Starting phenix.real_space_refine on Wed Sep 17 19:01:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqa_38571/09_2025/8xqa_38571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqa_38571/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xqa_38571/09_2025/8xqa_38571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqa_38571/09_2025/8xqa_38571.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xqa_38571/09_2025/8xqa_38571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqa_38571/09_2025/8xqa_38571.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.14, per 1000 atoms: 0.30 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: 1.09 Conformation dependent library (CDL) restraints added in 424.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.33 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: 2.03 Time building geometry restraints manager: 1.44 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: 0.02 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: 1.750 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.400 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 10798 Z= 0.253 Angle : 0.762 15.739 14638 Z= 0.438 Chirality : 0.048 0.168 1772 Planarity : 0.007 0.057 1796 Dihedral : 14.998 89.102 3904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.62 % Allowed : 11.50 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 583 TYR 0.015 0.002 TYR A 191 PHE 0.021 0.002 PHE B 455 TRP 0.017 0.002 TRP A 635 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00527 (10798) covalent geometry : angle 0.76164 (14638) hydrogen bonds : bond 0.10345 ( 909) hydrogen bonds : angle 5.68188 ( 2718) *********************** 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 : 0.408 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: 0.6415 (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: 0.8406 (tt) REVERT: A 479 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7240 (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: 0.7649 (m110) REVERT: A 531 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6845 (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: 0.7372 (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: 0.7406 (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: 0.6858 (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: 0.7178 (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: 0.8350 (tt) REVERT: B 390 ILE cc_start: 0.8477 (mm) cc_final: 0.8255 (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: 0.7167 (tp30) REVERT: B 450 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7866 (p) REVERT: B 499 ARG cc_start: 0.7647 (ptp90) cc_final: 0.7344 (ptp90) REVERT: B 500 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7450 (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: 0.7726 (tmmt) REVERT: B 907 ASN cc_start: 0.7574 (m-40) cc_final: 0.6486 (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: 0.1283 time to fit residues: 88.3465 Evaluate side-chains 478 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 443 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 450 VAL 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.123066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.104737 restraints weight = 19800.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108055 restraints weight = 9193.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110107 restraints weight = 5298.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111406 restraints weight = 3579.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112239 restraints weight = 2721.583| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1482 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= 0.163 Angle : 0.565 11.052 14638 Z= 0.305 Chirality : 0.039 0.262 1772 Planarity : 0.004 0.053 1796 Dihedral : 8.219 70.430 1504 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 6.01 % Allowed : 17.16 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.22), residues: 1344 helix: 0.94 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.91 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 910 TYR 0.016 0.001 TYR B 594 PHE 0.026 0.001 PHE B 163 TRP 0.027 0.002 TRP B 523 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00321 (10798) covalent geometry : angle 0.56550 (14638) hydrogen bonds : bond 0.04760 ( 909) hydrogen bonds : angle 4.43302 ( 2718) *********************** 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 535 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 466 time to evaluate : 0.398 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: A 76 LYS cc_start: 0.7465 (mmtm) cc_final: 0.7202 (mmtm) REVERT: A 85 CYS cc_start: 0.8391 (m) cc_final: 0.8050 (m) REVERT: A 112 ILE cc_start: 0.8380 (mt) cc_final: 0.8056 (mm) REVERT: A 124 GLU cc_start: 0.7635 (tp30) cc_final: 0.6723 (tp30) REVERT: A 128 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7402 (ttp-170) REVERT: A 160 MET cc_start: 0.7750 (mmm) cc_final: 0.7360 (mmt) REVERT: A 186 MET cc_start: 0.6723 (mtp) cc_final: 0.6466 (mtp) REVERT: A 205 MET cc_start: 0.7623 (mmm) cc_final: 0.7310 (mpp) REVERT: A 217 LEU cc_start: 0.8445 (mt) cc_final: 0.8184 (mt) REVERT: A 218 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7604 (mtmt) REVERT: A 237 ASN cc_start: 0.7941 (t0) cc_final: 0.7721 (t0) REVERT: A 257 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7523 (pp) REVERT: A 292 HIS cc_start: 0.8301 (m-70) cc_final: 0.7758 (m-70) REVERT: A 335 ASN cc_start: 0.8668 (t0) cc_final: 0.8315 (t0) REVERT: A 401 MET cc_start: 0.7165 (mtm) cc_final: 0.6958 (mtm) REVERT: A 406 PHE cc_start: 0.7703 (m-80) cc_final: 0.7370 (m-80) REVERT: A 454 LYS cc_start: 0.8405 (mttm) cc_final: 0.8093 (mttm) REVERT: A 477 LEU cc_start: 0.8637 (tt) cc_final: 0.8260 (tt) REVERT: A 479 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7419 (ttp80) REVERT: A 481 LEU cc_start: 0.8523 (mt) cc_final: 0.8234 (mt) REVERT: A 486 ILE cc_start: 0.8460 (mt) cc_final: 0.8198 (tt) REVERT: A 499 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7112 (ttp80) REVERT: A 502 HIS cc_start: 0.7785 (t-90) cc_final: 0.7209 (t-90) REVERT: A 506 ASN cc_start: 0.7948 (m-40) cc_final: 0.7390 (m-40) REVERT: A 514 SER cc_start: 0.8186 (p) cc_final: 0.7955 (p) REVERT: A 578 MET cc_start: 0.7991 (ttm) cc_final: 0.7756 (ttm) REVERT: A 579 MET cc_start: 0.7784 (mmm) cc_final: 0.7290 (mmm) REVERT: A 596 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7825 (tmmt) REVERT: A 597 GLN cc_start: 0.7458 (mt0) cc_final: 0.7238 (mt0) REVERT: A 613 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 622 LYS cc_start: 0.7911 (tttp) cc_final: 0.7665 (tttp) REVERT: A 645 LYS cc_start: 0.8903 (tptp) cc_final: 0.8286 (tptp) REVERT: A 843 TYR cc_start: 0.8612 (t80) cc_final: 0.7848 (t80) REVERT: A 848 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 852 LYS cc_start: 0.8178 (mttp) cc_final: 0.7935 (mttp) REVERT: A 862 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8319 (mmtm) REVERT: A 868 LYS cc_start: 0.8633 (mmmm) cc_final: 0.7862 (mmmm) REVERT: A 875 ARG cc_start: 0.7599 (tpt90) cc_final: 0.7140 (tpt90) REVERT: A 880 LYS cc_start: 0.8249 (tptp) cc_final: 0.7826 (tptp) REVERT: A 900 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7626 (tp40) REVERT: A 925 MET cc_start: 0.7866 (mmm) cc_final: 0.7539 (mmm) REVERT: B 77 VAL cc_start: 0.8290 (t) cc_final: 0.7966 (m) REVERT: B 84 SER cc_start: 0.8072 (t) cc_final: 0.7691 (p) REVERT: B 109 LEU cc_start: 0.7949 (mt) cc_final: 0.7682 (mt) REVERT: B 124 GLU cc_start: 0.7404 (tp30) cc_final: 0.7172 (tp30) REVERT: B 149 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6966 (tm-30) REVERT: B 205 MET cc_start: 0.8143 (mmp) cc_final: 0.7934 (mmp) REVERT: B 233 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 249 MET cc_start: 0.7526 (tmm) cc_final: 0.7065 (tmm) REVERT: B 278 TRP cc_start: 0.8366 (t-100) cc_final: 0.8039 (t-100) REVERT: B 300 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 337 GLU cc_start: 0.7700 (mp0) cc_final: 0.7409 (mp0) REVERT: B 351 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8068 (tpp-160) REVERT: B 384 ASP cc_start: 0.6889 (m-30) cc_final: 0.6546 (m-30) REVERT: B 388 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8340 (tt) REVERT: B 390 ILE cc_start: 0.8513 (mm) cc_final: 0.8285 (mm) REVERT: B 420 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7763 (mtm-85) REVERT: B 443 GLU cc_start: 0.7651 (tp30) cc_final: 0.7205 (tp30) REVERT: B 499 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7261 (ptp90) REVERT: B 500 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7445 (tpt90) REVERT: B 512 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8080 (tp) REVERT: B 527 THR cc_start: 0.8311 (p) cc_final: 0.7553 (p) REVERT: B 531 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6311 (mm-30) REVERT: B 579 MET cc_start: 0.7665 (mmm) cc_final: 0.7371 (mmm) REVERT: B 581 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5930 (pp20) REVERT: B 586 MET cc_start: 0.7490 (tmm) cc_final: 0.5948 (tmm) REVERT: B 588 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7741 (ttpp) REVERT: B 590 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 591 LYS cc_start: 0.8187 (mtmp) cc_final: 0.7917 (mtmp) REVERT: B 595 TRP cc_start: 0.7935 (m100) cc_final: 0.7667 (m100) REVERT: B 596 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8163 (mmmt) REVERT: B 613 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6942 (tm-30) REVERT: B 635 TRP cc_start: 0.5364 (m100) cc_final: 0.5147 (m100) REVERT: B 645 LYS cc_start: 0.8486 (tptp) cc_final: 0.7950 (tptp) REVERT: B 825 VAL cc_start: 0.8409 (t) cc_final: 0.8184 (p) REVERT: B 826 ASN cc_start: 0.7896 (t0) cc_final: 0.7545 (m110) REVERT: B 841 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8026 (ttmm) REVERT: B 843 TYR cc_start: 0.8325 (t80) cc_final: 0.7695 (t80) REVERT: B 847 GLU cc_start: 0.7898 (tp30) cc_final: 0.7530 (tp30) REVERT: B 848 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 876 LEU cc_start: 0.8220 (mt) cc_final: 0.7975 (mt) REVERT: B 881 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6832 (mm-30) REVERT: B 889 HIS cc_start: 0.8111 (m90) cc_final: 0.7119 (m90) REVERT: B 907 ASN cc_start: 0.7648 (m-40) cc_final: 0.6542 (m-40) REVERT: B 908 HIS cc_start: 0.7922 (m-70) cc_final: 0.7456 (m-70) REVERT: B 911 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6672 (mt-10) REVERT: B 913 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8757 (mt) REVERT: B 915 GLU cc_start: 0.7655 (tt0) cc_final: 0.7265 (tt0) REVERT: B 928 HIS cc_start: 0.7068 (t70) cc_final: 0.6784 (t70) outliers start: 69 outliers final: 35 residues processed: 496 average time/residue: 0.1346 time to fit residues: 88.4088 Evaluate side-chains 495 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 453 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 388 LEU 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 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 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 67 optimal weight: 0.0770 chunk 4 optimal weight: 0.1980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105514 restraints weight = 19763.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108872 restraints weight = 9188.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.110931 restraints weight = 5302.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112248 restraints weight = 3594.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113101 restraints weight = 2747.413| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10798 Z= 0.134 Angle : 0.567 13.058 14638 Z= 0.296 Chirality : 0.038 0.239 1772 Planarity : 0.004 0.046 1796 Dihedral : 7.147 67.838 1483 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.92 % Allowed : 19.86 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.23), residues: 1344 helix: 1.46 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -0.60 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 910 TYR 0.014 0.001 TYR A 392 PHE 0.022 0.001 PHE A 457 TRP 0.014 0.001 TRP B 523 HIS 0.011 0.001 HIS B 502 Details of bonding type rmsd covalent geometry : bond 0.00271 (10798) covalent geometry : angle 0.56732 (14638) hydrogen bonds : bond 0.04399 ( 909) hydrogen bonds : angle 4.21770 ( 2718) *********************** 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 527 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 459 time to evaluate : 0.422 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: 0.7401 (mmtm) cc_final: 0.6995 (mmtm) REVERT: A 85 CYS cc_start: 0.8347 (m) cc_final: 0.8016 (m) REVERT: A 112 ILE cc_start: 0.8389 (mt) cc_final: 0.8046 (mm) REVERT: A 124 GLU cc_start: 0.7631 (tp30) cc_final: 0.6760 (tp30) REVERT: A 125 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7077 (mt-10) REVERT: A 160 MET cc_start: 0.7744 (mmm) cc_final: 0.7377 (mmt) REVERT: A 186 MET cc_start: 0.6704 (mtp) cc_final: 0.6466 (mtp) REVERT: A 205 MET cc_start: 0.7594 (mmm) cc_final: 0.7359 (mmm) REVERT: A 217 LEU cc_start: 0.8314 (mt) cc_final: 0.8069 (mt) REVERT: A 237 ASN cc_start: 0.7914 (t0) cc_final: 0.7692 (t0) REVERT: A 257 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7519 (pp) REVERT: A 292 HIS cc_start: 0.8261 (m-70) cc_final: 0.7668 (m-70) REVERT: A 337 GLU cc_start: 0.7355 (mp0) cc_final: 0.6727 (mp0) REVERT: A 367 MET cc_start: 0.7633 (mtm) cc_final: 0.7410 (mtm) REVERT: A 387 TYR cc_start: 0.7938 (m-10) cc_final: 0.7575 (m-10) REVERT: A 454 LYS cc_start: 0.8400 (mttm) cc_final: 0.8178 (mttm) REVERT: A 477 LEU cc_start: 0.8609 (tt) cc_final: 0.8296 (tt) REVERT: A 479 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7450 (ttp80) REVERT: A 481 LEU cc_start: 0.8497 (mt) cc_final: 0.8274 (mt) REVERT: A 486 ILE cc_start: 0.8545 (mt) cc_final: 0.8231 (tt) REVERT: A 499 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7144 (ttp80) REVERT: A 502 HIS cc_start: 0.7793 (t-90) cc_final: 0.7310 (t-90) REVERT: A 506 ASN cc_start: 0.7930 (m-40) cc_final: 0.7456 (m-40) REVERT: A 514 SER cc_start: 0.8239 (p) cc_final: 0.7998 (p) REVERT: A 578 MET cc_start: 0.7999 (ttm) cc_final: 0.7785 (ttm) REVERT: A 579 MET cc_start: 0.7748 (mmm) cc_final: 0.7229 (mmm) REVERT: A 585 ARG cc_start: 0.8136 (ttp-170) cc_final: 0.7897 (ttt180) REVERT: A 596 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7779 (tmmt) REVERT: A 597 GLN cc_start: 0.7458 (mt0) cc_final: 0.7221 (mt0) REVERT: A 611 LEU cc_start: 0.8263 (tp) cc_final: 0.8007 (tp) REVERT: A 622 LYS cc_start: 0.7938 (tttp) cc_final: 0.7604 (tttp) REVERT: A 645 LYS cc_start: 0.8915 (tptp) cc_final: 0.8653 (tptp) REVERT: A 843 TYR cc_start: 0.8628 (t80) cc_final: 0.7870 (t80) REVERT: A 848 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7554 (mt-10) REVERT: A 849 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 862 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8395 (mmtm) REVERT: A 875 ARG cc_start: 0.7624 (tpt90) cc_final: 0.7157 (tpt90) REVERT: A 880 LYS cc_start: 0.8247 (tptp) cc_final: 0.7791 (tptp) REVERT: A 894 VAL cc_start: 0.8419 (t) cc_final: 0.8208 (p) REVERT: A 900 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7444 (tp40) REVERT: A 912 THR cc_start: 0.8470 (m) cc_final: 0.8226 (p) REVERT: A 925 MET cc_start: 0.7823 (mmm) cc_final: 0.7532 (mmm) REVERT: A 931 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7221 (mm-30) REVERT: A 940 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: B 81 ILE cc_start: 0.7939 (mt) cc_final: 0.7638 (mt) REVERT: B 84 SER cc_start: 0.8022 (t) cc_final: 0.7648 (p) REVERT: B 109 LEU cc_start: 0.7932 (mt) cc_final: 0.7616 (mt) REVERT: B 124 GLU cc_start: 0.7496 (tp30) cc_final: 0.7176 (tp30) REVERT: B 149 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6994 (tm-30) REVERT: B 152 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 191 TYR cc_start: 0.7791 (p90) cc_final: 0.7091 (p90) REVERT: B 199 MET cc_start: 0.7555 (tpp) cc_final: 0.7208 (mmm) REVERT: B 233 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 269 LEU cc_start: 0.8026 (tp) cc_final: 0.7666 (tp) REVERT: B 278 TRP cc_start: 0.8345 (t-100) cc_final: 0.8026 (t-100) REVERT: B 284 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7805 (mmmm) REVERT: B 300 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6940 (mt-10) REVERT: B 312 TYR cc_start: 0.8223 (t80) cc_final: 0.7769 (t80) REVERT: B 337 GLU cc_start: 0.7692 (mp0) cc_final: 0.7400 (mp0) REVERT: B 361 ASN cc_start: 0.8121 (m-40) cc_final: 0.7902 (m-40) REVERT: B 388 LEU cc_start: 0.8514 (tt) cc_final: 0.8312 (tt) REVERT: B 390 ILE cc_start: 0.8498 (mm) cc_final: 0.8278 (mm) REVERT: B 399 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8229 (tpt170) REVERT: B 420 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7432 (mtm-85) REVERT: B 475 GLN cc_start: 0.7476 (tp40) cc_final: 0.7166 (tp40) REVERT: B 499 ARG cc_start: 0.7485 (ptp90) cc_final: 0.7202 (ptp90) REVERT: B 500 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7414 (tpp80) REVERT: B 512 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8113 (tp) REVERT: B 527 THR cc_start: 0.8231 (p) cc_final: 0.7374 (p) REVERT: B 531 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6211 (mm-30) REVERT: B 579 MET cc_start: 0.7692 (mmm) cc_final: 0.7373 (mmm) REVERT: B 581 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5932 (pp20) REVERT: B 586 MET cc_start: 0.7599 (tmm) cc_final: 0.5995 (tmm) REVERT: B 588 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7780 (ttpp) REVERT: B 590 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6674 (mm-30) REVERT: B 591 LYS cc_start: 0.8101 (mtmp) cc_final: 0.7849 (mtmp) REVERT: B 595 TRP cc_start: 0.7972 (m100) cc_final: 0.7690 (m100) REVERT: B 596 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8217 (mmmt) REVERT: B 613 GLN cc_start: 0.7389 (tm-30) cc_final: 0.6927 (tm-30) REVERT: B 645 LYS cc_start: 0.8467 (tptp) cc_final: 0.7984 (tptp) REVERT: B 825 VAL cc_start: 0.8431 (t) cc_final: 0.8204 (p) REVERT: B 826 ASN cc_start: 0.7894 (t0) cc_final: 0.7498 (m110) REVERT: B 841 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8104 (ttmm) REVERT: B 843 TYR cc_start: 0.8230 (t80) cc_final: 0.7762 (t80) REVERT: B 847 GLU cc_start: 0.7864 (tp30) cc_final: 0.7533 (tp30) REVERT: B 848 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 850 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8022 (p) REVERT: B 872 GLU cc_start: 0.8150 (tp30) cc_final: 0.6997 (tp30) REVERT: B 876 LEU cc_start: 0.8222 (mt) cc_final: 0.7608 (mt) REVERT: B 881 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6816 (mm-30) REVERT: B 907 ASN cc_start: 0.7667 (m-40) cc_final: 0.6576 (m-40) REVERT: B 908 HIS cc_start: 0.7960 (m-70) cc_final: 0.7519 (m-70) REVERT: B 911 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6654 (mt-10) REVERT: B 915 GLU cc_start: 0.7631 (tt0) cc_final: 0.7217 (tt0) REVERT: B 924 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7659 (pp20) REVERT: B 928 HIS cc_start: 0.7065 (t70) cc_final: 0.6776 (t70) outliers start: 68 outliers final: 38 residues processed: 485 average time/residue: 0.1372 time to fit residues: 88.0525 Evaluate side-chains 505 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 460 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 175 VAL 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 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 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 921 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 94 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.0040 chunk 82 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN B 157 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105774 restraints weight = 20193.