Starting phenix.real_space_refine on Wed Jul 30 22:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1x_24807/07_2025/7s1x_24807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1x_24807/07_2025/7s1x_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_24807/07_2025/7s1x_24807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2025/7s1x_24807.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2025/7s1x_24807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2025/7s1x_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-5711/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: 15.61, per 1000 atoms: 1.23 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: 3.55 Conformation dependent library (CDL) restraints added in 2.2 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: 1.25 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: 4.19 Time building geometry restraints manager: 3.92 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: 0.07 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: 21.360 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 39.640 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.510 ------------------------------------------------------------------------------- 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 12956 Z= 0.239 Angle : 0.832 10.784 17668 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 Details of bonding type rmsd hydrogen bonds : bond 0.13218 ( 820) hydrogen bonds : angle 5.96336 ( 2382) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.87210 ( 4) covalent geometry : bond 0.00544 (12954) covalent geometry : angle 0.83154 (17664) *********************** 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 : 1.480 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: 0.9186 time to fit residues: 349.6505 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 : 1.457 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137160 restraints weight = 15657.132| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.89 r_work: 0.3538 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 12956 Z= 0.163 Angle : 0.684 10.657 17668 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 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 820) hydrogen bonds : angle 4.92913 ( 2382) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.82305 ( 4) covalent geometry : bond 0.00361 (12954) covalent geometry : angle 0.68436 (17664) *********************** 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 : 1.263 Fit side-chains REVERT: B 218 MET cc_start: 0.4377 (tpt) cc_final: 0.4072 (tpt) REVERT: B 242 SER cc_start: 0.7863 (t) cc_final: 0.7508 (m) REVERT: B 430 TRP cc_start: 0.7333 (m100) cc_final: 0.7132 (t-100) REVERT: B 485 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8382 (mm-30) REVERT: B 492 GLU cc_start: 0.8057 (tm-30) cc_final: 0.6876 (mt-10) REVERT: B 543 CYS cc_start: 0.7692 (t) cc_final: 0.6997 (m) REVERT: B 762 THR cc_start: 0.8718 (m) cc_final: 0.8502 (p) REVERT: B 834 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: B 889 LYS cc_start: 0.8505 (tttp) cc_final: 0.8246 (tttp) REVERT: A 218 MET cc_start: 0.4358 (tpt) cc_final: 0.4057 (tpt) REVERT: A 242 SER cc_start: 0.7873 (t) cc_final: 0.7530 (m) REVERT: A 430 TRP cc_start: 0.7336 (m100) cc_final: 0.7135 (t-100) REVERT: A 468 TYR cc_start: 0.7930 (m-80) cc_final: 0.7718 (m-80) REVERT: A 485 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 492 GLU cc_start: 0.8007 (tm-30) cc_final: 0.6800 (mt-10) REVERT: A 543 CYS cc_start: 0.7678 (t) cc_final: 0.7088 (m) REVERT: A 762 THR cc_start: 0.8734 (m) cc_final: 0.8513 (p) REVERT: A 834 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 889 LYS cc_start: 0.8501 (tttp) cc_final: 0.8245 (tttp) outliers start: 38 outliers final: 23 residues processed: 271 average time/residue: 0.9239 time to fit residues: 279.5527 Evaluate side-chains 245 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136122 restraints weight = 15732.448| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.92 r_work: 0.3520 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12956 Z= 0.155 Angle : 0.646 10.151 17668 Z= 0.340 Chirality : 0.045 0.327 2062 Planarity : 0.005 0.052 2216 Dihedral : 5.046 23.500 1880 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.38 % Allowed : 15.71 % Favored : 80.91 % 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: -0.12 (0.20), residues: 1730 helix: 1.16 (0.16), residues: 1006 sheet: 0.04 (0.57), residues: 92 loop : -2.23 (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 0.013 0.002 TYR A 353 ARG 0.007 0.001 ARG B1069 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 820) hydrogen bonds : angle 4.74459 ( 2382) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.63861 ( 4) covalent geometry : bond 0.00344 (12954) covalent geometry : angle 0.64600 (17664) *********************** 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 279 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 1.352 Fit side-chains REVERT: B 218 MET cc_start: 0.4273 (tpt) cc_final: 0.3999 (tpt) REVERT: B 242 SER cc_start: 0.7753 (t) cc_final: 0.7461 (m) REVERT: B 448 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7324 (t0) REVERT: B 468 TYR cc_start: 0.7968 (m-80) cc_final: 0.7720 (m-80) REVERT: B 485 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8257 (mm-30) REVERT: B 492 GLU cc_start: 0.8074 (tm-30) cc_final: 0.6833 (mt-10) REVERT: B 543 CYS cc_start: 0.7933 (t) cc_final: 0.7236 (m) REVERT: B 752 LYS cc_start: 0.6764 (tptt) cc_final: 0.6449 (tptp) REVERT: B 762 THR cc_start: 0.8736 (m) cc_final: 0.8456 (p) REVERT: B 834 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 218 MET cc_start: 0.4245 (tpt) cc_final: 0.3982 (tpt) REVERT: A 242 SER cc_start: 0.7761 (t) cc_final: 0.7450 (m) REVERT: A 468 TYR cc_start: 0.7950 (m-80) cc_final: 0.7670 (m-80) REVERT: A 485 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8268 (mm-30) REVERT: A 492 GLU cc_start: 0.8067 (tm-30) cc_final: 0.6839 (mt-10) REVERT: A 543 CYS cc_start: 0.7723 (t) cc_final: 0.7090 (m) REVERT: A 752 LYS cc_start: 0.6893 (tptt) cc_final: 0.6575 (tptp) REVERT: A 762 THR cc_start: 0.8739 (m) cc_final: 0.8459 (p) REVERT: A 834 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 1147 TYR cc_start: 0.6134 (m-10) cc_final: 0.5880 (m-10) outliers start: 40 outliers final: 23 residues processed: 262 average time/residue: 0.8901 time to fit residues: 261.7646 Evaluate side-chains 240 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 450 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 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 115 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 116 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 118 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- 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 B1203 ASN A 731 ASN A 799 ASN A1203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136360 restraints weight = 15705.652| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.91 r_work: 0.3519 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12956 Z= 0.144 Angle : 0.625 9.940 17668 Z= 0.326 Chirality : 0.044 0.145 2062 Planarity : 0.004 0.049 2216 Dihedral : 4.829 23.327 1880 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.22 % Allowed : 15.96 % Favored : 79.81 % 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: 0.03 (0.20), residues: 1730 helix: 1.39 (0.16), residues: 988 sheet: -0.07 (0.57), residues: 94 loop : -2.22 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B1028 HIS 0.007 0.001 HIS A 773 PHE 0.023 0.001 PHE B 608 TYR 0.013 0.001 TYR A 353 ARG 0.007 0.001 ARG A1069 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 820) hydrogen bonds : angle 4.60896 ( 2382) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.51255 ( 4) covalent geometry : bond 0.00320 (12954) covalent geometry : angle 0.62519 (17664) *********************** 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 287 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 237 time to evaluate : 1.435 Fit side-chains REVERT: B 218 MET cc_start: 0.4270 (tpt) cc_final: 0.4014 (tpt) REVERT: B 242 SER cc_start: 0.7850 (t) cc_final: 0.7532 (m) REVERT: B 469 LYS cc_start: 0.7508 (mmpt) cc_final: 0.7285 (mmmt) REVERT: B 492 GLU cc_start: 0.8102 (tm-30) cc_final: 0.6879 (mt-10) REVERT: B 543 CYS cc_start: 0.7961 (t) cc_final: 0.7220 (m) REVERT: B 752 LYS cc_start: 0.6976 (tptt) cc_final: 0.6688 (tptp) REVERT: B 762 THR cc_start: 0.8759 (m) cc_final: 0.8404 (p) REVERT: B 784 VAL cc_start: 0.8626 (t) cc_final: 0.8402 (t) REVERT: B 834 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 218 MET cc_start: 0.4268 (tpt) cc_final: 0.4014 (tpt) REVERT: A 242 SER cc_start: 0.7847 (t) cc_final: 0.7532 (m) REVERT: A 468 TYR cc_start: 0.7784 (m-80) cc_final: 0.7550 (m-80) REVERT: A 469 LYS cc_start: 0.7530 (mmpt) cc_final: 0.7259 (mmmt) REVERT: A 485 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 492 GLU cc_start: 0.8141 (tm-30) cc_final: 0.6990 (mt-10) REVERT: A 543 CYS cc_start: 0.7797 (t) cc_final: 0.7091 (m) REVERT: A 752 LYS cc_start: 0.6964 (tptt) cc_final: 0.6672 (tptp) REVERT: A 762 THR cc_start: 0.8763 (m) cc_final: 0.8412 (p) REVERT: A 784 VAL cc_start: 0.8666 (t) cc_final: 0.8454 (t) REVERT: A 834 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7604 (mp0) outliers start: 50 outliers final: 32 residues processed: 271 average time/residue: 0.8632 time to fit residues: 263.1666 Evaluate side-chains 