc_start: 0.7927 (tpt) cc_final: 0.7714 (tpt) REVERT: A 596 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7749 (tmmt) REVERT: A 597 GLN cc_start: 0.7402 (mt0) cc_final: 0.7171 (mt0) REVERT: A 602 MET cc_start: 0.6518 (tpp) cc_final: 0.6246 (tpp) REVERT: A 613 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 622 LYS cc_start: 0.7902 (tttp) cc_final: 0.7507 (tttp) REVERT: A 645 LYS cc_start: 0.8946 (tptp) cc_final: 0.8312 (tptp) REVERT: A 837 TYR cc_start: 0.8262 (t80) cc_final: 0.7902 (t80) REVERT: A 843 TYR cc_start: 0.8612 (t80) cc_final: 0.8004 (t80) REVERT: A 848 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 849 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 852 LYS cc_start: 0.8208 (mttp) cc_final: 0.7951 (tttp) REVERT: A 862 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8300 (mmtm) REVERT: A 867 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9021 (mm) REVERT: A 868 LYS cc_start: 0.8526 (mmmm) cc_final: 0.7691 (mmmm) REVERT: A 875 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7271 (tpt170) REVERT: A 880 LYS cc_start: 0.8258 (tptp) cc_final: 0.7754 (tptp) REVERT: A 881 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6945 (tm-30) REVERT: A 900 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7875 (tp40) REVERT: A 910 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7734 (ttm-80) REVERT: A 923 ASP cc_start: 0.7638 (p0) cc_final: 0.7340 (p0) REVERT: A 931 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 937 LYS cc_start: 0.8726 (mttm) cc_final: 0.8250 (mtpp) REVERT: A 938 MET cc_start: 0.8553 (mmm) cc_final: 0.8285 (mmm) REVERT: A 940 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7676 (tpp80) REVERT: B 84 SER cc_start: 0.7990 (t) cc_final: 0.7551 (p) REVERT: B 109 LEU cc_start: 0.7940 (mt) cc_final: 0.7691 (mt) REVERT: B 120 VAL cc_start: 0.8510 (t) cc_final: 0.8102 (p) REVERT: B 149 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 199 MET cc_start: 0.7595 (mmm) cc_final: 0.6963 (tpt) REVERT: B 246 ASN cc_start: 0.8017 (m-40) cc_final: 0.7736 (m-40) REVERT: B 278 TRP cc_start: 0.8373 (t-100) cc_final: 0.8075 (t-100) REVERT: B 300 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: B 337 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: B 351 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8267 (tpp-160) REVERT: B 361 ASN cc_start: 0.8124 (m-40) cc_final: 0.7774 (m110) REVERT: B 366 MET cc_start: 0.8094 (tpp) cc_final: 0.7618 (tpp) REVERT: B 384 ASP cc_start: 0.7232 (m-30) cc_final: 0.6944 (m-30) REVERT: B 387 TYR cc_start: 0.7783 (m-10) cc_final: 0.7381 (m-10) REVERT: B 420 ARG cc_start: 0.8115 (mtm180) cc_final: 0.7635 (mtm-85) REVERT: B 443 GLU cc_start: 0.7696 (tp30) cc_final: 0.7026 (tp30) REVERT: B 475 GLN cc_start: 0.7491 (tp40) cc_final: 0.7194 (tp40) REVERT: B 499 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7207 (ptp90) REVERT: B 500 ARG cc_start: 0.7780 (tpt90) cc_final: 0.7388 (tpp80) REVERT: B 512 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 523 TRP cc_start: 0.7642 (m100) cc_final: 0.7128 (m100) REVERT: B 527 THR cc_start: 0.7989 (p) cc_final: 0.7249 (p) REVERT: B 531 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5930 (mm-30) REVERT: B 579 MET cc_start: 0.7706 (mmm) cc_final: 0.7378 (mmm) REVERT: B 586 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6158 (tmm) REVERT: B 588 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7912 (ttpp) REVERT: B 590 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6790 (mm-30) REVERT: B 595 TRP cc_start: 0.7992 (m100) cc_final: 0.7664 (m100) REVERT: B 596 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8283 (mmmt) REVERT: B 600 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.6226 (m-70) REVERT: B 613 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 645 LYS cc_start: 0.8448 (tptp) cc_final: 0.7951 (tptp) REVERT: B 825 VAL cc_start: 0.8499 (t) cc_final: 0.8282 (p) REVERT: B 826 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7632 (m110) REVERT: B 841 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8267 (ttmm) REVERT: B 847 GLU cc_start: 0.7660 (tp30) cc_final: 0.7429 (tp30) REVERT: B 848 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7779 (mt-10) REVERT: B 850 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (p) REVERT: B 872 GLU cc_start: 0.7808 (tp30) cc_final: 0.7444 (tp30) REVERT: B 881 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7281 (mm-30) REVERT: B 903 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6280 (mtm180) REVERT: B 907 ASN cc_start: 0.7699 (m-40) cc_final: 0.6346 (m110) REVERT: B 911 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6599 (mp0) REVERT: B 925 MET cc_start: 0.7443 (tmm) cc_final: 0.7150 (tmm) REVERT: B 928 HIS cc_start: 0.7160 (t70) cc_final: 0.6807 (t70) REVERT: B 929 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7217 (mtpp) REVERT: B 941 LEU cc_start: 0.8687 (tp) cc_final: 0.8483 (tt) outliers start: 67 outliers final: 50 residues processed: 467 average time/residue: 0.2884 time to