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109135 restraints weight = 9318.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111241 restraints weight = 5383.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112553 restraints weight = 3660.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113375 restraints weight = 2820.078| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10798 Z= 0.135 Angle : 0.553 14.000 14638 Z= 0.288 Chirality : 0.038 0.214 1772 Planarity : 0.004 0.043 1796 Dihedral : 6.465 58.393 1477 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.27 % Allowed : 20.47 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.23), residues: 1344 helix: 1.76 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.76 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 910 TYR 0.017 0.001 TYR A 392 PHE 0.016 0.001 PHE A 457 TRP 0.013 0.001 TRP B 523 HIS 0.004 0.000 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00276 (10798) covalent geometry : angle 0.55305 (14638) hydrogen bonds : bond 0.04198 ( 909) hydrogen bonds : angle 4.12091 ( 2718) *********************** 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 523 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 451 time to evaluate : 0.414 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: 0.7294 (mmtm) cc_final: 0.7022 (mmtm) REVERT: A 85 CYS cc_start: 0.8313 (m) cc_final: 0.7951 (m) REVERT: A 112 ILE cc_start: 0.8387 (mt) cc_final: 0.8061 (mm) REVERT: A 124 GLU cc_start: 0.7618 (tp30) cc_final: 0.6903 (tp30) REVERT: A 160 MET cc_start: 0.7742 (mmm) cc_final: 0.7362 (mmt) REVERT: A 186 MET cc_start: 0.6670 (mtp) cc_final: 0.6449 (mtp) REVERT: A 194 ASN cc_start: 0.8372 (p0) cc_final: 0.8165 (p0) REVERT: A 199 MET cc_start: 0.7670 (mmm) cc_final: 0.7341 (mmm) REVERT: A 205 MET cc_start: 0.7599 (mmm) cc_final: 0.7255 (mmm) REVERT: A 217 LEU cc_start: 0.8301 (mt) cc_final: 0.8051 (mt) REVERT: A 218 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7513 (ttmt) REVERT: A 237 ASN cc_start: 0.7940 (t0) cc_final: 0.7709 (t0) REVERT: A 292 HIS cc_start: 0.8203 (m-70) cc_final: 0.7578 (m-70) REVERT: A 319 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6599 (mt) REVERT: A 335 ASN cc_start: 0.8637 (t0) cc_final: 0.8355 (t0) REVERT: A 337 GLU cc_start: 0.7341 (mp0) cc_final: 0.6717 (mp0) REVERT: A 367 MET cc_start: 0.7659 (mtm) cc_final: 0.7428 (mtm) REVERT: A 387 TYR cc_start: 0.7898 (m-10) cc_final: 0.7586 (m-10) REVERT: A 427 TRP cc_start: 0.8663 (t-100) cc_final: 0.8456 (t-100) REVERT: A 431 ARG cc_start: 0.8292 (mmt180) cc_final: 0.8089 (mmt180) REVERT: A 454 LYS cc_start: 0.8422 (mttm) cc_final: 0.8126 (mttm) REVERT: A 477 LEU cc_start: 0.8569 (tt) cc_final: 0.8262 (tt) REVERT: A 479 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7462 (ttp80) REVERT: A 481 LEU cc_start: 0.8483 (mt) cc_final: 0.8221 (mt) REVERT: A 486 ILE cc_start: 0.8552 (mt) cc_final: 0.8195 (tt) REVERT: A 499 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7114 (ttp80) REVERT: A 502 HIS cc_start: 0.7854 (t-90) cc_final: 0.7373 (t-90) REVERT: A 506 ASN cc_start: 0.7929 (m-40) cc_final: 0.7464 (m-40) REVERT: A 578 MET cc_start: 0.8087 (ttm) cc_final: 0.7857 (ttm) REVERT: A 579 MET cc_start: 0.7848 (mmm) cc_final: 0.7318 (mmm) REVERT: A 596 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7794 (tmmt) REVERT: A 597 GLN cc_start: 0.7427 (mt0) cc_final: 0.7216 (mt0) REVERT: A 611 LEU cc_start: 0.8270 (tp) cc_final: 0.7985 (tp) REVERT: A 613 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 616 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 645 LYS cc_start: 0.8949 (tptp) cc_final: 0.8341 (tptp) REVERT: A 843 TYR cc_start: 0.8636 (t80) cc_final: 0.7877 (t80) REVERT: A 848 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 849 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 862 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8378 (mmtm) REVERT: A 875 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7311 (tpt90) REVERT: A 880 LYS cc_start: 0.8273 (tptp) cc_final: 0.7853 (tptp) REVERT: A 881 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6933 (tm-30) REVERT: A 894 VAL cc_start: 0.8435 (t) cc_final: 0.8210 (p) REVERT: A 900 GLN cc_start: 0.8174 (tm130) cc_final: 0.7459 (tp40) REVERT: A 912 THR cc_start: 0.8492 (m) cc_final: 0.8236 (p) REVERT: A 925 MET cc_start: 0.7908 (mmm) cc_final: 0.7672 (mmm) REVERT: A 931 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 940 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7472 (ttm-80) REVERT: B 81 ILE cc_start: 0.7961 (mt) cc_final: 0.7650 (mt) REVERT: B 84 SER cc_start: 0.8006 (t) cc_final: 0.7623 (p) REVERT: B 109 LEU cc_start: 0.7947 (mt) cc_final: 0.7613 (mt) REVERT: B 124 GLU cc_start: 0.7479 (tp30) cc_final: 0.7162 (tp30) REVERT: B 149 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7024 (tm-30) REVERT: B 152 PHE cc_start: 0.8238 (t80) cc_final: 0.7905 (t80) REVERT: B 199 MET cc_start: 0.7454 (tpp) cc_final: 0.7155 (tpp) REVERT: B 233 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 246 ASN cc_start: 0.8131 (m-40) cc_final: 0.7898 (m-40) REVERT: B 269 LEU cc_start: 0.8026 (tp) cc_final: 0.7692 (tp) REVERT: B 278 TRP cc_start: 0.8356 (t-100) cc_final: 0.8061 (t-100) REVERT: B 300 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6827 (mt-10) REVERT: B 312 TYR cc_start: 0.8272 (t80) cc_final: 0.7952 (t80) REVERT: B 335 ASN cc_start: 0.8241 (t0) cc_final: 0.7960 (t0) REVERT: B 337 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: B 351 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8033 (tpp-160) REVERT: B 388 LEU cc_start: 0.8504 (tt) cc_final: 0.8288 (tt) REVERT: B 390 ILE cc_start: 0.8515 (mm) cc_final: 0.8299 (mm) REVERT: B 399 ARG cc_start: 0.8510 (ttt90) cc_final: 0.8186 (tpt170) REVERT: B 420 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7535 (mtm-85) REVERT: B 443 GLU cc_start: 0.7686 (tp30) cc_final: 0.7075 (tp30) REVERT: B 454 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7674 (tttm) REVERT: B 475 GLN cc_start: 0.7469 (tp40) cc_final: 0.7171 (tp40) REVERT: B 499 ARG cc_start: 0.7506 (ptp90) cc_final: 0.7208 (ptp90) REVERT: B 500 ARG cc_start: 0.7782 (tpt90) cc_final: 0.7430 (tpp80) REVERT: B 527 THR cc_start: 0.8270 (p) cc_final: 0.7267 (p) REVERT: B 579 MET cc_start: 0.7699 (mmm) cc_final: 0.7283 (mmm) REVERT: B 581 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5919 (pp20) REVERT: B 586 MET cc_start: 0.7579 (tmm) cc_final: 0.5909 (tmm) REVERT: B 588 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7798 (ttpp) REVERT: B 590 GLU cc_start: 0.7630 (mm-30) cc_final: 0.6668 (mm-30) REVERT: B 591 LYS cc_start: 0.8072 (mtmp) cc_final: 0.7795 (mtmp) REVERT: B 595 TRP cc_start: 0.7940 (m100) cc_final: 0.7653 (m100) REVERT: B 613 GLN cc_start: 0.7432 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 645 LYS cc_start: 0.8515 (tptp) cc_final: 0.7998 (tptp) REVERT: B 825 VAL cc_start: 0.8500 (t) cc_final: 0.8271 (p) REVERT: B 826 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7535 (m110) REVERT: B 841 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8152 (ttmm) REVERT: B 843 TYR cc_start: 0.8136 (t80) cc_final: 0.7817 (t80) REVERT: B 847 GLU cc_start: 0.7846 (tp30) cc_final: 0.7578 (tp30) REVERT: B 848 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 850 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7997 (p) REVERT: B 872 GLU cc_start: 0.8008 (tp30) cc_final: 0.7514 (tp30) REVERT: B 875 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7378 (ttt-90) REVERT: B 876 LEU cc_start: 0.8138 (mt) cc_final: 0.7840 (mt) REVERT: B 880 LYS cc_start: 0.8028 (tmmt) cc_final: 0.7578 (tmmt) REVERT: B 881 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7046 (mm-30) REVERT: B 907 ASN cc_start: 0.7682 (m-40) cc_final: 0.6606 (m-40) REVERT: B 908 HIS cc_start: 0.7972 (m-70) cc_final: 0.7537 (m-70) REVERT: B 911 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6665 (mt-10) REVERT: B 928 HIS cc_start: 0.7045 (t70) cc_final: 0.6771 (t70) REVERT: B 929 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7226 (mtpp) outliers start: 72 outliers final: 40 residues processed: 477 average time/residue: 0.1327 time to fit residues: 84.2541 Evaluate side-chains 493 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 447 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 ARG 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 337 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 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 ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104720 restraints weight = 19973.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108082 restraints weight = 9269.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110195 restraints weight = 5371.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111486 restraints weight = 3660.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112312 restraints weight = 2825.802| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2298 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= 0.162 Angle : 0.588 15.099 14638 Z= 0.301 Chirality : 0.039 0.216 1772 Planarity : 0.004 0.048 1796 Dihedral : 5.955 59.038 1465 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.75 % Allowed : 21.