Starting phenix.real_space_refine on Mon Dec 30 09:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1x_24807/12_2024/7s1x_24807.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.148 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 74 5.16 5 Cl 2 4.86 5 C 8264 2.51 5 N 2130 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12658 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 871, 6302 Classifications: {'peptide': 871} Incomplete info: {'backbone_only': 29, 'truncation_to_alanine': 117} Link IDs: {'PTRANS': 31, 'TRANS': 839} Chain breaks: 2 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 19, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 13.20, per 1000 atoms: 1.04 Number of scatterers: 12658 At special positions: 0 Unit cell: (111.3, 107.06, 145.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 74 16.00 O 2186 8.00 N 2130 7.00 C 8264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 82U B1301 " pdb=" CB 82U A1301 " Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 4 sheets defined 64.1% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.640A pdb=" N ARG B 228 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.259A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 343 removed outlier: 3.923A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 398 Proline residue: B 362 - end of helix removed outlier: 3.862A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.517A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 454 removed outlier: 4.075A pdb=" N GLU B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 477 Processing helix chain 'B' and resid 486 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 504 through 511 removed outlier: 4.831A pdb=" N GLY B 509 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 544 removed outlier: 4.218A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 571 removed outlier: 4.010A pdb=" N LEU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.944A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 632 removed outlier: 3.942A pdb=" N GLY B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 651 through 669 Processing helix chain 'B' and resid 670 through 699 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 730 Processing helix chain 'B' and resid 731 through 753 Processing helix chain 'B' and resid 760 through 779 removed outlier: 3.516A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 801 through 811 removed outlier: 3.596A pdb=" N PHE B 811 " --> pdb=" O LEU B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 849 removed outlier: 3.727A pdb=" N LYS B 833 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 840 " --> pdb=" O SER B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 874 Processing helix chain 'B' and resid 896 through 913 Processing helix chain 'B' and resid 1034 through 1046 Proline residue: B1040 - end of helix Processing helix chain 'B' and resid 1064 through 1079 Processing helix chain 'B' and resid 1097 through 1109 Processing helix chain 'B' and resid 1110 through 1112 No H-bonds generated for 'chain 'B' and resid 1110 through 1112' Processing helix chain 'B' and resid 1120 through 1128 Processing helix chain 'B' and resid 1136 through 1140 removed outlier: 3.778A pdb=" N LEU B1139 " --> pdb=" O ASP B1136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B1140 " --> pdb=" O ASN B1137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1136 through 1140' Processing helix chain 'B' and resid 1141 through 1160 Processing helix chain 'B' and resid 1161 through 1163 No H-bonds generated for 'chain 'B' and resid 1161 through 1163' Processing helix chain 'B' and resid 1179 through 1192 Processing helix chain 'A' and resid 223 through 228 removed outlier: 3.639A pdb=" N ARG A 228 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.259A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.923A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 398 Proline residue: A 362 - end of helix removed outlier: 3.862A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 4.518A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 4.075A pdb=" N GLU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 477 Processing helix chain 'A' and resid 486 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 504 through 511 removed outlier: 4.831A pdb=" N GLY A 509 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 544 removed outlier: 4.217A pdb=" N LEU A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 571 removed outlier: 4.010A pdb=" N LEU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.944A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.943A pdb=" N GLY A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 651 through 669 