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 359 SER 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 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 1029 LEU Chi-restraints excluded: chain B residue 1076 LEU 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 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 448 ASP 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 1029 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 93 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.166124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132311 restraints weight = 15748.895| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.90 r_work: 0.3467 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12956 Z= 0.189 Angle : 0.660 10.184 17668 Z= 0.344 Chirality : 0.046 0.173 2062 Planarity : 0.005 0.049 2216 Dihedral : 4.876 23.953 1880 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.81 % Allowed : 17.23 % Favored : 77.96 % 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: -0.06 (0.20), residues: 1730 helix: 1.31 (0.16), residues: 990 sheet: -0.09 (0.56), residues: 94 loop : -2.27 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B1028 HIS 0.006 0.001 HIS B 822 PHE 0.020 0.002 PHE B 608 TYR 0.016 0.002 TYR B 746 ARG 0.008 0.001 ARG A1069 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 820) hydrogen bonds : angle 4.63691 ( 2382) SS BOND : bond 0.00144 ( 2) SS BOND : angle 0.58697 ( 4) covalent geometry : bond 0.00444 (12954) covalent geometry : angle 0.66042 (17664) *********************** 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 269 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 1.592 Fit side-chains REVERT: B 242 SER cc_start: 0.7721 (t) cc_final: 0.7362 (m) REVERT: B 440 VAL cc_start: 0.8271 (t) cc_final: 0.7993 (t) REVERT: B 492 GLU cc_start: 0.8153 (tm-30) cc_final: 0.6870 (mt-10) REVERT: B 543 CYS cc_start: 0.8064 (t) cc_final: 0.7181 (m) REVERT: B 595 MET cc_start: 0.8297 (tmm) cc_final: 0.8049 (tmm) REVERT: B 752 LYS cc_start: 0.6974 (tptt) cc_final: 0.6647 (tptp) REVERT: B 762 THR cc_start: 0.8814 (m) cc_final: 0.8387 (p) REVERT: B 799 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 834 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 242 SER cc_start: 0.7701 (t) cc_final: 0.7345 (m) REVERT: A 468 TYR cc_start: 0.7879 (m-80) cc_final: 0.7617 (m-80) REVERT: A 485 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8210 (mm-30) REVERT: A 492 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7027 (mt-10) REVERT: A 543 CYS cc_start: 0.7897 (t) cc_final: 0.7055 (m) REVERT: A 752 LYS cc_start: 0.6949 (tptt) cc_final: 0.6614 (tptp) REVERT: A 762 THR cc_start: 0.8820 (m) cc_final: 0.8390 (p) REVERT: A 799 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7911 (p0) REVERT: A 834 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7710 (mp0) outliers start: 57 outliers final: 37 residues processed: 252 average time/residue: 0.8754 time to fit residues: 249.9325 Evaluate side-chains 239 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 359 SER 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 448 ASP Chi-restraints excluded: chain B residue 450 VAL 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 613 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 359 SER 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 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 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 160 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 79 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.0000 chunk 87 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.171521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138572 restraints weight = 15726.907| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.90 r_work: 0.3547 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12956 Z= 0.127 Angle : 0.595 9.392 17668 Z= 0.310 Chirality : 0.042 0.169 2062 Planarity : 0.004 0.046 2216 Dihedral : 4.614 22.445 1880 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.97 % Allowed : 19.00 % Favored : 77.03 % 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: 1.51 (0.16), residues: 988 sheet: -0.71 (0.49), residues: 118 loop : -2.22 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1028 HIS 0.005 0.001 HIS B 773 PHE 0.020 0.001 PHE B 449 TYR 0.014 0.001 TYR A 353 ARG 0.007 0.001 ARG B1069 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 820) hydrogen bonds : angle 4.44077 ( 2382) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.45802 ( 4) covalent geometry : bond 0.00270 (12954) covalent geometry : angle 0.59506 (17664) *********************** 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 265 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.420 