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.23), residues: 1344 helix: 1.78 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.47 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 585 TYR 0.013 0.001 TYR A 313 PHE 0.012 0.001 PHE A 517 TRP 0.012 0.001 TRP B 635 HIS 0.002 0.001 HIS B 458 Details of bonding type rmsd covalent geometry : bond 0.00332 (10798) covalent geometry : angle 0.58779 (14638) hydrogen bonds : bond 0.04301 ( 909) hydrogen bonds : angle 4.13000 ( 2718) *********************** 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 518 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 452 time to evaluate : 0.502 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: A 76 LYS cc_start: 0.7319 (mmtm) cc_final: 0.7064 (mmtm) REVERT: A 85 CYS cc_start: 0.8347 (m) cc_final: 0.8029 (m) REVERT: A 124 GLU cc_start: 0.7610 (tp30) cc_final: 0.6986 (tp30) REVERT: A 155 ASP cc_start: 0.7361 (t0) cc_final: 0.7144 (t0) REVERT: A 160 MET cc_start: 0.7757 (mmm) cc_final: 0.7360 (mmt) REVERT: A 186 MET cc_start: 0.6578 (mtp) cc_final: 0.6372 (mtp) REVERT: A 199 MET cc_start: 0.7623 (mmm) cc_final: 0.7245 (mmm) REVERT: A 205 MET cc_start: 0.7599 (mmm) cc_final: 0.7259 (mmm) REVERT: A 217 LEU cc_start: 0.8367 (mt) cc_final: 0.8119 (mt) REVERT: A 225 GLN cc_start: 0.7822 (pm20) cc_final: 0.7617 (pm20) REVERT: A 237 ASN cc_start: 0.7931 (t0) cc_final: 0.7705 (t0) REVERT: A 250 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7479 (mtmm) REVERT: A 292 HIS cc_start: 0.8223 (m-70) cc_final: 0.7637 (m-70) REVERT: A 319 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6643 (mt) REVERT: A 335 ASN cc_start: 0.8651 (t0) cc_final: 0.8408 (t0) REVERT: A 337 GLU cc_start: 0.7341 (mp0) cc_final: 0.6721 (mp0) REVERT: A 387 TYR cc_start: 0.7906 (m-10) cc_final: 0.7510 (m-10) REVERT: A 431 ARG cc_start: 0.8330 (mmt180) cc_final: 0.8118 (mmt180) REVERT: A 454 LYS cc_start: 0.8417 (mttm) cc_final: 0.8142 (mttm) REVERT: A 477 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 479 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7515 (ttp80) REVERT: A 481 LEU cc_start: 0.8504 (mt) cc_final: 0.8229 (mt) REVERT: A 499 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7103 (ttp80) REVERT: A 502 HIS cc_start: 0.7867 (t-90) cc_final: 0.7376 (t-90) REVERT: A 506 ASN cc_start: 0.7951 (m-40) cc_final: 0.7465 (m-40) REVERT: A 578 MET cc_start: 0.8083 (ttm) cc_final: 0.7857 (ttm) REVERT: A 579 MET cc_start: 0.7845 (mmm) cc_final: 0.7341 (mmm) REVERT: A 596 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7779 (tmmt) REVERT: A 597 GLN cc_start: 0.7442 (mt0) cc_final: 0.7205 (mt0) REVERT: A 611 LEU cc_start: 0.8260 (tp) cc_final: 0.7973 (tp) REVERT: A 613 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 645 LYS cc_start: 0.8963 (tptp) cc_final: 0.8361 (tptp) REVERT: A 843 TYR cc_start: 0.8658 (t80) cc_final: 0.7983 (t80) REVERT: A 848 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 849 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 862 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8368 (mmtm) REVERT: A 868 LYS cc_start: 0.8559 (mmmm) cc_final: 0.7763 (mmmm) REVERT: A 875 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7396 (tpt90) REVERT: A 880 LYS cc_start: 0.8286 (tptp) cc_final: 0.7845 (tptp) REVERT: A 881 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6966 (tm-30) REVERT: A 900 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7488 (tp40) REVERT: A 910 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7865 (ttm-80) REVERT: A 925 MET cc_start: 0.7959 (mmm) cc_final: 0.7716 (mmm) REVERT: A 931 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7392 (mm-30) REVERT: B 81 ILE cc_start: 0.7940 (mt) cc_final: 0.7649 (mt) REVERT: B 84 SER cc_start: 0.8027 (t) cc_final: 0.7626 (p) REVERT: B 109 LEU cc_start: 0.7929 (mt) cc_final: 0.7607 (mt) REVERT: B 120 VAL cc_start: 0.8518 (t) cc_final: 0.8120 (p) REVERT: B 149 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7046 (tm-30) REVERT: B 152 PHE cc_start: 0.8226 (t80) cc_final: 0.7876 (t80) REVERT: B 269 LEU cc_start: 0.8048 (tp) cc_final: 0.7709 (tp) REVERT: B 278 TRP cc_start: 0.8375 (t-100) cc_final: 0.8072 (t-100) REVERT: B 300 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6972 (mt-10) REVERT: B 335 ASN cc_start: 0.8268 (t0) cc_final: 0.8066 (t0) REVERT: B 337 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 351 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8068 (tpp-160) REVERT: B 361 ASN cc_start: 0.8139 (m-40) cc_final: 0.7651 (m110) REVERT: B 388 LEU cc_start: 0.8523 (tt) cc_final: 0.8295 (tt) REVERT: B 390 ILE cc_start: 0.8525 (mm) cc_final: 0.8312 (mm) REVERT: B 399 ARG cc_start: 0.8518 (ttt90) cc_final: 0.8152 (tpt170) REVERT: B 420 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7429 (mtm-85) REVERT: B 443 GLU cc_start: 0.7710 (tp30) cc_final: 0.7133 (tp30) REVERT: B 475 GLN cc_start: 0.7481 (tp40) cc_final: 0.7179 (tp40) REVERT: B 499 ARG cc_start: 0.7532 (ptp90) cc_final: 0.7225 (ptp90) REVERT: B 500 ARG cc_start: 0.7814 (tpt90) cc_final: 0.7475 (tpp80) REVERT: B 512 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8158 (tp) REVERT: B 527 THR cc_start: 0.8069 (p) cc_final: 0.7582 (p) REVERT: B 579 MET cc_start: 0.7670 (mmm) cc_final: 0.7278 (mmm) REVERT: B 581 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5927 (pp20) REVERT: B 586 MET cc_start: 0.7542 (tmm) cc_final: 0.5906 (tmm) REVERT: B 588 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7805 (ttpp) REVERT: B 590 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6650 (mm-30) REVERT: B 591 LYS cc_start: 0.8086 (mtmp) cc_final: 0.7783 (mtmp) REVERT: B 595 TRP cc_start: 0.7959 (m100) cc_final: 0.7659 (m100) REVERT: B 613 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 645 LYS cc_start: 0.8524 (tptp) cc_final: 0.7994 (tptp) REVERT: B 825 VAL cc_start: 0.8513 (t) cc_final: 0.8280 (p) REVERT: B 826 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7572 (m110) REVERT: B 847 GLU cc_start: 0.7835 (tp30) cc_final: 0.7568 (tp30) REVERT: B 848 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 850 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.7978 (p) REVERT: B 872 GLU cc_start: 0.7995 (tp30) cc_final: 0.7545 (tp30) REVERT: B 876 LEU cc_start: 0.8137 (mt) cc_final: 0.7846 (mt) REVERT: B 880 LYS cc_start: 0.8093 (tmmt) cc_final: 0.7681 (tmmt) REVERT: B 881 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7195 (mm-30) REVERT: B 907 ASN cc_start: 0.7670 (m-40) cc_final: 0.6502 (m-40) REVERT: B 908 HIS cc_start: 0.7988 (m-70) cc_final: 0.7547 (m-70) REVERT: B 911 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6624 (mp0) REVERT: B 928 HIS cc_start: 0.7084 (t70) cc_final: 0.6782 (t70) outliers start: 66 outliers final: 44 residues processed: 473 average time/residue: 0.1354 time to fit residues: 84.8887 Evaluate side-chains 503 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 450 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 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 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS 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 132 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 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 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 93 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105240 restraints weight = 20023.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108597 restraints weight = 9344.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110689 restraints weight = 5439.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112015 restraints weight = 3718.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112872 restraints weight = 2862.894| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2435 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= 0.149 Angle : 0.593 15.827 14638 Z= 0.303 Chirality : 0.040 0.273 1772 Planarity : 0.004 0.054 1796 Dihedral : 5.925 58.497 1465 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.01 % Allowed : 22.