Processing helix chain 'A' and resid 670 through 699 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 712 through 730 Processing helix chain 'A' and resid 731 through 753 Processing helix chain 'A' and resid 760 through 779 removed outlier: 3.517A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 801 through 811 removed outlier: 3.596A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 849 removed outlier: 3.727A pdb=" N LYS A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 874 Processing helix chain 'A' and resid 896 through 913 Processing helix chain 'A' and resid 1034 through 1046 Proline residue: A1040 - end of helix Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1110 through 1112 No H-bonds generated for 'chain 'A' and resid 1110 through 1112' Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.779A pdb=" N LEU A1139 " --> pdb=" O ASP A1136 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A1140 " --> pdb=" O ASN A1137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1136 through 1140' Processing helix chain 'A' and resid 1141 through 1160 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1179 through 1192 Processing sheet with id=AA1, first strand: chain 'B' and resid 547 through 548 Processing sheet with id=AA2, first strand: chain 'B' and resid 854 through 859 removed outlier: 6.736A pdb=" N CYS B 791 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY B 821 " --> pdb=" O CYS B 791 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 793 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL B 823 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B1026 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLY B1059 " --> pdb=" O VAL B1026 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B1056 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU B1089 " --> pdb=" O VAL B1056 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B1058 " --> pdb=" O LEU B1089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA4, first strand: chain 'A' and resid 854 through 859 removed outlier: 6.736A pdb=" N CYS A 791 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A 821 " --> pdb=" O CYS A 791 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 793 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL A 823 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A1026 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLY A1059 " --> pdb=" O VAL A1026 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1056 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A1089 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A1058 " --> pdb=" O LEU A1089 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2382 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: 4.42 Time building geometry restraints manager: 4.08 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: 3964 1.34 - 1.46: 2241 1.46 - 1.58: 6627 1.58 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 12954 Sorted by residual: bond pdb=" N 82U A1301 " pdb=" CA 82U A1301 " ideal model delta sigma weight residual 1.366 1.443 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" N 82U B1301 " pdb=" CA 82U B1301 " ideal model delta sigma weight residual 1.366 1.443 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" NE1 82U B1301 " pdb=" S1 82U B1301 " ideal model delta sigma weight residual 1.647 1.705 -0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" NE1 82U A1301 " pdb=" S1 82U A1301 " ideal model delta sigma weight residual 1.647 1.704 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" C17 82U A1301 " pdb=" O4 82U A1301 " ideal model delta sigma weight residual 1.245 1.294 -0.049 2.00e-02 2.50e+03 5.97e+00 ... (remaining 12949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17153 2.16 - 4.31: 426 4.31 - 6.47: 62 6.47 - 8.63: 19 8.63 - 10.78: 4 Bond angle restraints: 17664 Sorted by residual: angle pdb=" C HIS B 229 " pdb=" N THR B 230 " pdb=" CA THR B 230 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C HIS A 229 " pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C TRP B1027 " pdb=" N TRP B1028 " pdb=" CA TRP B1028 " ideal model delta sigma weight residual 123.12 117.81 5.31 1.52e+00 4.33e-01 1.22e+01 angle pdb=" C TRP A1027 " pdb=" N TRP A1028 " pdb=" CA TRP A1028 " ideal model delta sigma weight residual 123.12 117.82 5.30 1.52e+00 4.33e-01 1.21e+01 angle pdb=" C VAL A1026 " pdb=" N TRP A1027 " pdb=" CA TRP A1027 " ideal model delta sigma weight residual 123.23 117.77 5.46 1.57e+00 4.06e-01 1.21e+01 ... (remaining 17659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 6797 15.25 - 30.50: 495 30.50 - 45.75: 106 45.75 - 61.00: 17 61.00 - 76.25: 15 Dihedral angle restraints: 7430 sinusoidal: 2514 harmonic: 4916 Sorted by