Fit side-chains REVERT: B 360 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8584 (pt) REVERT: B 440 VAL cc_start: 0.8231 (t) cc_final: 0.7928 (t) REVERT: B 492 GLU cc_start: 0.8138 (tm-30) cc_final: 0.6857 (mt-10) REVERT: B 543 CYS cc_start: 0.8155 (t) cc_final: 0.7198 (m) REVERT: B 752 LYS cc_start: 0.7016 (tptt) cc_final: 0.6698 (tptp) REVERT: B 834 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: A 360 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8578 (pt) REVERT: A 440 VAL cc_start: 0.8233 (t) cc_final: 0.7960 (t) REVERT: A 468 TYR cc_start: 0.7783 (m-80) cc_final: 0.7510 (m-80) REVERT: A 485 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 492 GLU cc_start: 0.8102 (tm-30) cc_final: 0.6767 (mt-10) REVERT: A 543 CYS cc_start: 0.7883 (t) cc_final: 0.7049 (m) REVERT: A 752 LYS cc_start: 0.7004 (tptt) cc_final: 0.6683 (tptp) REVERT: A 834 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7791 (mm-30) outliers start: 47 outliers final: 27 residues processed: 247 average time/residue: 0.7921 time to fit residues: 222.9897 Evaluate side-chains 225 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1076 LEU 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 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 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1101 ILE 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 11 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.169684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136600 restraints weight = 15562.951| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.89 r_work: 0.3521 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12956 Z= 0.146 Angle : 0.616 9.688 17668 Z= 0.319 Chirality : 0.043 0.148 2062 Planarity : 0.004 0.045 2216 Dihedral : 4.600 22.294 1880 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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: 0.18 (0.20), residues: 1730 helix: 1.57 (0.16), residues: 978 sheet: -0.79 (0.48), residues: 118 loop : -2.12 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1028 HIS 0.005 0.001 HIS B 822 PHE 0.016 0.001 PHE B 608 TYR 0.016 0.001 TYR A 746 ARG 0.009 0.001 ARG A1069 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 820) hydrogen bonds : angle 4.42399 ( 2382) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.49071 ( 4) covalent geometry : bond 0.00331 (12954) covalent geometry : angle 0.61577 (17664) *********************** 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 251 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 1.730 Fit side-chains REVERT: B 360 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8644 (pt) REVERT: B 440 VAL cc_start: 0.8145 (t) cc_final: 0.7760 (t) REVERT: B 444 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (mt) REVERT: B 492 GLU cc_start: 0.8199 (tm-30) cc_final: 0.6913 (mt-10) REVERT: B 752 LYS cc_start: 0.6993 (tptt) cc_final: 0.6679 (tptp) REVERT: B 762 THR cc_start: 0.8790 (m) cc_final: 0.8398 (p) REVERT: B 834 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: A 360 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8632 (pt) REVERT: A 468 TYR cc_start: 0.7818 (m-80) cc_final: 0.7564 (m-80) REVERT: A 485 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8217 (mm-30) REVERT: A 492 GLU cc_start: 0.8148 (tm-30) cc_final: 0.6840 (mt-10) REVERT: A 493 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 543 CYS cc_start: 0.7971 (t) cc_final: 0.7080 (m) REVERT: A 752 LYS cc_start: 0.6977 (tptt) cc_final: 0.6660 (tptp) REVERT: A 762 THR cc_start: 0.8775 (m) cc_final: 0.8387 (p) REVERT: A 834 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7508 (mp0) outliers start: 51 outliers final: 32 residues processed: 235 average time/residue: 0.8132 time to fit residues: 217.4468 Evaluate side-chains 230 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain B residue 360 LEU 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 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 1076 LEU 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 359 SER 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 425 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 493 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 609 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 14 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 799 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137087 restraints weight = 15691.958| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.86 r_work: 0.3526 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12956 Z= 0.143 Angle : 0.614 9.749 17668 Z= 0.318 Chirality : 0.043 0.145 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.577 23.041 1880 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.48 % Allowed : 19.43 % Favored : 76.10 % 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: 0.20 (0.20), residues: 1730 helix: 1.60 (0.16), residues: 978 sheet: -0.82 (0.48), residues: 118 loop : -2.11 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1028 HIS 0.005 0.001 HIS B 822 PHE 0.016 0.001 PHE B 608 TYR 0.017 0.001 TYR B 746 ARG 0.008 0.000 ARG A1069 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 820) hydrogen bonds : angle 4.40868 ( 2382) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.50318 ( 4) covalent geometry : bond 0.00323 (12954) covalent geometry : angle 0.61389 (17664) *********************** 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 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 189 time to evaluate : 1.255 Fit side-chains REVERT: B 360 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8666 (pt) REVERT: B 440 VAL cc_start: 0.8190 (t) cc_final: 0.7892 (t) REVERT: B 492 GLU cc_start: 0.8100 (tm-30) cc_final: 0.6723 (mt-10) REVERT: B 752 LYS cc_start: 0.6991 (tptt) cc_final: 0.6681 (tptp) REVERT: B 762 THR cc_start: 0.8783 (m) cc_final: 0.8424 (p) REVERT: B 834 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: A 360 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8663 (pt) REVERT: A 468 TYR cc_start: 0.7817 (m-80) cc_final: 0.7561 (m-80) REVERT: A 485 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 492 GLU cc_start: 0.8136 (tm-30) cc_final: 0.6871 (mt-10) REVERT: A 543 CYS cc_start: 0.8005 (t) cc_final: 0.7102 (m) REVERT: A 752 LYS cc_start: 0.6991 (tptt) cc_final: 0.6681 (tptp) REVERT: A 762 THR cc_start: 0.8772 (m) cc_final: 0.8416 (p) REVERT: A 834 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7842 (mm-30) outliers start: 53 outliers final: 33 residues processed: 225 average time/residue: 0.8272 time to fit residues: 211.1885 Evaluate side-chains 224 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain B residue 360 LEU 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 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 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 359 SER 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 425 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 609 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 114 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 B1203 ASN A 731 ASN A 799 ASN A1203 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.135932 restraints weight = 15634.305| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.88 r_work: 0.3513 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12956 Z= 0.153 Angle : 0.631 9.956 17668 Z= 0.326 Chirality : 0.044 0.168 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.594 23.351 1880 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.14 % Allowed : 19.85 % Favored : 76.01 % 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: 0.22 (0.20), residues: 1730 helix: 1.60 (0.16), residues: 976 sheet: -0.19 (0.53), residues: 94 loop : -2.15 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1028 HIS 0.005 0.001 HIS B 822 PHE 0.015 0.001 PHE A 608 TYR 0.018 0.001 TYR A 746 ARG 0.008 0.000 ARG B1069 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 820) hydrogen bonds : angle 4.42236 ( 2382) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.53222 ( 4) covalent geometry : bond 0.00353 (12954) covalent geometry : angle 0.63095 (17664) *********************** 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 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 1.361 Fit side-chains REVERT: B 242 SER cc_start: 0.7778 (t) cc_final: 0.7398 (m) REVERT: B 360 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8691 (pt) REVERT: B 440 VAL cc_start: 0.8172 (t) cc_final: 0.7907 (t) REVERT: B 492 GLU cc_start: 0.8104 (tm-30) cc_final: 0.6717 (mt-10) REVERT: B 752 LYS cc_start: 0.6988 (tptt) cc_final: 0.6678 (tptp) REVERT: B 762 THR cc_start: 0.8803 (m) cc_final: 0.8426 (p) REVERT: B 834 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: A 242 SER cc_start: 0.7769 (t) cc_final: 0.7393 (m) REVERT: A 360 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8686 (pt) REVERT: A 444 LEU cc_start: 0.8163 (mp) cc_final: 0.7910 (mt) REVERT: A 468 TYR cc_start: 0.7836 (m-80) cc_final: 0.7577 (m-80) REVERT: A 485 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 492 GLU cc_start: 0.8171 (tm-30) cc_final: 0.6857 (mt-10) REVERT: A 543 CYS cc_start: 0.8059 (t) cc_final: 0.7140 (m) REVERT: A 752 LYS cc_start: 0.6974 (tptt) cc_final: 0.6662 (tttp) REVERT: A 762 THR cc_start: 0.8780 (m) cc_final: 0.8410 (p) REVERT: A 834 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7812 (mm-30) outliers start: 49 outliers final: 35 residues processed: 225 average time/residue: 0.8418 time to