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.23), residues: 1344 helix: 1.83 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.48 (0.47), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 585 TYR 0.014 0.001 TYR A 313 PHE 0.020 0.001 PHE B 288 TRP 0.022 0.001 TRP B 635 HIS 0.002 0.000 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00310 (10798) covalent geometry : angle 0.59349 (14638) hydrogen bonds : bond 0.04232 ( 909) hydrogen bonds : angle 4.10969 ( 2718) *********************** 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 519 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 450 time to evaluate : 0.442 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 85 CYS cc_start: 0.8343 (m) cc_final: 0.8015 (m) REVERT: A 124 GLU cc_start: 0.7539 (tp30) cc_final: 0.7083 (tp30) REVERT: A 155 ASP cc_start: 0.7350 (t0) cc_final: 0.7140 (t0) REVERT: A 160 MET cc_start: 0.7773 (mmm) cc_final: 0.7353 (mmt) REVERT: A 186 MET cc_start: 0.6551 (mtp) cc_final: 0.6335 (mtp) REVERT: A 205 MET cc_start: 0.7572 (mmm) cc_final: 0.7296 (mpp) REVERT: A 217 LEU cc_start: 0.8345 (mt) cc_final: 0.8084 (mt) REVERT: A 218 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7480 (ttmt) REVERT: A 237 ASN cc_start: 0.7925 (t0) cc_final: 0.7692 (t0) REVERT: A 250 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7447 (mtmm) REVERT: A 292 HIS cc_start: 0.8215 (m-70) cc_final: 0.7644 (m-70) REVERT: A 319 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6616 (mt) REVERT: A 335 ASN cc_start: 0.8642 (t0) cc_final: 0.8369 (t0) REVERT: A 337 GLU cc_start: 0.7331 (mp0) cc_final: 0.6680 (mp0) REVERT: A 346 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6694 (mt-10) REVERT: A 387 TYR cc_start: 0.7835 (m-10) cc_final: 0.7605 (m-10) REVERT: A 454 LYS cc_start: 0.8361 (mttm) cc_final: 0.8092 (mttm) REVERT: A 477 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8259 (tt) REVERT: A 479 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7508 (ttp80) REVERT: A 481 LEU cc_start: 0.8533 (mt) cc_final: 0.8271 (mt) REVERT: A 486 ILE cc_start: 0.8486 (mt) cc_final: 0.8137 (tt) REVERT: A 499 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7085 (ttp80) REVERT: A 506 ASN cc_start: 0.7950 (m-40) cc_final: 0.7534 (m-40) REVERT: A 512 LEU cc_start: 0.8570 (tp) cc_final: 0.8216 (tt) REVERT: A 578 MET cc_start: 0.8032 (ttm) cc_final: 0.7814 (ttm) REVERT: A 579 MET cc_start: 0.7846 (mmm) cc_final: 0.7348 (mmm) REVERT: A 596 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7713 (tmmt) REVERT: A 597 GLN cc_start: 0.7424 (mt0) cc_final: 0.7164 (mt0) REVERT: A 611 LEU cc_start: 0.8260 (tp) cc_final: 0.7965 (tp) REVERT: A 613 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 645 LYS cc_start: 0.8938 (tptp) cc_final: 0.8329 (tptp) REVERT: A 843 TYR cc_start: 0.8659 (t80) cc_final: 0.7968 (t80) REVERT: A 848 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 849 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 862 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8372 (mmtm) REVERT: A 868 LYS cc_start: 0.8583 (mmmm) cc_final: 0.7765 (mmmm) REVERT: A 875 ARG cc_start: 0.7652 (tpt90) cc_final: 0.7378 (tpt90) REVERT: A 880 LYS cc_start: 0.8286 (tptp) cc_final: 0.7832 (tptp) REVERT: A 881 GLU cc_start: 0.7546 (mm-30) cc_final: 0.6941 (tm-30) REVERT: A 900 GLN cc_start: 0.8186 (tm130) cc_final: 0.7976 (tp40) REVERT: A 931 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 81 ILE cc_start: 0.7938 (mt) cc_final: 0.7652 (mt) REVERT: B 84 SER cc_start: 0.8026 (t) cc_final: 0.7626 (p) REVERT: B 109 LEU cc_start: 0.7930 (mt) cc_final: 0.7615 (mt) REVERT: B 149 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7040 (tm-30) REVERT: B 152 PHE cc_start: 0.8219 (t80) cc_final: 0.7853 (t80) REVERT: B 199 MET cc_start: 0.7618 (mmm) cc_final: 0.6962 (tpp) REVERT: B 269 LEU cc_start: 0.8040 (tp) cc_final: 0.7724 (tp) REVERT: B 278 TRP cc_start: 0.8382 (t-100) cc_final: 0.8077 (t-100) REVERT: B 300 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6960 (mt-10) REVERT: B 337 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: B 351 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8073 (tpp-160) REVERT: B 388 LEU cc_start: 0.8518 (tt) cc_final: 0.8278 (tt) REVERT: B 420 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7550 (mtm-85) REVERT: B 443 GLU cc_start: 0.7704 (tp30) cc_final: 0.7108 (tp30) REVERT: B 475 GLN cc_start: 0.7479 (tp40) cc_final: 0.7183 (tp40) REVERT: B 499 ARG cc_start: 0.7542 (ptp90) cc_final: 0.7211 (ptp90) REVERT: B 500 ARG cc_start: 0.7808 (tpt90) cc_final: 0.7459 (tpp80) REVERT: B 512 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 527 THR cc_start: 0.7976 (p) cc_final: 0.7678 (p) REVERT: B 579 MET cc_start: 0.7680 (mmm) cc_final: 0.7346 (mmm) REVERT: B 581 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5823 (pp20) REVERT: B 586 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6004 (tmm) REVERT: B 588 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7952 (ttpp) REVERT: B 590 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6746 (mm-30) REVERT: B 595 TRP cc_start: 0.7988 (m100) cc_final: 0.7680 (m100) REVERT: B 596 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8271 (mmmt) REVERT: B 613 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7110 (tm-30) REVERT: B 645 LYS cc_start: 0.8502 (tptp) cc_final: 0.7974 (tptp) REVERT: B 825 VAL cc_start: 0.8498 (t) cc_final: 0.8263 (p) REVERT: B 826 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7565 (m110) REVERT: B 847 GLU cc_start: 0.7766 (tp30) cc_final: 0.7504 (tp30) REVERT: B 848 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 850 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (p) REVERT: B 872 GLU cc_start: 0.7947 (tp30) cc_final: 0.7590 (tp30) REVERT: B 876 LEU cc_start: 0.8102 (mt) cc_final: 0.7868 (mt) REVERT: B 881 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7216 (mm-30) REVERT: B 907 ASN cc_start: 0.7684 (m-40) cc_final: 0.6477 (m-40) REVERT: B 908 HIS cc_start: 0.7950 (m-70) cc_final: 0.7508 (m-70) REVERT: B 911 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6605 (mp0) REVERT: B 928 HIS cc_start: 0.7051 (t70) cc_final: 0.6790 (t70) REVERT: B 929 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7241 (mtpp) outliers start: 69 outliers final: 48 residues processed: 473 average time/residue: 0.1341 time to fit residues: 84.4470 Evaluate side-chains 504 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 447 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 128 ARG 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 372 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 850 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 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 270 GLN A 943 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106173 restraints weight = 19972.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109521 restraints weight = 9314.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111617 restraints weight = 5432.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.112937 restraints weight = 3709.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113704 restraints weight = 2856.326| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10798 Z= 0.131 Angle : 0.587 16.172 14638 Z= 0.297 Chirality : 0.039 0.245 1772 Planarity : 0.004 0.046 1796 Dihedral : 5.844 56.820 1465 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.10 % Allowed : 23.61 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.23), residues: 1344 helix: 1.97 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.61 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 910 TYR 0.012 0.001 TYR A 313 PHE 0.011 0.001 PHE A 245 TRP 0.019 0.001 TRP B 635 HIS 0.004 0.000 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00269 (10798) covalent geometry : angle 0.58665 (14638) hydrogen bonds : bond 0.04070 ( 909) hydrogen bonds : angle 4.05239 ( 2718) *********************** 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 525 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 455 time to evaluate : 0.401 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 85 CYS cc_start: 0.8316 (m) cc_final: 0.7905 (m) REVERT: A 103 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7800 (p) REVERT: A 124 GLU cc_start: 0.7477 (tp30) cc_final: 0.6680 (tp30) REVERT: A 160 MET cc_start: 0.7775 (mmm) cc_final: 0.7343 (mmt) REVERT: A 186 MET cc_start: 0.6535 (mtp) cc_final: 0.6315 (mtp) REVERT: A 199 MET cc_start: 0.7837 (mmm) cc_final: 0.7543 (mmm) REVERT: A 205 MET cc_start: 0.7551 (mmm) cc_final: 0.7058 (mpp) REVERT: A 217 LEU cc_start: 0.8326 (mt) cc_final: 0.8062 (mt) REVERT: A 218 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7452 (ttmt) REVERT: A 237 ASN cc_start: 0.7888 (t0) cc_final: 0.7669 (t0) REVERT: A 250 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7374 (mtmm) REVERT: A 292 HIS cc_start: 0.8213 (m-70) cc_final: 0.7610 (m-70) REVERT: A 319 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6642 (mt) REVERT: A 322 SER cc_start: 0.8070 (t) cc_final: 0.7705 (p) REVERT: A 335 ASN cc_start: 0.8614 (t0) cc_final: 0.8095 (t0) REVERT: A 337 GLU cc_start: 0.7320 (mp0) cc_final: 0.6688 (mp0) REVERT: A 387 TYR cc_start: 0.7821 (m-10) cc_final: 0.7556 (m-10) REVERT: A 454 LYS cc_start: 0.8348 (mttm) cc_final: 0.8131 (mttm) REVERT: A 476 THR cc_start: 0.8354 (m) cc_final: 0.7727 (p) REVERT: A 477 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (tt) REVERT: A 479 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7523 (ttp80) REVERT: A 481 LEU cc_start: 0.8502 (mt) cc_final: 0.8239 (mt) REVERT: A 486 ILE cc_start: 0.8486 (mt) cc_final: 0.8119 (tt) REVERT: A 499 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7152 (ttp80) REVERT: A 506 ASN cc_start: 0.7948 (m-40) cc_final: 0.7505 (m-40) REVERT: A 512 LEU cc_start: 0.8509 (tp) cc_final: 0.8172 (tt) REVERT: A 578 MET cc_start: 0.8075 (ttm) cc_final: 0.7837 (ttm) REVERT: A 579 MET cc_start: 0.7866 (mmm) cc_final: 0.7364 (mmm) REVERT: A 596 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7707 (tmmt) REVERT: A 597 GLN cc_start: 0.7463 (mt0) cc_final: 0.7207 (mt0) REVERT: A 611 LEU cc_start: 0.8264 (tp) cc_final: 0.7962 (tp) REVERT: A 613 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 645 LYS cc_start: 0.8935 (tptp) cc_final: 0.8328 (tptp) REVERT: A 843 TYR cc_start: 0.8662 (t80) cc_final: 0.7994 (t80) REVERT: A 848 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 849 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 862 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8391 (mmtm) REVERT: A 868 LYS cc_start: 0.8543 (mmmm) cc_final: 0.7698 (mmmm) REVERT: A 880 LYS cc_start: 0.8298 (tptp) cc_final: 0.7815 (tptp) REVERT: A 881 GLU cc_start: 0.7538 (mm-30) cc_final: 0.6960 (tm-30) REVERT: A 900 GLN cc_start: 0.8198 (tm130) cc_final: 0.7987 (tp40) REVERT: B 81 ILE cc_start: 0.7917 (mt) cc_final: 0.7626 (mt) REVERT: B 84 SER cc_start: 0.8017 (t) cc_final: 