residual: dihedral pdb=" CB CYS B 577 " pdb=" SG CYS B 577 " pdb=" SG CYS B 582 " pdb=" CB CYS B 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.73 71.27 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CA THR A 795 " pdb=" C THR A 795 " pdb=" N GLY A 796 " pdb=" CA GLY A 796 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA THR B 795 " pdb=" C THR B 795 " pdb=" N GLY B 796 " pdb=" CA GLY B 796 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 7427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1506 0.052 - 0.105: 462 0.105 - 0.157: 81 0.157 - 0.210: 11 0.210 - 0.262: 2 Chirality restraints: 2062 Sorted by residual: chirality pdb=" CG LEU B1156 " pdb=" CB LEU B1156 " pdb=" CD1 LEU B1156 " pdb=" CD2 LEU B1156 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU A1156 " pdb=" CB LEU A1156 " pdb=" CD1 LEU A1156 " pdb=" CD2 LEU A1156 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ARG B 705 " pdb=" N ARG B 705 " pdb=" C ARG B 705 " pdb=" CB ARG B 705 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 2059 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1027 " 0.039 2.00e-02 2.50e+03 4.25e-02 4.52e+01 pdb=" CG TRP A1027 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP A1027 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP A1027 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A1027 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A1027 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1027 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1027 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1027 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A1027 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1027 " -0.038 2.00e-02 2.50e+03 4.24e-02 4.50e+01 pdb=" CG TRP B1027 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP B1027 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP B1027 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B1027 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP B1027 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1027 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1027 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1027 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1027 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1028 " -0.035 2.00e-02 2.50e+03 3.34e-02 2.78e+01 pdb=" CG TRP A1028 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 TRP A1028 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A1028 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP A1028 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1028 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A1028 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1028 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1028 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A1028 " -0.005 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 172 2.65 - 3.27: 15033 3.27 - 3.90: 25595 3.90 - 4.52: 34553 4.52 - 5.14: 52775 Nonbonded interactions: 128128 Sorted by model distance: nonbonded pdb=" SG CYS A 563 " pdb=" SG CYS A 568 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " model vdw 2.033 3.760 nonbonded pdb=" NH1 ARG B 705 " pdb=" O PHE A1079 " model vdw 2.052 3.120 nonbonded pdb=" O PHE B1079 " pdb=" NH1 ARG A 705 " model vdw 2.053 3.120 nonbonded pdb=" OH TYR B 686 " pdb="CL CL B1303 " model vdw 2.061 3.190 ... (remaining 128123 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: 0.00 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 individual isotropic 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.250 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:13.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 0.077 12954 Z= 0.370 Angle : 0.832 10.784 17664 Z= 0.442 Chirality : 0.051 0.262 2062 Planarity : 0.005 0.063 2216 Dihedral : 12.055 76.247 4300 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.17 % Allowed : 0.51 % Favored : 99.32 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1730 helix: 0.74 (0.16), residues: 982 sheet: -0.13 (0.57), residues: 92 loop : -2.36 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.007 TRP A1027 HIS 0.010 0.003 HIS B1067 PHE 0.055 0.003 PHE A 608 TYR 0.018 0.002 TYR A 353 ARG 0.009 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 242 SER cc_start: 0.7446 (t) cc_final: 0.7070 (m) REVERT: B 346 PHE cc_start: 0.7749 (t80) cc_final: 0.7449 (t80) REVERT: B 485 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8112 (mm-30) REVERT: B 492 GLU cc_start: 0.7120 (tm-30) cc_final: 0.5853 (mt-10) REVERT: B 543 CYS cc_start: 0.7573 (t) cc_final: 0.6898 (m) REVERT: B 762 THR cc_start: 0.8076 (m) cc_final: 0.7692 (p) REVERT: B 1205 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 