fit residues: 215.4849 Evaluate side-chains 224 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain B residue 360 LEU 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 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 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 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 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 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 728 PHE 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 15 optimal weight: 40.0000 chunk 64 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 B1203 ASN A 731 ASN A 799 ASN A 868 GLN A1203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.167783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.134613 restraints weight = 15597.066| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.88 r_work: 0.3496 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12956 Z= 0.168 Angle : 0.643 10.534 17668 Z= 0.332 Chirality : 0.045 0.168 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.651 24.904 1880 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.97 % Allowed : 20.27 % Favored : 75.76 % 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: 1.53 (0.16), residues: 980 sheet: -0.31 (0.51), residues: 98 loop : -2.16 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1028 HIS 0.006 0.001 HIS B 822 PHE 0.016 0.001 PHE A 907 TYR 0.019 0.001 TYR B 746 ARG 0.008 0.000 ARG B1069 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 820) hydrogen bonds : angle 4.45223 ( 2382) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.56102 ( 4) covalent geometry : bond 0.00390 (12954) covalent geometry : angle 0.64291 (17664) ********************** 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 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 1.398 Fit side-chains REVERT: B 242 SER cc_start: 0.7688 (t) cc_final: 0.7284 (m) REVERT: B 360 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8711 (pt) REVERT: B 440 VAL cc_start: 0.8185 (t) cc_final: 0.7915 (t) REVERT: B 492 GLU cc_start: 0.8120 (tm-30) cc_final: 0.6729 (mt-10) REVERT: B 607 ILE cc_start: 0.7430 (mt) cc_final: 0.7220 (mp) REVERT: B 752 LYS cc_start: 0.6993 (tptt) cc_final: 0.6680 (tttp) REVERT: B 762 THR cc_start: 0.8816 (m) cc_final: 0.8424 (p) REVERT: B 834 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: A 242 SER cc_start: 0.7677 (t) cc_final: 0.7277 (m) REVERT: A 360 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8703 (pt) REVERT: A 444 LEU cc_start: 0.8215 (mp) cc_final: 0.7963 (mt) REVERT: A 468 TYR cc_start: 0.7835 (m-80) cc_final: 0.7580 (m-80) REVERT: A 485 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 492 GLU cc_start: 0.8168 (tm-30) cc_final: 0.6855 (mt-10) REVERT: A 543 CYS cc_start: 0.8074 (t) cc_final: 0.7145 (m) REVERT: A 752 LYS cc_start: 0.6984 (tptt) cc_final: 0.6676 (tttp) REVERT: A 762 THR cc_start: 0.8805 (m) cc_final: 0.8418 (p) REVERT: A 834 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7819 (mm-30) outliers start: 47 outliers final: 35 residues processed: 223 average time/residue: 0.8573 time to fit residues: 216.1771 Evaluate side-chains 226 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain B residue 360 LEU 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 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 360 LEU 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 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 609 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 46 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 B1203 ASN A 731 ASN A 799 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136934 restraints weight = 15542.905| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.88 r_work: 0.3525 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12956 Z= 0.138 Angle : 0.622 10.198 17668 Z= 0.322 Chirality : 0.043 0.158 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.574 24.361 1880 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.46 % Allowed : 20.61 % Favored : 75.93 % 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: 0.21 (0.20), residues: 1730 helix: 1.59 (0.16), residues: 978 sheet: -0.60 (0.48), residues: 114 loop : -2.13 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B1028 HIS 0.006 0.001 HIS B1204 PHE 0.014 0.001 PHE A 608 TYR 0.017 0.001 TYR B 746 ARG 0.009 0.000 ARG A1069 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 820) hydrogen bonds : angle 4.39473 ( 2382) SS BOND : bond 0.00180 ( 2) SS BOND : angle 0.50573 ( 4) covalent geometry : bond 0.00307 (12954) covalent geometry : angle 0.62157 (17664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10221.56 seconds wall clock time: 175 minutes 54.65 seconds (10554.65 seconds total)