0.7613 (p) REVERT: B 109 LEU cc_start: 0.7903 (mt) cc_final: 0.7649 (mt) REVERT: B 149 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 199 MET cc_start: 0.7516 (mmm) cc_final: 0.6912 (tpt) REVERT: B 249 MET cc_start: 0.7506 (ttm) cc_final: 0.7212 (ttp) REVERT: B 269 LEU cc_start: 0.7989 (tp) cc_final: 0.7692 (tp) REVERT: B 278 TRP cc_start: 0.8364 (t-100) cc_final: 0.8008 (t-100) REVERT: B 300 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6921 (mt-10) REVERT: B 337 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 351 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8048 (tpp-160) REVERT: B 361 ASN cc_start: 0.8156 (m-40) cc_final: 0.7652 (m110) REVERT: B 366 MET cc_start: 0.8152 (tpp) cc_final: 0.7876 (tpp) REVERT: B 388 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (tt) REVERT: B 420 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7529 (mtm-85) REVERT: B 425 MET cc_start: 0.7720 (ttm) cc_final: 0.7514 (ttt) REVERT: B 443 GLU cc_start: 0.7693 (tp30) cc_final: 0.7052 (tp30) REVERT: B 475 GLN cc_start: 0.7465 (tp40) cc_final: 0.7179 (tp40) REVERT: B 485 ASP cc_start: 0.8554 (p0) cc_final: 0.8330 (p0) REVERT: B 499 ARG cc_start: 0.7543 (ptp90) cc_final: 0.7193 (ptp90) REVERT: B 500 ARG cc_start: 0.7803 (tpt90) cc_final: 0.7454 (tpp80) REVERT: B 509 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8237 (mm) REVERT: B 512 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8204 (tp) REVERT: B 523 TRP cc_start: 0.7621 (m100) cc_final: 0.7019 (m100) REVERT: B 527 THR cc_start: 0.7923 (p) cc_final: 0.7659 (p) REVERT: B 579 MET cc_start: 0.7704 (mmm) cc_final: 0.7372 (mmm) REVERT: B 581 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5831 (pp20) REVERT: B 586 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6064 (tmm) REVERT: B 588 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7815 (ttpp) REVERT: B 590 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6708 (mm-30) REVERT: B 591 LYS cc_start: 0.8083 (mtmp) cc_final: 0.7775 (mtmp) REVERT: B 595 TRP cc_start: 0.8000 (m100) cc_final: 0.7677 (m100) REVERT: B 596 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8270 (mmmt) REVERT: B 613 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 645 LYS cc_start: 0.8460 (tptp) cc_final: 0.7981 (tptp) REVERT: B 825 VAL cc_start: 0.8509 (t) cc_final: 0.8267 (p) REVERT: B 826 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7560 (m110) REVERT: B 837 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.6578 (m-80) REVERT: B 847 GLU cc_start: 0.7757 (tp30) cc_final: 0.7487 (tp30) REVERT: B 848 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 850 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 872 GLU cc_start: 0.7949 (tp30) cc_final: 0.7597 (tp30) REVERT: B 876 LEU cc_start: 0.8097 (mt) cc_final: 0.7858 (mt) REVERT: B 881 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7232 (mm-30) REVERT: B 903 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6096 (mtp-110) REVERT: B 907 ASN cc_start: 0.7705 (m-40) cc_final: 0.6486 (m-40) REVERT: B 911 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6601 (mp0) REVERT: B 928 HIS cc_start: 0.7070 (t70) cc_final: 0.6778 (t70) REVERT: B 929 LYS cc_start: 0.7684 (mtpp) cc_final: 0.7225 (mtpp) outliers start: 70 outliers final: 43 residues processed: 479 average time/residue: 0.1340 time to fit residues: 85.4272 Evaluate side-chains 501 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 444 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 921 LEU 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 372 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 903 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 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.0970 chunk 90 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110508 restraints weight = 20016.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113895 restraints weight = 9310.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116011 restraints weight = 5373.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117374 restraints weight = 3619.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118169 restraints weight = 2751.100| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10798 Z= 0.142 Angle : 0.611 16.641 14638 Z= 0.310 Chirality : 0.039 0.260 1772 Planarity : 0.004 0.045 1796 Dihedral : 5.850 56.984 1465 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.84 % Allowed : 24.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.23), residues: 1344 helix: 1.96 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -0.56 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 910 TYR 0.012 0.001 TYR A 313 PHE 0.023 0.001 PHE B 288 TRP 0.019 0.001 TRP B 635 HIS 0.002 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00297 (10798) covalent geometry : angle 0.61112 (14638) hydrogen bonds : bond 0.04113 ( 909) hydrogen bonds : angle 4.04639 ( 2718) *********************** 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 524 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 457 time to evaluate : 0.419 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: 0.8308 (m) cc_final: 0.7934 (m) REVERT: A 103 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 124 GLU cc_start: 0.7472 (tp30) cc_final: 0.6671 (tp30) REVERT: A 160 MET cc_start: 0.7745 (mmm) cc_final: 0.7348 (mmt) REVERT: A 186 MET cc_start: 0.6559 (mtp) cc_final: 0.6332 (mtp) REVERT: A 199 MET cc_start: 0.7752 (mmm) cc_final: 0.7425 (mmm) REVERT: A 205 MET cc_start: 0.7558 (mmm) cc_final: 0.7057 (mpp) REVERT: A 217 LEU cc_start: 0.8329 (mt) cc_final: 0.8046 (mt) REVERT: A 218 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7444 (ttmt) REVERT: A 225 GLN cc_start: 0.7829 (pm20) cc_final: 0.7597 (pm20) REVERT: A 237 ASN cc_start: 0.7881 (t0) cc_final: 0.7677 (t0) REVERT: A 250 LYS cc_start: 0.8149 (mtmm) cc_final: 0.7373 (mtmm) REVERT: A 292 HIS cc_start: 0.8232 (m-70) cc_final: 0.7643 (m-70) REVERT: A 319 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6635 (mt) REVERT: A 322 SER cc_start: 0.8064 (t) cc_final: 0.7697 (p) REVERT: A 335 ASN cc_start: 0.8623 (t0) cc_final: 0.8354 (t0) REVERT: A 337 GLU cc_start: 0.7328 (mp0) cc_final: 0.6678 (mp0) REVERT: A 387 TYR cc_start: 0.7829 (m-10) cc_final: 0.7535 (m-10) REVERT: A 454 LYS cc_start: 0.8346 (mttm) cc_final: 0.7927 (mmtp) REVERT: A 476 THR cc_start: 0.8362 (m) cc_final: 0.7727 (p) REVERT: A 477 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 479 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7538 (ttp80) REVERT: A 481 LEU cc_start: 0.8511 (mt) cc_final: 0.8239 (mt) REVERT: A 499 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7117 (ttp80) REVERT: A 506 ASN cc_start: 0.7937 (m110) cc_final: 0.7531 (m110) REVERT: A 512 LEU cc_start: 0.8522 (tp) cc_final: 0.8171 (tt) REVERT: A 578 MET cc_start: 0.7953 (ttm) cc_final: 0.7740 (ttm) REVERT: A 579 MET cc_start: 0.7744 (mmm) cc_final: 0.7289 (mmm) REVERT: A 596 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7736 (tmmt) REVERT: A 597 GLN cc_start: 0.7425 (mt0) cc_final: 0.7181 (mt0) REVERT: A 611 LEU cc_start: 0.8252 (tp) cc_final: 0.7942 (tp) REVERT: A 613 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7587 (tm-30) REVERT: A 622 LYS cc_start: 0.7797 (tttp) cc_final: 0.7411 (tttp) REVERT: A 645 LYS cc_start: 0.8945 (tptp) cc_final: 0.8313 (tptp) REVERT: A 843 TYR cc_start: 0.8639 (t80) cc_final: 0.7942 (t80) REVERT: A 848 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7575 (mt-10) REVERT: A 849 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 862 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8341 (mmtm) REVERT: A 868 LYS cc_start: 0.8453 (mmmm) cc_final: 0.7672 (mmmm) REVERT: A 875 ARG cc_start: 0.7659 (tpt90) cc_final: 0.7280 (tpt170) REVERT: A 880 LYS cc_start: 0.8280 (tptp) cc_final: 0.7806 (tptp) REVERT: A 881 GLU cc_start: 0.7566 (mm-30) cc_final: 0.6986 (tm-30) REVERT: A 931 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7179 (tm-30) REVERT: A 937 LYS cc_start: 0.8671 (mttt) cc_final: 0.8425 (mtpp) REVERT: B 81 ILE cc_start: 0.7926 (mt) cc_final: 0.7640 (mt) REVERT: B 84 SER cc_start: 0.8016 (t) cc_final: 0.7614 (p) REVERT: B 149 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7042 (tm-30) REVERT: B 199 MET cc_start: 0.7525 (mmm) cc_final: 0.6904 (tpt) REVERT: B 269 LEU cc_start: 0.7999 (tp) cc_final: 0.7705 (tp) REVERT: B 278 TRP cc_start: 0.8376 (t-100) cc_final: 0.8048 (t-100) REVERT: B 300 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6932 (mt-10) REVERT: B 337 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: B 351 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8055 (tpp-160) REVERT: B 366 MET cc_start: 0.8159 (tpp) cc_final: 0.7865 (tpp) REVERT: B 388 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 420 ARG cc_start: 0.8017 (mtm180) cc_final: 0.7556 (mtm-85) REVERT: B 425 MET cc_start: 0.7709 (ttm) cc_final: 0.7507 (ttt) REVERT: B 443 GLU cc_start: 0.7672 (tp30) cc_final: 0.7022 (tp30) REVERT: B 475 GLN cc_start: 0.7467 (tp40) cc_final: 0.7179 (tp40) REVERT: B 499 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7156 (ptp90) REVERT: B 500 ARG cc_start: 0.7793 (tpt90) cc_final: 0.7444 (tpp80) REVERT: B 512 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8217 (tp) REVERT: B 517 PHE cc_start: 0.7518 (m-10) cc_final: 0.7273 (m-80) REVERT: B 523 TRP cc_start: 0.7629 (m100) cc_final: 0.7004 (m100) REVERT: B 579 MET cc_start: 0.7640 (mmm) cc_final: 0.7374 (mmm) REVERT: B 581 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: B 586 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6011 (tmm) REVERT: B 588 LYS cc_start: 0.8263 (ttpp) cc_final: 0.7966 (ttpp) REVERT: B 590 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6680 (mm-30) REVERT: B 595 TRP cc_start: 0.7979 (m100) cc_final: 0.7689 (m100) REVERT: B 613 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 645 LYS cc_start: 0.8402 (tptp) cc_final: 0.7931 (tptp) REVERT: B 825 VAL cc_start: 0.8487 (t) cc_final: 0.8254 (p) REVERT: B 826 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7606 (m110) REVERT: B 837 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: B 841 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8160 (ttmm) REVERT: B 847 GLU cc_start: 0.7718 (tp30) cc_final: 0.7485 (tp30) REVERT: B 848 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 850 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7878 (p) REVERT: B 872 GLU cc_start: 0.7896 (tp30) cc_final: 0.7541 (tp30) REVERT: B 881 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7241 (mm-30) REVERT: B 903 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: B 907 ASN cc_start: 0.7711 (m-40) cc_final: 0.6468 (m-40) REVERT: B 911 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6577 (mp0) REVERT: B 928 HIS cc_start: 0.7068 (t70) cc_final: 0.6776 (t70) REVERT: B 929 LYS cc_start: 0.7679 (mtpp) cc_final: 0.7197 (mtpp) outliers start: 67 outliers final: 43 residues processed: 480 average time/residue: 0.1346 time to fit residues: 86.1346 Evaluate side-chains 507 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 451 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 183 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 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 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 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 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 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 130 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 41 optimal weight: 0.0470 chunk 98 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 421 ASN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 361 ASN B 506 ASN ** B 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.128627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110138 restraints weight = 20054.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113509 restraints weight = 9333.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115648 restraints weight = 5398.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116996 restraints weight = 3634.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117673 restraints weight = 2755.811| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10798 Z= 0.152 Angle : 0.633 16.617 14638 Z= 0.321 Chirality : 0.041 0.290 1772 Planarity : 0.005 0.122 1796 Dihedral : 5.775 57.432 1463 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 6.10 % Allowed : 24.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.23), residues: 1344 helix: 1.97 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.60 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 609 TYR 0.012 0.001 TYR A 313 PHE 0.016 0.001 PHE B 455 TRP 0.021 0.001 TRP B 635 HIS 0.008 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00319 (10798) covalent geometry : angle 0.63287 (14638) hydrogen bonds : bond 0.04170 ( 909) hydrogen bonds : angle 4.07562 ( 2718) *********************** 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 523 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 0.526 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: 0.8310 (m) cc_final: 0.7940 (m) REVERT: A 103 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7829 (p) REVERT: A 124 GLU cc_start: 0.7458 (tp30) cc_final: 0.6660 (tp30) REVERT: A 160 MET cc_start: 0.7655 (mmm) cc_final: 0.7237 (mmt) REVERT: A 186 MET cc_start: 0.6561 (mtp) cc_final: 0.6348 (mtp) REVERT: A 205 MET cc_start: 0.7556 (mmm) cc_final: 0.7046 (mpp) REVERT: A 217 LEU cc_start: 0.8327 (mt) cc_final: 0.8059 (mt) REVERT: A 218 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7476 (ttmt) REVERT: A 225 GLN cc_start: 0.7857 (pm20) cc_final: 0.7624 (pm20) REVERT: A 237 ASN cc_start: 0.7891 (t0) cc_final: 0.7678 (t0) REVERT: A 250 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7367 (mtmm) REVERT: A 292 HIS cc_start: 0.8234 (m-70) cc_final: 0.7636 (m-70) REVERT: A 319 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6653 (mt) REVERT: A 322 SER cc_start: 0.8061 (t) cc_final: 0.7698 (p) REVERT: A 335 ASN cc_start: 0.8590 (t0) cc_final: 0.8359 (t0) REVERT: A 337 GLU cc_start: 0.7329 (mp0) cc_final: 0.6698 (mp0) REVERT: A 387 TYR cc_start: 0.7831 (m-10) cc_final: 0.7527 (m-10) REVERT: A 401 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6655 (mtm) REVERT: A 454 LYS cc_start: 0.8346 (mttm) cc_final: 0.8043 (mtpp) REVERT: A 476 THR cc_start: 0.8357 (m) cc_final: 0.7684 (p) REVERT: A 477 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 479 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7550 (ttp80) REVERT: A 481 LEU cc_start: 0.8519 (mt) cc_final: 0.8249 (mt) REVERT: A 499 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7106 (ttp80) REVERT: A 506 ASN cc_start: 0.7880 (m110) cc_final: 0.7506 (m110) REVERT: A 512 LEU cc_start: 0.8506 (tp) cc_final: 0.8163 (tt) REVERT: A 578 MET cc_start: 0.7967 (ttm) cc_final: 0.7755 (ttm) REVERT: A 579 MET cc_start: 0.7772 (mmm) cc_final: 0.7311 (mmm) REVERT: A 596 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7746 (tmmt) REVERT: A 597 GLN cc_start: 0.7430 (mt0) cc_final: 0.7208 (mt0) REVERT: A 613 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 622 LYS cc_start: 0.7842 (tttp) cc_final: 0.7442 (tttp) REVERT: A 645 LYS cc_start: 0.8922 (tptp) cc_final: 0.8296 (tptp) REVERT: A 843 TYR cc_start: 0.8644 (t80) cc_final: 0.7960 (t80) REVERT: A 848 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 849 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 862 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8306 (mmtm) REVERT: A 868 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7594 (mmmm) REVERT: A 875 ARG cc_start: 0.7681 (tpt90) cc_final: 0.7348 (tpt170) REVERT: A 880 LYS cc_start: 0.8274 (tptp) cc_final: 0.7805 (tptp) REVERT: A 881 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6978 (tm-30) REVERT: A 931 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7187 (tm-30) REVERT: A 937 LYS cc_start: 0.8697 (mttt) cc_final: 0.8422 (mtpp) REVERT: B 81 ILE cc_start: 0.7935 (mt) cc_final: 0.7641 (mt) REVERT: B 84 SER cc_start: 0.8027 (t) cc_final: 0.7612 (p) REVERT: B 149 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 199 MET cc_start: 0.7537 (mmm) cc_final: 0.6883 (tpt) REVERT: B 269 LEU cc_start: 0.8005 (tp) cc_final: 0.7730 (tp) REVERT: B 278 TRP cc_start: 0.8381 (t-100) cc_final: 0.8093 (t-100) REVERT: B 300 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: B 337 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 351 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8076 (tpp-160) REVERT: B 361 ASN cc_start: 0.8156 (m-40) cc_final: 0.7656 (m110) REVERT: B 366 MET cc_start: 0.8158 (tpp) cc_final: 0.7861 (tpp) REVERT: B 388 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 420 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7547 (mtm-85) REVERT: B 443 GLU cc_start: 0.7679 (tp30) cc_final: 0.7037 (tp30) REVERT: B 475 GLN cc_start: 0.7476 (tp40) cc_final: 0.7163 (tp40) REVERT: B 499 ARG cc_start: 0.7545 (ptp90) cc_final: 0.7183 (ptp90) REVERT: B 500 ARG cc_start: 0.7783 (tpt90) cc_final: 0.7456 (tpp80) REVERT: B 512 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 523 TRP cc_start: 0.7734 (m100) cc_final: 0.7219 (m100) REVERT: B 579 MET cc_start: 0.7628 (mmm) cc_final: 0.7401 (mmm) REVERT: B 581 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5806 (pp20) REVERT: B 586 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: B 588 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7972 (ttpp) REVERT: B 590 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 595 TRP cc_start: 0.7994 (m100) cc_final: 0.7706 (m100) REVERT: B 613 GLN cc_start: 0.7520 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 645 LYS cc_start: 0.8400 (tptp) cc_final: 0.7932 (tptp) REVERT: B 825 VAL cc_start: 0.8475 (t) cc_final: 0.8243 (p) REVERT: B 826 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7555 (m110) REVERT: B 837 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: B 841 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8159 (ttmm) REVERT: B 847 GLU cc_start: 0.7655 (tp30) cc_final: 0.7423 (tp30) REVERT: B 848 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 881 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 903 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6376 (mtm180) REVERT: B 907 ASN cc_start: 0.7705 (m-40) cc_final: 0.6461 (m-40) REVERT: B 911 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6599 (mp0) REVERT: B 928 HIS cc_start: 0.7067 (t70) cc_final: 0.6772 (t70) REVERT: B 929 LYS cc_start: 0.7689 (mtpp) cc_final: 0.7244 (mtpp) REVERT: B 941 LEU cc_start: 0.8710 (tp) cc_final: 0.8493 (tt) outliers start: 70 outliers final: 50 residues processed: 477 average time/residue: 0.1337 time to fit residues: 84.6987 Evaluate side-chains 510 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 446 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 388 LEU 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 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 826 ASN Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 33 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 900 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 506 ASN B 624 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.128866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110405 restraints weight = 19931.