Starting phenix.real_space_refine on Fri Jul 3 07:14:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_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 { model { file = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1x_24807/07_2026/7s1x_24807.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12658 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" 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: {'ASN:plan1': 14, 'HIS:plan': 1, 'GLN:plan1': 5, 'GLU:plan': 26, 'ASP:plan': 19, 'ARG:plan': 6, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 283 Chain: "B" 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: A Time building chain proxies: 5.31, per 1000 atoms: 0.42 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=4, 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 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 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: 1.05 Conformation dependent library (CDL) restraints added in 513.4 milliseconds 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: 0.33 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: 2.23 Time building geometry restraints manager: 1.36 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: 496 30.50 - 45.75: 109 45.75 - 61.00: 18 61.00 - 76.25: 16 Dihedral angle restraints: 7436 sinusoidal: 2520 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=" CB CYS A 577 " pdb=" SG CYS A 577 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 21.75 71.25 1 1.00e+01 1.00e-02 6.51e+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 ... (remaining 7433 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: 2.05 - 2.67: 216 2.67 - 3.29: 15469 3.29 - 3.90: 25452 3.90 - 4.52: 34532 4.52 - 5.14: 52453 Nonbonded interactions: 128122 Sorted by model distance: 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 nonbonded pdb=" OH TYR A 686 " pdb="CL CL A1303 " model vdw 2.061 3.190 nonbonded pdb=" OD2 ASP B1032 " pdb=" OG1 THR B1036 " model vdw 2.138 3.040 ... (remaining 128117 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 12958 Z= 0.239 Angle : 0.832 10.784 17672 Z= 0.442 Chirality : 0.051 0.262 2062 Planarity : 0.005 0.063 2216 Dihedral : 12.055 76.247 4300 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.009 0.001 ARG A 546 TYR 0.018 0.002 TYR A 353 PHE 0.055 0.003 PHE A 608 TRP 0.109 0.007 TRP A1027 HIS 0.010 0.003 HIS B1067 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 (12954) covalent geometry : angle 0.83154 / 0.44 (17664) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.87788 / 0.50 ( 8) hydrogen bonds : bond 0.13218 / 8.92 ( 820) hydrogen bonds : angle 5.96336 / 4.33 ( 2382) *********************** 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 : 0.452 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: 0.8077 (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: 0.7433 (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: 0.7690 (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: 0.3810 time to fit residues: 145.1446 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 GLN B 589 ASN B 731 ASN B 799 ASN B 806 HIS B 849 ASN B1149 GLN B1159 HIS B1203 ASN A 435 GLN A 589 ASN A 731 ASN A 799 ASN A 806 HIS A 849 ASN A1149 GLN A1159 HIS A1203 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136433 restraints weight = 15722.531| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.87 r_work: 0.3525 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12958 Z= 0.167 Angle : 0.685 10.779 17672 Z= 0.358 Chirality : 0.046 0.172 2062 Planarity : 0.005 0.052 2216 Dihedral : 5.311 24.179 1880 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.38 % Allowed : 12.67 % Favored : 83.95 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1730 helix: 1.02 (0.16), residues: 1000 sheet: -0.07 (0.56), residues: 92 loop : -2.29 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1069 TYR 0.014 0.002 TYR B 353 PHE 0.037 0.002 PHE A 608 TRP 0.036 0.003 TRP A1027 HIS 0.006 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (12954) covalent geometry : angle 0.68516 / 0.36 (17664) SS BOND : bond 0.00219 / 0.11 ( 4) SS BOND : angle 0.88914 / 0.51 ( 8) hydrogen bonds : bond 0.04808 / 3.31 ( 820) hydrogen bonds : angle 4.90302 / 3.59 ( 2382) *********************** 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: 40 poor density : 253 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: B 218 MET cc_start: 0.4340 (tpt) cc_final: 0.4040 (tpt) REVERT: B 242 SER cc_start: 0.7786 (t) cc_final: 0.7469 (m) REVERT: B 430 TRP cc_start: 0.7406 (m100) cc_final: 0.7200 (t-100) REVERT: B 485 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8379 (mm-30) REVERT: B 492 GLU cc_start: 0.8081 (tm-30) cc_final: 0.6852 (mt-10) REVERT: B 543 CYS cc_start: 0.7729 (t) cc_final: 0.6984 (m) REVERT: B 762 THR cc_start: 0.8711 (m) cc_final: 0.8487 (p) REVERT: B 834 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: B 889 LYS cc_start: 0.8494 (tttp) cc_final: 0.8243 (tttp) REVERT: B 1205 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8295 (mm110) REVERT: A 218 MET cc_start: 0.4330 (tpt) cc_final: 0.4036 (tpt) REVERT: A 242 SER cc_start: 0.7798 (t) cc_final: 0.7476 (m) REVERT: A 430 TRP cc_start: 0.7322 (m100) cc_final: 0.7119 (t-100) REVERT: A 485 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8383 (mm-30) REVERT: A 492 GLU cc_start: 0.8029 (tm-30) cc_final: 0.6763 (mt-10) REVERT: A 543 CYS cc_start: 0.7662 (t) cc_final: 0.7056 (m) REVERT: A 762 THR cc_start: 0.8730 (m) cc_final: 0.8504 (p) REVERT: A 834 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 889 LYS cc_start: 0.8488 (tttp) cc_final: 0.8241 (tttp) outliers start: 40 outliers final: 25 residues processed: 271 average time/residue: 0.3813 time to fit residues: 115.7736 Evaluate side-chains 243 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 419 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain 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 419 ILE 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 609 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 21 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 119 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 76 optimal weight: 0.0070 chunk 170 optimal weight: 0.9980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 515 GLN B 731 ASN B 799 ASN A 515 GLN A 731 ASN A 799 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.168638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134978 restraints weight = 15853.089| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.94 r_work: 0.3502 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12958 Z= 0.161 Angle : 0.649 10.188 17672 Z= 0.342 Chirality : 0.046 0.340 2062 Planarity : 0.005 0.051 2216 Dihedral : 5.054 23.689 1880 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.63 % Allowed : 15.71 % Favored : 80.66 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1730 helix: 1.21 (0.16), residues: 992 sheet: 0.01 (0.57), residues: 92 loop : -2.24 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1069 TYR 0.013 0.002 TYR A 353 PHE 0.028 0.002 PHE B 608 TRP 0.028 0.002 TRP B1028 HIS 0.006 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (12954) covalent geometry : angle 0.64917 / 0.34 (17664) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.64006 / 0.36 ( 8) hydrogen bonds : bond 0.04580 / 3.14 ( 820) hydrogen bonds : angle 4.73317 / 3.46 ( 2382) *********************** 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 272 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 0.293 Fit side-chains REVERT: B 218 MET cc_start: 0.4260 (tpt) cc_final: 0.3993 (tpt) REVERT: B 242 SER cc_start: 0.7747 (t) cc_final: 0.7434 (m) REVERT: B 448 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 468 TYR cc_start: 0.7973 (m-80) cc_final: 0.7717 (m-80) REVERT: B 492 GLU cc_start: 0.8084 (tm-30) cc_final: 0.6814 (mt-10) REVERT: B 543 CYS cc_start: 0.7898 (t) cc_final: 0.7196 (m) REVERT: B 752 LYS cc_start: 0.6831 (tptt) cc_final: 0.6519 (tptp) REVERT: B 762 THR cc_start: 0.8752 (m) cc_final: 0.8449 (p) REVERT: B 834 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 218 MET cc_start: 0.4235 (tpt) cc_final: 0.3971 (tpt) REVERT: A 242 SER cc_start: 0.7739 (t) cc_final: 0.7431 (m) REVERT: A 485 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 492 GLU cc_start: 0.8070 (tm-30) cc_final: 0.6852 (mt-10) REVERT: A 543 CYS cc_start: 0.7872 (t) cc_final: 0.7214 (m) REVERT: A 752 LYS cc_start: 0.6891 (tptt) cc_final: 0.6574 (tptp) REVERT: A 762 THR cc_start: 0.8748 (m) cc_final: 0.8447 (p) REVERT: A 834 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7690 (mp0) outliers start: 43 outliers final: 26 residues processed: 253 average time/residue: 0.3631 time to fit residues: 103.3920 Evaluate side-chains 248 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 419 ILE 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 419 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 VAL 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 Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1101 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A1203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132618 restraints weight = 15730.773| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.91 r_work: 0.3479 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12958 Z= 0.176 Angle : 0.653 10.238 17672 Z= 0.340 Chirality : 0.045 0.157 2062 Planarity : 0.005 0.051 2216 Dihedral : 4.956 24.609 1880 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.81 % Allowed : 15.20 % Favored : 79.98 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1730 helix: 1.32 (0.16), residues: 988 sheet: -0.23 (0.56), residues: 94 loop : -2.27 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1069 TYR 0.012 0.001 TYR B 353 PHE 0.023 0.002 PHE B 608 TRP 0.031 0.002 TRP B1028 HIS 0.007 0.001 HIS B 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (12954) covalent geometry : angle 0.65348 / 0.34 (17664) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.61657 / 0.35 ( 8) hydrogen bonds : bond 0.04591 / 3.15 ( 820) hydrogen bonds : angle 4.66306 / 3.40 ( 2382) *********************** 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 282 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.449 Fit side-chains REVERT: B 242 SER cc_start: 0.7759 (t) cc_final: 0.7412 (m) REVERT: B 469 LYS cc_start: 0.7538 (mmpt) cc_final: 0.7312 (mmmt) REVERT: B 492 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7024 (mt-10) REVERT: B 543 CYS cc_start: 0.7975 (t) cc_final: 0.7153 (m) REVERT: B 752 LYS cc_start: 0.6974 (tptt) cc_final: 0.6685 (tptp) REVERT: B 762 THR cc_start: 0.8817 (m) cc_final: 0.8400 (p) REVERT: B 790 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: B 834 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: A 218 MET cc_start: 0.4216 (tpt) cc_final: 0.4004 (tpt) REVERT: A 242 SER cc_start: 0.7772 (t) cc_final: 0.7426 (m) REVERT: A 469 LYS cc_start: 0.7557 (mmpt) cc_final: 0.7271 (mmmt) REVERT: A 485 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 492 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7013 (mt-10) REVERT: A 543 CYS cc_start: 0.8013 (t) cc_final: 0.7238 (m) REVERT: A 752 LYS cc_start: 0.6958 (tptt) cc_final: 0.6667 (tptp) REVERT: A 762 THR cc_start: 0.8823 (m) cc_final: 0.8404 (p) REVERT: A 784 VAL cc_start: 0.8686 (t) cc_final: 0.8475 (t) REVERT: A 790 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: A 834 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7569 (mp0) outliers start: 57 outliers final: 36 residues processed: 263 average time/residue: 0.3250 time to fit residues: 97.4746 Evaluate side-chains 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 ILE 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 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 790 GLN 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 312 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 450 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 712 ASN Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 105 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 680 ASN B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 799 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 = 0.4011 r_free = 0.4011 target = 0.168731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.135439 restraints weight = 15763.176| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.90 r_work: 0.3511 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12958 Z= 0.143 Angle : 0.616 9.632 17672 Z= 0.322 Chirality : 0.043 0.166 2062 Planarity : 0.004 0.047 2216 Dihedral : 4.768 23.368 1880 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.65 % Allowed : 17.23 % Favored : 78.12 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.20), residues: 1730 helix: 1.40 (0.16), residues: 988 sheet: -0.17 (0.56), residues: 94 loop : -2.27 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1069 TYR 0.016 0.001 TYR B 746 PHE 0.019 0.001 PHE A 608 TRP 0.027 0.002 TRP B1028 HIS 0.005 0.001 HIS B 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12954) covalent geometry : angle 0.61590 / 0.32 (17664) SS BOND : bond 0.00191 / 0.09 ( 4) SS BOND : angle 0.51593 / 0.29 ( 8) hydrogen bonds : bond 0.04266 / 2.93 ( 820) hydrogen bonds : angle 4.55633 / 3.34 ( 2382) *********************** 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 280 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.461 Fit side-chains REVERT: B 242 SER cc_start: 0.7794 (t) cc_final: 0.7453 (m) REVERT: B 360 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8542 (pt) REVERT: B 468 TYR cc_start: 0.7960 (m-80) cc_final: 0.7646 (m-80) REVERT: B 492 GLU cc_start: 0.8226 (tm-30) cc_final: 0.6994 (mt-10) REVERT: B 543 CYS cc_start: 0.8081 (t) cc_final: 0.7167 (m) REVERT: B 752 LYS cc_start: 0.6965 (tptt) cc_final: 0.6641 (tptp) REVERT: B 762 THR cc_start: 0.8756 (m) cc_final: 0.8366 (p) REVERT: B 784 VAL cc_start: 0.8686 (t) cc_final: 0.8479 (t) REVERT: B 834 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 242 SER cc_start: 0.7809 (t) cc_final: 0.7480 (m) REVERT: A 360 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (pt) REVERT: A 440 VAL cc_start: 0.8226 (t) cc_final: 0.7891 (t) REVERT: A 485 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 492 GLU cc_start: 0.8216 (tm-30) cc_final: 0.6985 (mt-10) REVERT: A 543 CYS cc_start: 0.8022 (t) cc_final: 0.7201 (m) REVERT: A 752 LYS cc_start: 0.6948 (tptt) cc_final: 0.6618 (tptp) REVERT: A 762 THR cc_start: 0.8785 (m) cc_final: 0.8412 (p) REVERT: A 784 VAL cc_start: 0.8654 (t) cc_final: 0.8442 (t) REVERT: A 790 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: A 834 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7695 (mp0) outliers start: 55 outliers final: 33 residues processed: 260 average time/residue: 0.4141 time to fit residues: 121.0337 Evaluate side-chains 236 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 419 ILE 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 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 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 419 ILE 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 712 ASN Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 156 optimal weight: 0.0020 chunk 45 optimal weight: 0.2980 chunk 157 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4020 r_free = 0.4020 target = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136483 restraints weight = 15581.924| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.89 r_work: 0.3520 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12958 Z= 0.134 Angle : 0.605 9.521 17672 Z= 0.315 Chirality : 0.043 0.163 2062 Planarity : 0.004 0.045 2216 Dihedral : 4.649 22.799 1880 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.48 % Allowed : 18.41 % Favored : 77.11 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.20), residues: 1730 helix: 1.46 (0.16), residues: 988 sheet: -0.12 (0.55), residues: 94 loop : -2.24 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1069 TYR 0.013 0.001 TYR B 353 PHE 0.017 0.001 PHE A 608 TRP 0.024 0.001 TRP B1028 HIS 0.005 0.001 HIS B 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12954) covalent geometry : angle 0.60478 / 0.32 (17664) SS BOND : bond 0.00196 / 0.10 ( 4) SS BOND : angle 0.46365 / 0.26 ( 8) hydrogen bonds : bond 0.04124 / 2.83 ( 820) hydrogen bonds : angle 4.45967 / 3.26 ( 2382) *********************** 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 262 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.552 Fit side-chains REVERT: B 360 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8551 (pt) REVERT: B 492 GLU cc_start: 0.8223 (tm-30) cc_final: 0.6921 (mt-10) REVERT: B 543 CYS cc_start: 0.8127 (t) cc_final: 0.7180 (m) REVERT: B 752 LYS cc_start: 0.7003 (tptt) cc_final: 0.6680 (tptp) REVERT: B 762 THR cc_start: 0.8740 (m) cc_final: 0.8353 (p) REVERT: B 784 VAL cc_start: 0.8618 (t) cc_final: 0.8390 (t) REVERT: B 799 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7771 (p0) REVERT: B 834 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: A 242 SER cc_start: 0.7770 (t) cc_final: 0.7440 (m) REVERT: A 360 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8553 (pt) REVERT: A 469 LYS cc_start: 0.7393 (mmpt) cc_final: 0.7175 (mmmt) REVERT: A 485 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8224 (mm-30) REVERT: A 492 GLU cc_start: 0.8165 (tm-30) cc_final: 0.6851 (mt-10) REVERT: A 543 CYS cc_start: 0.8151 (t) cc_final: 0.7262 (m) REVERT: A 752 LYS cc_start: 0.6989 (tptt) cc_final: 0.6661 (tptp) REVERT: A 762 THR cc_start: 0.8773 (m) cc_final: 0.8405 (p) REVERT: A 784 VAL cc_start: 0.8600 (t) cc_final: 0.8388 (t) REVERT: A 799 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7738 (p0) REVERT: A 834 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7492 (mp0) outliers start: 53 outliers final: 30 residues processed: 245 average time/residue: 0.3688 time to fit residues: 103.0057 Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 419 ILE 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 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE 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 609 SER Chi-restraints excluded: chain A residue 710 TYR 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 1028 TRP Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 7 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 20 optimal weight: 9.9990 chunk 74 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 680 ASN B 731 ASN B 799 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 = 0.4037 r_free = 0.4037 target = 0.171427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138466 restraints weight = 15647.883| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.89 r_work: 0.3545 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12958 Z= 0.126 Angle : 0.591 9.554 17672 Z= 0.307 Chirality : 0.042 0.151 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.505 21.785 1880 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.48 % Allowed : 18.67 % Favored : 76.