242 SER cc_start: 0.7330 (t) cc_final: 0.6944 (m) REVERT: A 346 PHE cc_start: 0.7726 (t80) cc_final: 0.7434 (t80) REVERT: A 485 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 492 GLU cc_start: 0.7047 (tm-30) cc_final: 0.5750 (mt-10) REVERT: A 531 LEU cc_start: 0.6300 (tp) cc_final: 0.6020 (mp) REVERT: A 543 CYS cc_start: 0.7553 (t) cc_final: 0.6954 (m) REVERT: A 762 THR cc_start: 0.8077 (m) cc_final: 0.7689 (p) REVERT: A 879 MET cc_start: 0.8292 (mtt) cc_final: 0.8082 (mtm) REVERT: A 1205 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7367 (mm-40) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.9729 time to fit residues: 369.0114 Evaluate side-chains 219 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 GLN B 589 ASN B 731 ASN B 799 ASN B 806 HIS B1149 GLN B1159 HIS B1203 ASN A 435 GLN A 589 ASN A 731 ASN A 799 ASN A 806 HIS A1149 GLN A1159 HIS A1203 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12954 Z= 0.245 Angle : 0.684 10.657 17664 Z= 0.358 Chirality : 0.045 0.167 2062 Planarity : 0.005 0.051 2216 Dihedral : 5.294 23.976 1880 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.21 % Allowed : 12.67 % Favored : 84.12 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1730 helix: 0.99 (0.16), residues: 1014 sheet: -0.09 (0.56), residues: 92 loop : -2.33 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A1027 HIS 0.005 0.001 HIS B 822 PHE 0.036 0.002 PHE B 608 TYR 0.015 0.002 TYR A 353 ARG 0.007 0.001 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 1.355 Fit side-chains REVERT: B 218 MET cc_start: 0.3989 (tpt) cc_final: 0.3715 (tpt) REVERT: B 242 SER cc_start: 0.7322 (t) cc_final: 0.7047 (m) REVERT: B 346 PHE cc_start: 0.7782 (t80) cc_final: 0.7566 (t80) REVERT: B 430 TRP cc_start: 0.6960 (m100) cc_final: 0.6749 (t-100) REVERT: B 485 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 492 GLU cc_start: 0.7133 (tm-30) cc_final: 0.5859 (mt-10) REVERT: B 543 CYS cc_start: 0.7277 (t) cc_final: 0.6423 (m) REVERT: B 762 THR cc_start: 0.7966 (m) cc_final: 0.7718 (p) REVERT: B 834 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: B 889 LYS cc_start: 0.8171 (tttp) cc_final: 0.7792 (tttp) REVERT: A 218 MET cc_start: 0.3983 (tpt) cc_final: 0.3713 (tpt) REVERT: A 242 SER cc_start: 0.7319 (t) cc_final: 0.7054 (m) REVERT: A 346 PHE cc_start: 0.7768 (t80) cc_final: 0.7545 (t80) REVERT: A 430 TRP cc_start: 0.6957 (m100) cc_final: 0.6751 (t-100) REVERT: A 468 TYR cc_start: 0.7966 (m-80) cc_final: 0.7652 (m-80) REVERT: A 485 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 492 GLU cc_start: 0.7059 (tm-30) cc_final: 0.5753 (mt-10) REVERT: A 543 CYS cc_start: 0.7294 (t) cc_final: 0.6531 (m) REVERT: A 762 THR cc_start: 0.7967 (m) cc_final: 0.7715 (p) REVERT: A 834 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: A 889 LYS cc_start: 0.8159 (tttp) cc_final: 0.7789 (tttp) REVERT: A 1205 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7644 (mm-40) outliers start: 38 outliers final: 23 residues processed: 271 average time/residue: 0.9764 time to fit residues: 295.0158 Evaluate side-chains 248 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 731 ASN Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1101 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 126 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN B 799 ASN A 515 GLN A 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12954 Z= 0.218 Angle : 0.639 10.061 17664 Z= 0.336 Chirality : 0.045 0.315 2062 Planarity : 0.005 0.051 2216 Dihedral : 5.023 23.246 1880 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.29 % Allowed : 15.37 % Favored : 81.33 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1730 helix: 1.17 (0.16), residues: 1006 sheet: 0.07 (0.57), residues: 92 loop : -2.22 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B1028 HIS 0.006 0.001 HIS A 773 PHE 0.029 0.002 PHE A 608 TYR 0.014 0.002 TYR A 353 ARG 0.007 0.001 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 1.481 Fit side-chains REVERT: B 218 MET cc_start: 0.3895 (tpt) cc_final: 0.3661 (tpt) REVERT: B 242 SER cc_start: 0.7251 (t) cc_final: 0.7028 (m) REVERT: B 346 PHE cc_start: 0.7785 (t80) cc_final: 0.7543 (t80) REVERT: B 359 SER cc_start: 0.8045 (t) cc_final: 0.7797 (m) REVERT: B 430 TRP cc_start: 0.7113 (m100) cc_final: 0.6863 (t-100) REVERT: B 448 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7383 (t0) REVERT: B 468 TYR cc_start: 0.7927 (m-80) cc_final: 0.7603 (m-80) REVERT: B 485 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8016 (mm-30) REVERT: B 492 GLU cc_start: 0.7081 (tm-30) cc_final: 0.5773 (mt-10) REVERT: B 543 CYS cc_start: 0.7460 (t) cc_final: 0.6646 (m) REVERT: B 752 LYS cc_start: 0.6246 (tptt) cc_final: 0.5967 (tptp) REVERT: B 