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113830 restraints weight = 9304.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115957 restraints weight = 5343.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.117260 restraints weight = 3586.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118159 restraints weight = 2730.274| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2875 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= 0.137 Angle : 0.642 16.704 14638 Z= 0.321 Chirality : 0.041 0.288 1772 Planarity : 0.004 0.042 1796 Dihedral : 5.777 56.172 1463 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.84 % Allowed : 25.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.23), residues: 1344 helix: 2.01 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.57 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 585 TYR 0.013 0.001 TYR A 313 PHE 0.025 0.001 PHE B 288 TRP 0.019 0.001 TRP B 635 HIS 0.004 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00291 (10798) covalent geometry : angle 0.64224 (14638) hydrogen bonds : bond 0.04073 ( 909) hydrogen bonds : angle 4.06578 ( 2718) ********************** 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 519 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 452 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 CYS cc_start: 0.8293 (m) cc_final: 0.7908 (m) REVERT: A 103 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7793 (p) REVERT: A 124 GLU cc_start: 0.7454 (tp30) cc_final: 0.6640 (tp30) REVERT: A 147 ILE cc_start: 0.8082 (mp) cc_final: 0.7680 (mt) REVERT: A 160 MET cc_start: 0.7659 (mmm) cc_final: 0.7260 (mmt) REVERT: A 186 MET cc_start: 0.6557 (mtp) cc_final: 0.6337 (mtp) REVERT: A 217 LEU cc_start: 0.8329 (mt) cc_final: 0.8056 (mt) REVERT: A 218 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7452 (ttmt) REVERT: A 225 GLN cc_start: 0.7821 (pm20) cc_final: 0.7582 (pm20) REVERT: A 237 ASN cc_start: 0.7878 (t0) cc_final: 0.7656 (t0) REVERT: A 250 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7358 (mtmm) REVERT: A 292 HIS cc_start: 0.8198 (m-70) cc_final: 0.7539 (m-70) REVERT: A 319 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6642 (mt) REVERT: A 322 SER cc_start: 0.8040 (t) cc_final: 0.7676 (p) REVERT: A 335 ASN cc_start: 0.8578 (t0) cc_final: 0.8342 (t0) REVERT: A 337 GLU cc_start: 0.7327 (mp0) cc_final: 0.6637 (mp0) REVERT: A 387 TYR cc_start: 0.7820 (m-10) cc_final: 0.7534 (m-10) REVERT: A 401 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6656 (mtm) REVERT: A 454 LYS cc_start: 0.8359 (mttm) cc_final: 0.8071 (mtpp) REVERT: A 476 THR cc_start: 0.8346 (m) cc_final: 0.7716 (p) REVERT: A 477 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 479 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7534 (ttp80) REVERT: A 481 LEU cc_start: 0.8496 (mt) cc_final: 0.8190 (mt) REVERT: A 499 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7173 (ttp80) REVERT: A 506 ASN cc_start: 0.7897 (m110) cc_final: 0.7519 (m110) REVERT: A 512 LEU cc_start: 0.8479 (tp) cc_final: 0.8149 (tt) REVERT: A 579 MET cc_start: 0.7709 (mmm) cc_final: 0.7273 (mmm) REVERT: A 596 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7750 (tmmt) REVERT: A 613 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7575 (tm-30) REVERT: A 645 LYS cc_start: 0.8906 (tptp) cc_final: 0.8282 (tptp) REVERT: A 837 TYR cc_start: 0.8231 (t80) cc_final: 0.7910 (t80) REVERT: A 843 TYR cc_start: 0.8636 (t80) cc_final: 0.8032 (t80) REVERT: A 848 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 849 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 862 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8281 (mmtm) REVERT: A 868 LYS cc_start: 0.8339 (mmmm) cc_final: 0.7572 (mmmm) REVERT: A 875 ARG cc_start: 0.7706 (tpt90) cc_final: 0.7361 (tpt170) REVERT: A 880 LYS cc_start: 0.8270 (tptp) cc_final: 0.7777 (tptp) REVERT: A 881 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6983 (tm-30) REVERT: A 937 LYS cc_start: 0.8670 (mttt) cc_final: 0.8397 (mtpp) REVERT: A 940 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7730 (tpp80) REVERT: B 81 ILE cc_start: 0.7910 (mt) cc_final: 0.7625 (mt) REVERT: B 84 SER cc_start: 0.8003 (t) cc_final: 0.7599 (p) REVERT: B 120 VAL cc_start: 0.8492 (t) cc_final: 0.8112 (p) REVERT: B 149 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7022 (tm-30) REVERT: B 155 ASP cc_start: 0.7545 (t0) cc_final: 0.7226 (t0) REVERT: B 199 MET cc_start: 0.7514 (mmm) cc_final: 0.6895 (tpt) REVERT: B 234 SER cc_start: 0.7836 (m) cc_final: 0.7595 (p) REVERT: B 269 LEU cc_start: 0.8000 (tp) cc_final: 0.7701 (tp) REVERT: B 278 TRP cc_start: 0.8362 (t-100) cc_final: 0.8040 (t-100) REVERT: B 300 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6862 (mt-10) REVERT: B 337 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: B 351 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8073 (tpp-160) REVERT: B 366 MET cc_start: 0.8152 (tpp) cc_final: 0.7869 (tpp) REVERT: B 388 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8294 (tt) REVERT: B 420 ARG cc_start: 0.8009 (mtm180) cc_final: 0.7528 (mtm-85) REVERT: B 443 GLU cc_start: 0.7674 (tp30) cc_final: 0.7005 (tp30) REVERT: B 475 GLN cc_start: 0.7528 (tp40) cc_final: 0.7225 (tp40) REVERT: B 499 ARG cc_start: 0.7494 (ptp90) cc_final: 0.7140 (ptp90) REVERT: B 500 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7413 (tpp80) REVERT: B 512 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8135 (tp) REVERT: B 517 PHE cc_start: 0.7495 (m-10) cc_final: 0.7278 (m-80) REVERT: B 523 TRP cc_start: 0.7753 (m100) cc_final: 0.7256 (m100) REVERT: B 579 MET cc_start: 0.7602 (mmm) cc_final: 0.7398 (mmm) REVERT: B 581 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: B 586 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6141 (tmm) REVERT: B 588 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7961 (ttpp) REVERT: B 590 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6913 (mm-30) REVERT: B 595 TRP cc_start: 0.7937 (m100) cc_final: 0.7636 (m100) REVERT: B 596 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8332 (mmmt) REVERT: B 613 GLN cc_start: 0.7482 (tm-30) cc_final: 0.7036 (tm-30) REVERT: B 645 LYS cc_start: 0.8387 (tptp) cc_final: 0.7920 (tptp) REVERT: B 825 VAL cc_start: 0.8503 (t) cc_final: 0.8283 (p) REVERT: B 826 ASN cc_start: 0.7914 (t0) cc_final: 0.7619 (m110) REVERT: B 837 TYR cc_start: 0.8413 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: B 841 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8118 (ttmm) REVERT: B 847 GLU cc_start: 0.7641 (tp30) cc_final: 0.7370 (tp30) REVERT: B 848 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 881 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7209 (mm-30) REVERT: B 903 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6362 (mtm180) REVERT: B 907 ASN cc_start: 0.7710 (m-40) cc_final: 0.6455 (m-40) REVERT: B 911 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6579 (mp0) REVERT: B 928 HIS cc_start: 0.7065 (t70) cc_final: 0.6749 (t70) REVERT: B 929 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7220 (mtpp) REVERT: B 941 LEU cc_start: 0.8700 (tp) cc_final: 0.8488 (tt) outliers start: 67 outliers final: 47 residues processed: 474 average time/residue: 0.1321 time to fit residues: 83.2370 Evaluate side-chains 507 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 447 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 425 MET 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 852 LYS Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 257 LEU 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 372 VAL Chi-restraints excluded: chain B residue 388 LEU 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 502 HIS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 586 MET Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 903 ARG Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 108 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 133 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN A 900 GLN ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 361 ASN B 506 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109471 restraints weight = 20047.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112901 restraints weight = 9341.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115020 restraints weight = 5358.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.116404 restraints weight = 3606.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.117113 restraints weight = 2716.065| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10798 Z= 0.149 Angle : 0.654 16.482 14638 Z= 0.331 Chirality : 0.041 0.308 1772 Planarity : 0.004 0.042 1796 Dihedral : 5.719 56.790 1462 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.66 % Allowed : 25.61 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.23), residues: 1344 helix: 1.94 (0.15), residues: 1158 sheet: None (None), residues: 0 loop : -0.41 (0.48), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 609 TYR 0.012 0.001 TYR A 313 PHE 0.020 0.001 PHE A 625 TRP 0.021 0.001 TRP B 635 HIS 0.003 0.000 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00317 (10798) covalent geometry : angle 0.65403 (14638) hydrogen bonds : bond 0.04138 ( 909) hydrogen bonds : angle 4.08284 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2366.91 seconds wall clock time: 41 minutes 36.32 seconds (2496.32 seconds total)