fit residues: 177.8825 Evaluate side-chains 501 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 439 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 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 894 VAL Chi-restraints excluded: chain A residue 900 GLN 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 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 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 498 VAL 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 626 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL 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 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 0.0370 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.5862 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.128846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110301 restraints weight = 19970.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113689 restraints weight = 9343.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115795 restraints weight = 5414.368| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10798 Z= 0.201 Angle : 0.635 16.076 14638 Z= 0.325 Chirality : 0.041 0.235 1772 Planarity : 0.004 0.053 1796 Dihedral : 5.785 55.998 1464 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.57 % Allowed : 25.52 % Favored : 68.90 % 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: 2.34 (0.23), residues: 1344 helix: 1.92 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.62 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 643 HIS 0.004 0.000 HIS A 157 PHE 0.020 0.001 PHE B 625 TYR 0.012 0.001 TYR B 843 ARG 0.007 0.001 ARG A 399 ********************** 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 503 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 439 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8279 (m) cc_final: 0.7892 (m) REVERT: A 112 ILE cc_start: 0.8392 (mt) cc_final: 0.8110 (mm) REVERT: A 124 GLU cc_start: 0.7452 (tp30) cc_final: 0.6635 (tp30) REVERT: A 160 MET cc_start: 0.7628 (mmm) cc_final: 0.7230 (mmt) REVERT: A 205 MET cc_start: 0.7546 (mmm) cc_final: 0.6985 (mpp) REVERT: A 217 LEU cc_start: 0.8383 (mt) cc_final: 0.8111 (mt) REVERT: A 218 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7654 (ttmt) REVERT: A 237 ASN cc_start: 0.7893 (t0) cc_final: 0.7675 (t0) REVERT: A 292 HIS cc_start: 0.8242 (m-70) cc_final: 0.7594 (m-70) REVERT: A 319 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6656 (mt) REVERT: A 322 SER cc_start: 0.8064 (t) cc_final: 0.7702 (p) REVERT: A 335 ASN cc_start: 0.8592 (t0) cc_final: 0.8360 (t0) REVERT: A 337 GLU cc_start: 0.7301 (mp0) cc_final: 0.6688 (mp0) REVERT: A 387 TYR cc_start: 0.7859 (m-10) cc_final: 0.7567 (m-10) REVERT: A 401 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6589 (mtm) REVERT: A 431 ARG cc_start: 0.8150 (mmt180) cc_final: 0.7933 (mmt-90) REVERT: A 454 LYS cc_start: 0.8346 (mttm) cc_final: 0.8060 (mtpp) REVERT: A 476 THR cc_start: 0.8302 (m) cc_final: 0.7655 (p) REVERT: A 477 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 479 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7580 (ttp80) REVERT: A 481 LEU cc_start: 0.8524 (mt) cc_final: 0.8260 (mt) REVERT: A 499 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7325 (ttp80) REVERT: A 506 ASN cc_start: 0.7980 (m-40) cc_final: 0.7601 (m-40) REVERT: A 512 LEU cc_start: 0.8449 (tp) cc_final: 0.8122 (tt) REVERT: A 578 MET cc_start: 0.8035 (ttm) cc_final: 0.7821 (ttm) REVERT: A 579 MET cc_start: 0.7799 (mmm) cc_final: 0.7298 (mmm) REVERT: A 586 MET cc_start: 0.7873 (tpt) cc_final: 0.7672 (tpt) REVERT: A 596 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7764 (tmmt) REVERT: A 602 MET cc_start: 0.6638 (tpp) cc_final: 0.6340 (tpp) REVERT: A 613 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 616 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 622 LYS cc_start: 0.7920 (tttp) cc_final: 0.7484 (tttp) REVERT: A 645 LYS cc_start: 0.8952 (tptp) cc_final: 0.8406 (tptp) REVERT: A 647 LYS cc_start: 0.8724 (mppt) cc_final: 0.8466 (mptt) REVERT: A 843 TYR cc_start: 0.8594 (t80) cc_final: 0.8007 (t80) REVERT: A 848 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 849 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7913 (mm-30) REVERT: A 852 LYS cc_start: 0.8183 (mttp) cc_final: 0.7941 (tttp) REVERT: A 862 LYS cc_start: 0.8489 (mmtm) cc_final: 0.8265 (mmtm) REVERT: A 867 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9101 (mm) REVERT: A 875 ARG cc_start: 0.7701 (tpt90) cc_final: 0.7303 (tpt170) REVERT: A 880 LYS cc_start: 0.8259 (tptp) cc_final: 0.7768 (tptp) REVERT: A 881 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6953 (tm-30) REVERT: A 900 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (tp40) REVERT: A 910 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7827 (ttm-80) REVERT: A 923 ASP cc_start: 0.7655 (p0) cc_final: 0.7386 (p0) REVERT: A 931 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 937 LYS cc_start: 0.8737 (mttm) cc_final: 0.8240 (ttmm) REVERT: A 