762 THR cc_start: 0.7931 (m) cc_final: 0.7658 (p) REVERT: B 834 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6947 (mp0) REVERT: B 889 LYS cc_start: 0.8075 (tttp) cc_final: 0.7795 (tttp) REVERT: B 1095 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8351 (tmtt) REVERT: A 218 MET cc_start: 0.3893 (tpt) cc_final: 0.3663 (tpt) REVERT: A 242 SER cc_start: 0.7250 (t) cc_final: 0.7028 (m) REVERT: A 346 PHE cc_start: 0.7783 (t80) cc_final: 0.7541 (t80) REVERT: A 359 SER cc_start: 0.8024 (t) cc_final: 0.7778 (m) REVERT: A 468 TYR cc_start: 0.7985 (m-80) cc_final: 0.7620 (m-80) REVERT: A 485 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8006 (mm-30) REVERT: A 492 GLU cc_start: 0.7090 (tm-30) cc_final: 0.5767 (mt-10) REVERT: A 543 CYS cc_start: 0.7304 (t) cc_final: 0.6521 (m) REVERT: A 752 LYS cc_start: 0.6381 (tptt) cc_final: 0.6073 (tptp) REVERT: A 762 THR cc_start: 0.7901 (m) cc_final: 0.7636 (p) REVERT: A 834 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: A 889 LYS cc_start: 0.8047 (tttp) cc_final: 0.7779 (tttp) REVERT: A 1095 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8345 (tmtt) REVERT: A 1147 TYR cc_start: 0.5591 (m-10) cc_final: 0.5336 (m-10) outliers start: 39 outliers final: 22 residues processed: 265 average time/residue: 0.9416 time to fit residues: 279.7990 Evaluate side-chains 249 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 834 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 799 ASN B1203 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A1203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12954 Z= 0.306 Angle : 0.675 10.562 17664 Z= 0.351 Chirality : 0.046 0.162 2062 Planarity : 0.005 0.053 2216 Dihedral : 5.016 24.781 1880 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.81 % Allowed : 15.71 % Favored : 79.48 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1730 helix: 1.28 (0.16), residues: 988 sheet: -0.26 (0.56), residues: 94 loop : -2.27 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1028 HIS 0.007 0.002 HIS B 773 PHE 0.023 0.002 PHE B 608 TYR 0.013 0.002 TYR B 227 ARG 0.006 0.001 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 1.426 Fit side-chains REVERT: B 242 SER cc_start: 0.7242 (t) cc_final: 0.6961 (m) REVERT: B 346 PHE cc_start: 0.7909 (t80) cc_final: 0.7643 (t80) REVERT: B 469 LYS cc_start: 0.7188 (mmpt) cc_final: 0.6972 (mmmt) REVERT: B 492 GLU cc_start: 0.7185 (tm-30) cc_final: 0.5901 (mt-10) REVERT: B 543 CYS cc_start: 0.7587 (t) cc_final: 0.6595 (m) REVERT: B 752 LYS cc_start: 0.6448 (tptt) cc_final: 0.6166 (tptp) REVERT: B 762 THR cc_start: 0.7977 (m) cc_final: 0.7548 (p) REVERT: B 834 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: A 242 SER cc_start: 0.7236 (t) cc_final: 0.6960 (m) REVERT: A 468 TYR cc_start: 0.7833 (m-80) cc_final: 0.7489 (m-80) REVERT: A 469 LYS cc_start: 0.7083 (mmpt) cc_final: 0.6819 (mmmt) REVERT: A 485 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 492 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6023 (mt-10) REVERT: A 543 CYS cc_start: 0.7481 (t) cc_final: 0.6506 (m) REVERT: A 752 LYS cc_start: 0.6439 (tptt) cc_final: 0.6157 (tptp) REVERT: A 762 THR cc_start: 0.7974 (m) cc_final: 0.7543 (p) REVERT: A 834 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6814 (mp0) outliers start: 57 outliers final: 33 residues processed: 265 average time/residue: 0.9142 time to fit residues: 273.9922 Evaluate side-chains 244 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 150 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12954 Z= 0.226 Angle : 0.630 9.695 17664 Z= 0.330 Chirality : 0.044 0.164 2062 Planarity : 0.005 0.049 2216 Dihedral : 4.878 23.838 1880 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.31 % Allowed : 17.65 % Favored : 78.04 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1730 helix: 1.43 (0.16), residues: 976 sheet: -0.25 (0.56), residues: 94 loop : -2.22 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1028 HIS 0.005 0.001 HIS B 773 PHE 0.019 0.001 PHE B 608 TYR 0.015 0.001 TYR B 746 ARG 0.006 0.000 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.462 Fit side-chains REVERT: B 242 SER cc_start: 0.7209 (t) cc_final: 0.6918 (m) REVERT: B 440 VAL cc_start: 0.7817 (t) cc_final: 0.7605 (t) REVERT: B 468 TYR cc_start: 0.7916 (m-80) cc_final: 0.7562 (m-80) REVERT: B 492 GLU cc_start: 0.7170 (tm-30) cc_final: 0.5800 (mt-10) REVERT: B 543 CYS cc_start: 0.7665 (t) cc_final: 0.6627 (m) REVERT: B 595 MET cc_start: 0.7941 (tmm) cc_final: 0.7659 (tmm) REVERT: B 752 LYS cc_start: 0.6448 (tptt) cc_final: 0.6180 (tptp) REVERT: B 762 THR cc_start: 0.7971 (m) cc_final: 0.7599 (p) REVERT: B 799 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7564 (p0) REVERT: B 834 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 1095 LYS cc_start: 0.8621 (tmtt) cc_final: 0.8347 (tmtt) REVERT: A 242 SER cc_start: 0.7198 (t) cc_final: 0.6914 (m) REVERT: A 384 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7957 (p) REVERT: A 440 VAL cc_start: 0.7740 (t) cc_final: 0.7531 (t) REVERT: A 468 TYR cc_start: 0.7839 (m-80) cc_final: 0.7492 (m-80) REVERT: A 485 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7973 (mm-30) REVERT: A 492 GLU cc_start: 0.7311 (tm-30) cc_final: 0.5957 (mt-10) REVERT: A 543 CYS cc_start: 0.7472 (t) cc_final: 0.6478 (m) REVERT: A 752 LYS cc_start: 0.6438 (tptt) cc_final: 0.6169 (tptp) REVERT: A 762 THR cc_start: 0.7967 (m) cc_final: 0.7593 (p) REVERT: A 799 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7560 (p0) REVERT: A 834 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: A 1095 LYS cc_start: 0.8636 (tmtt) cc_final: 0.8383 (tmtt) REVERT: A 1154 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6844 (tp30) outliers start: 51 outliers final: 29 residues processed: 256 average time/residue: 0.9166 time to fit residues: 264.2703 Evaluate side-chains 239 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN B 799 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12954 Z= 0.237 Angle : 0.628 9.549 17664 Z= 0.328 Chirality : 0.044 0.187 2062 Planarity : 0.004 0.047 2216 Dihedral : 4.785 23.557 1880 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 4.73 % Allowed : 17.91 % Favored : 77.36 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1730 helix: 1.48 (0.16), residues: 974 sheet: -0.30 (0.55), residues: 94 loop : -2.21 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1028 HIS 0.005 0.001 HIS B 773 PHE 0.017 0.001 PHE A 608 TYR 0.013 0.001 TYR A 353 ARG 0.009 0.001 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.428 Fit side-chains REVERT: B 242 SER cc_start: 0.7113 (t) cc_final: 0.6802 (m) REVERT: B 359 SER cc_start: 0.8112 (t) cc_final: 0.7910 (m) REVERT: B 440 VAL cc_start: 0.7793 (t) cc_final: 0.7506 (t) REVERT: B 492 GLU cc_start: 0.7204 (tm-30) cc_final: 0.5807 (mt-10) REVERT: B 543 CYS cc_start: 0.7803 (t) cc_final: 0.6642 (m) REVERT: B 595 MET cc_start: 0.7990 (tmm) cc_final: 0.7725 (tmm) REVERT: B 752 LYS cc_start: 0.6444 (tptt) cc_final: 0.6131 (tptp) REVERT: B 762 THR cc_start: 0.7941 (m) cc_final: 0.7555 (p) REVERT: B 834 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: B 1095 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8406 (tmtt) REVERT: A 242 SER cc_start: 0.7103 (t) cc_final: 0.6795 (m) REVERT: A 384 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7963 (p) REVERT: A 440 VAL cc_start: 0.7709 (t) cc_final: 0.7499 (t) REVERT: A 468 TYR cc_start: 0.7787 (m-80) cc_final: 0.7433 (m-80) REVERT: A 485 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7970 (mm-30) REVERT: A 492 GLU cc_start: 0.7231 (tm-30) cc_final: 0.5862 (mt-10) REVERT: A 543 CYS cc_start: 0.7526 (t) cc_final: 0.6481 (m) REVERT: A 752 LYS cc_start: 0.6524 (tptt) cc_final: 0.6209 (tptp) REVERT: A 762 THR cc_start: 0.7936 (m) cc_final: 0.7545 (p) REVERT: A 834 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 1095 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8409 (tmtt) outliers start: 56 outliers final: 33 residues processed: 250 average time/residue: 0.8345 time to fit residues: 237.5560 Evaluate side-chains 237 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.0370 chunk 94 optimal weight: 0.7980 chunk 167 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN B 799 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12954 Z= 0.211 Angle : 0.615 10.194 17664 Z= 0.321 Chirality : 0.044 0.199 2062 Planarity : 0.004 0.045 2216 Dihedral : 4.708 23.187 1880 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.14 % Allowed : 18.67 % Favored : 77.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1730 helix: 1.50 (0.16), residues: 974 sheet: -0.26 (0.55), residues: 94 loop : -2.18 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1028 HIS 0.004 0.001 HIS B 773 PHE 0.016 0.001 PHE A 608 TYR 0.016 0.001 TYR B 746 ARG 0.008 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 1.458 Fit side-chains REVERT: B 242 SER cc_start: 0.7103 (t) cc_final: 0.6783 (m) REVERT: B 307 ARG cc_start: 0.6503 (mtp-110) cc_final: 0.6248 (mtp-110) REVERT: B 440 VAL cc_start: 0.7718 (t) cc_final: 0.7400 (t) REVERT: B 444 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 492 GLU cc_start: 0.7236 (tm-30) cc_final: 0.5883 (mt-10) REVERT: B 595 MET cc_start: 0.7951 (tmm) cc_final: 0.7576 (tmm) REVERT: B 752 LYS cc_start: 0.6526 (tptt) cc_final: 0.6217 (tptp) REVERT: B 762 THR cc_start: 0.7956 (m) cc_final: 0.7586 (p) REVERT: B 834 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: B 1095 