938 MET cc_start: 0.8549 (mmm) cc_final: 0.8308 (mmm) REVERT: A 940 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7688 (tpp80) REVERT: B 84 SER cc_start: 0.8016 (t) cc_final: 0.7561 (p) REVERT: B 109 LEU cc_start: 0.7948 (mt) cc_final: 0.7714 (mt) REVERT: B 128 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7616 (ttp-110) REVERT: B 149 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7032 (tm-30) REVERT: B 199 MET cc_start: 0.7595 (mmm) cc_final: 0.6959 (tpt) REVERT: B 246 ASN cc_start: 0.8035 (m-40) cc_final: 0.7735 (m-40) REVERT: B 278 TRP cc_start: 0.8385 (t-100) cc_final: 0.8099 (t-100) REVERT: B 300 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 337 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: B 351 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8270 (tpp-160) REVERT: B 366 MET cc_start: 0.8066 (tpp) cc_final: 0.7612 (tpp) REVERT: B 384 ASP cc_start: 0.7225 (m-30) cc_final: 0.6961 (m-30) REVERT: B 387 TYR cc_start: 0.7794 (m-10) cc_final: 0.7387 (m-10) REVERT: B 420 ARG cc_start: 0.8093 (mtm180) cc_final: 0.7665 (mtm-85) REVERT: B 421 ASN cc_start: 0.8170 (m-40) cc_final: 0.7775 (m110) REVERT: B 443 GLU cc_start: 0.7689 (tp30) cc_final: 0.7045 (tp30) REVERT: B 475 GLN cc_start: 0.7513 (tp40) cc_final: 0.7220 (tp40) REVERT: B 499 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7207 (ptp90) REVERT: B 500 ARG cc_start: 0.7766 (tpt90) cc_final: 0.7405 (tpp80) REVERT: B 512 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 523 TRP cc_start: 0.7669 (m100) cc_final: 0.7335 (m100) REVERT: B 527 THR cc_start: 0.8007 (p) cc_final: 0.7251 (p) REVERT: B 531 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6111 (mm-30) REVERT: B 579 MET cc_start: 0.7664 (mmm) cc_final: 0.7376 (mmm) REVERT: B 586 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6117 (tmm) REVERT: B 588 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7908 (ttpp) REVERT: B 590 GLU cc_start: 0.7712 (mm-30) cc_final: 0.6789 (mm-30) REVERT: B 595 TRP cc_start: 0.7989 (m100) cc_final: 0.7651 (m100) REVERT: B 596 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8274 (mmmt) REVERT: B 600 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6150 (m-70) REVERT: B 613 GLN cc_start: 0.7490 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 645 LYS cc_start: 0.8419 (tptp) cc_final: 0.7934 (tptp) REVERT: B 825 VAL cc_start: 0.8498 (t) cc_final: 0.8283 (p) REVERT: B 826 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7632 (m110) REVERT: B 841 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8147 (ttmm) REVERT: B 847 GLU cc_start: 0.7635 (tp30) cc_final: 0.7381 (tp30) REVERT: B 848 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 881 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7205 (mm-30) REVERT: B 903 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6294 (mtm180) REVERT: B 907 ASN cc_start: 0.7706 (m-40) cc_final: 0.6384 (m110) REVERT: B 911 GLU cc_start: 0.7450 (mt-10) cc_final: 0.6633 (mp0) REVERT: B 925 MET cc_start: 0.7415 (tmm) cc_final: 0.7098 (tmm) REVERT: B 928 HIS cc_start: 0.7180 (t70) cc_final: 0.6818 (t70) REVERT: B 929 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7255 (mtpp) REVERT: B 941 LEU cc_start: 0.8677 (tp) cc_final: 0.8473 (tt) outliers start: 64 outliers final: 49 residues processed: 463 average time/residue: 0.2854 time to fit residues: 174.0845 Evaluate side-chains 498 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 437 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 894 VAL Chi-restraints excluded: chain A residue 900 GLN 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 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 383 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 498 VAL 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 626 ILE Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 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 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 108 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 55 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106789 restraints weight = 19854.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110201 restraints weight = 9324.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112284 restraints weight = 5440.853| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10798 Z= 0.189 Angle : 0.632 15.857 14638 Z= 0.321 Chirality : 0.040 0.221 1772 Planarity : 0.004 0.042 1796 Dihedral : 5.750 55.482 1464 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.75 % Allowed : 25.26 % Favored : 68.99 % 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: 2.35 (0.23), residues: 1344 helix: 1.92 (0.15), residues: 1150 sheet: None (None), residues: 0 loop : -0.59 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 643 HIS 0.002 0.000 HIS B 292 PHE 0.023 0.001 PHE B 288 TYR 0.014 0.001 TYR B 843 ARG 0.010 0.001 ARG A 399 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4195.07 seconds wall clock time: 76 minutes 36.05 seconds (4596.05 seconds total)