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8441 (tmtt) REVERT: A 242 SER cc_start: 0.7093 (t) cc_final: 0.6777 (m) REVERT: A 384 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 440 VAL cc_start: 0.7730 (t) cc_final: 0.7521 (t) REVERT: A 468 TYR cc_start: 0.7793 (m-80) cc_final: 0.7449 (m-80) REVERT: A 485 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7950 (mm-30) REVERT: A 492 GLU cc_start: 0.7322 (tm-30) cc_final: 0.5907 (mt-10) REVERT: A 543 CYS cc_start: 0.7555 (t) cc_final: 0.6500 (m) REVERT: A 595 MET cc_start: 0.8083 (tmm) cc_final: 0.7811 (tmm) REVERT: A 752 LYS cc_start: 0.6519 (tptt) cc_final: 0.6211 (tptp) REVERT: A 762 THR cc_start: 0.8011 (m) cc_final: 0.7626 (p) REVERT: A 834 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: A 1095 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8482 (tmtt) outliers start: 49 outliers final: 32 residues processed: 239 average time/residue: 0.8470 time to fit residues: 229.6053 Evaluate side-chains 237 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 114 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 40.0000 chunk 131 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN B 799 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12954 Z= 0.233 Angle : 0.621 10.302 17664 Z= 0.323 Chirality : 0.044 0.217 2062 Planarity : 0.004 0.045 2216 Dihedral : 4.688 23.169 1880 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.31 % Allowed : 19.26 % Favored : 76.44 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1730 helix: 1.49 (0.16), residues: 976 sheet: -0.96 (0.47), residues: 122 loop : -2.12 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1028 HIS 0.005 0.001 HIS A 822 PHE 0.016 0.001 PHE B 608 TYR 0.018 0.001 TYR A 746 ARG 0.008 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 1.406 Fit side-chains REVERT: B 242 SER cc_start: 0.7184 (t) cc_final: 0.6864 (m) REVERT: B 419 ILE cc_start: 0.7594 (mm) cc_final: 0.7340 (mt) REVERT: B 440 VAL cc_start: 0.7736 (t) cc_final: 0.7414 (t) REVERT: B 444 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 492 GLU cc_start: 0.7274 (tm-30) cc_final: 0.5920 (mt-10) REVERT: B 595 MET cc_start: 0.7944 (tmm) cc_final: 0.7636 (tmm) REVERT: B 752 LYS cc_start: 0.6525 (tptt) cc_final: 0.6219 (tptp) REVERT: B 762 THR cc_start: 0.7970 (m) cc_final: 0.7576 (p) REVERT: B 834 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: B 1095 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8454 (tmtt) REVERT: A 242 SER cc_start: 0.7170 (t) cc_final: 0.6857 (m) REVERT: A 384 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 440 VAL cc_start: 0.7743 (t) cc_final: 0.7533 (t) REVERT: A 468 TYR cc_start: 0.7791 (m-80) cc_final: 0.7446 (m-80) REVERT: A 485 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 492 GLU cc_start: 0.7307 (tm-30) cc_final: 0.5880 (mt-10) REVERT: A 543 CYS cc_start: 0.7582 (t) cc_final: 0.6504 (m) REVERT: A 595 MET cc_start: 0.7946 (tmm) cc_final: 0.7703 (tmm) REVERT: A 752 LYS cc_start: 0.6515 (tptt) cc_final: 0.6208 (tptp) REVERT: A 762 THR cc_start: 0.8019 (m) cc_final: 0.7654 (p) REVERT: A 834 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: A 1154 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6685 (tp30) outliers start: 51 outliers final: 36 residues processed: 242 average time/residue: 0.8497 time to fit residues: 232.6906 Evaluate side-chains 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 165 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B 731 ASN B 799 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A 868 GLN A1203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12954 Z= 0.240 Angle : 0.629 10.505 17664 Z= 0.326 Chirality : 0.044 0.159 2062 Planarity : 0.004 0.045 2216 Dihedral : 4.688 24.613 1880 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.48 % Allowed : 19.00 % Favored : 76.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.20), residues: 1730 helix: 1.48 (0.16), residues: 978 sheet: -0.40 (0.53), residues: 98 loop : -2.15 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1028 HIS 0.005 0.001 HIS A 822 PHE 0.016 0.001 PHE A 608 TYR 0.018 0.001 TYR A 746 ARG 0.009 0.000 ARG B1069 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.434 Fit side-chains REVERT: B 242 SER cc_start: 0.7190 (t) cc_final: 0.6861 (m) REVERT: B 419 ILE cc_start: 0.7602 (mm) cc_final: 0.7348 (mt) REVERT: B 444 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 492 GLU cc_start: 0.7331 (tm-30) cc_final: 0.5876 (mt-10) REVERT: B 595 MET cc_start: 0.7918 (tmm) cc_final: 0.7632 (tmm) REVERT: B 752 LYS cc_start: 0.6523 (tptt) cc_final: 0.6218 (tptp) REVERT: B 762 THR cc_start: 0.8018 (m) cc_final: 0.7654 (p) REVERT: B 834 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: B 1095 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8476 (tmtt) REVERT: A 242 SER cc_start: 0.7174 (t) cc_final: 0.6854 (m) REVERT: A 384 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7928 (p) REVERT: A 468 TYR cc_start: 0.7788 (m-80) cc_final: 0.7443 (m-80) REVERT: A 485 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 492 GLU cc_start: 0.7227 (tm-30) cc_final: 0.5758 (mt-10) REVERT: A 543 CYS cc_start: 0.7651 (t) cc_final: 0.6545 (m) REVERT: A 595 MET cc_start: 0.7972 (tmm) cc_final: 0.7704 (tmm) REVERT: A 752 LYS cc_start: 0.6509 (tptt) cc_final: 0.6205 (tptp) REVERT: A 762 THR cc_start: 0.8024 (m) cc_final: 0.7652 (p) REVERT: A 834 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: A 1154 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6692 (tp30) outliers start: 53 outliers final: 35 residues processed: 236 average time/residue: 0.8755 time to fit residues: 233.7186 Evaluate side-chains 232 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 713 MET Chi-restraints excluded: chain B residue 728 PHE Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 0.0070 chunk 173 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 680 ASN B 731 ASN B 799 ASN B1203 ASN A 680 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN A1203 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12954 Z= 0.212 Angle : 0.618 10.204 17664 Z= 0.321 Chirality : 0.043 0.150 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.621 24.605 1880 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.22 % Allowed : 19.26 % Favored : 76.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1730 helix: 1.52 (0.16), residues: 978 sheet: -0.25 (0.53), residues: 98 loop : -2.14 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1028 HIS 0.004 0.001 HIS A1204 PHE 0.015 0.001 PHE A 494 TYR 0.017 0.001 TYR A 746 ARG 0.009 0.001 ARG A1069 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3460 Ramachandran restraints generated. 1730 Oldfield, 0 Emsley, 1730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 1.490 Fit side-chains REVERT: B 242 SER cc_start: 0.7179 (t) cc_final: 0.6848 (m) REVERT: B 419 ILE cc_start: 0.7599 (mm) cc_final: 0.7346 (mt) REVERT: B 444 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 492 GLU cc_start: 0.7293 (tm-30) cc_final: 0.5868 (mt-10) REVERT: B 595 MET cc_start: 0.7932 (tmm) cc_final: 0.7701 (tmm) REVERT: B 752 LYS cc_start: 0.6514 (tptt) cc_final: 0.6203 (tttp) REVERT: B 762 THR cc_start: 0.7976 (m) cc_final: 0.7628 (p) REVERT: B 834 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: B 889 LYS cc_start: 0.7810 (tttp) cc_final: 0.7541 (tttp) REVERT: B 1095 LYS cc_start: 0.8708 (tmtt) cc_final: 0.8475 (tmtt) REVERT: A 242 SER cc_start: 0.7163 (t) cc_final: 0.6844 (m) REVERT: A 384 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7923 (p) REVERT: A 468 TYR cc_start: 0.7789 (m-80) cc_final: 0.7435 (m-80) REVERT: A 485 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 492 GLU cc_start: 0.7124 (tm-30) cc_final: 0.5627 (mt-10) REVERT: A 543 CYS cc_start: 0.7648 (t) cc_final: 0.6548 (m) REVERT: A 595 MET cc_start: 0.7969 (tmm) cc_final: 0.7712 (tmm) REVERT: A 752 LYS cc_start: 0.6503 (tptt) cc_final: 0.6191 (tttp) REVERT: A 762 THR cc_start: 0.7978 (m) cc_final: 0.7622 (p) REVERT: A 834 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: A 1154 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6687 (tp30) outliers start: 50 outliers final: 33 residues processed: 234 average time/residue: 0.8893 time to fit residues: 235.2370 Evaluate side-chains 228 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain B residue 1203 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 593 MET Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain A residue 1203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 731 ASN B 799 ASN A 731 ASN ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137810 restraints weight = 15415.872| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.86 r_work: 0.3535 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12954 Z= 0.207 Angle : 0.617 10.423 17664 Z= 0.321 Chirality : 0.044 0.226 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.587 25.690 1880 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.80 % Allowed : 19.59 % Favored : 76.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1730 helix: 1.54 (0.16), residues: 978 sheet: -0.76 (0.48), residues: 122 loop : -2.09 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1028 HIS 0.005 0.001 HIS B1204 PHE 0.016 0.001 PHE B 494 TYR 0.017 0.001 TYR A 746 ARG 0.009 0.001 ARG A1069 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4652.60 seconds wall clock time: 84 minutes 42.13 seconds (5082.13 seconds total)