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1730 helix: 1.62 (0.17), residues: 978 sheet: -0.74 (0.49), residues: 118 loop : -2.10 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1069 TYR 0.018 0.001 TYR B 746 PHE 0.016 0.001 PHE A 608 TRP 0.022 0.001 TRP B1028 HIS 0.004 0.001 HIS B 859 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12954) covalent geometry : angle 0.59115 / 0.31 (17664) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 0.45640 / 0.26 ( 8) hydrogen bonds : bond 0.04004 / 2.75 ( 820) hydrogen bonds : angle 4.38082 / 3.20 ( 2382) *********************** 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 256 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.299 Fit side-chains REVERT: B 492 GLU cc_start: 0.8199 (tm-30) cc_final: 0.6941 (mt-10) REVERT: B 752 LYS cc_start: 0.7000 (tptt) cc_final: 0.6699 (tptp) REVERT: B 784 VAL cc_start: 0.8592 (t) cc_final: 0.8364 (t) REVERT: B 834 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: A 242 SER cc_start: 0.7830 (t) cc_final: 0.7417 (m) REVERT: A 485 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 492 GLU cc_start: 0.8218 (tm-30) cc_final: 0.6935 (mt-10) REVERT: A 543 CYS cc_start: 0.8187 (t) cc_final: 0.7272 (m) REVERT: A 752 LYS cc_start: 0.6989 (tptt) cc_final: 0.6684 (tptp) REVERT: A 784 VAL cc_start: 0.8530 (t) cc_final: 0.8325 (t) REVERT: A 834 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (mm-30) outliers start: 53 outliers final: 39 residues processed: 237 average time/residue: 0.3112 time to fit residues: 83.9102 Evaluate side-chains 225 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 ILE 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 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 710 TYR Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 799 ASN Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE 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 593 MET 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 799 ASN Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1028 TRP 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 10 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 62 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 108 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 731 ASN B 799 ASN A 680 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 = 0.4016 r_free = 0.4016 target = 0.169390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.136145 restraints weight = 15459.542| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.88 r_work: 0.3516 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.003 0.037 12958 Z= 0.152 Angle : 0.615 9.358 17672 Z= 0.318 Chirality : 0.044 0.215 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.534 22.123 1880 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.81 % Allowed : 18.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1730 helix: 1.60 (0.17), residues: 978 sheet: -0.76 (0.48), residues: 118 loop : -2.10 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1069 TYR 0.017 0.001 TYR B 746 PHE 0.016 0.001 PHE A 494 TRP 0.024 0.002 TRP B1028 HIS 0.005 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12954) covalent geometry : angle 0.61466 / 0.32 (17664) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.49786 / 0.28 ( 8) hydrogen bonds : bond 0.04162 / 2.86 ( 820) hydrogen bonds : angle 4.42992 / 3.23 ( 2382) *********************** 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 248 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.354 Fit side-chains REVERT: B 492 GLU cc_start: 0.8185 (tm-30) cc_final: 0.6807 (mt-10) REVERT: B 752 LYS cc_start: 0.7010 (tptt) cc_final: 0.6708 (tptp) REVERT: B 762 THR cc_start: 0.8791 (m) cc_final: 0.8427 (p) REVERT: B 784 VAL cc_start: 0.8596 (t) cc_final: 0.8370 (t) REVERT: B 834 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: A 242 SER cc_start: 0.7811 (t) cc_final: 0.7366 (m) REVERT: A 485 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 492 GLU cc_start: 0.8142 (tm-30) cc_final: 0.6783 (mt-10) REVERT: A 543 CYS cc_start: 0.8262 (t) cc_final: 0.7291 (m) REVERT: A 752 LYS cc_start: 0.6997 (tptt) cc_final: 0.6693 (tttp) REVERT: A 762 THR cc_start: 0.8794 (m) cc_final: 0.8432 (p) REVERT: A 784 VAL cc_start: 0.8552 (t) cc_final: 0.8321 (t) REVERT: A 834 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7853 (mm-30) outliers start: 57 outliers final: 38 residues processed: 229 average time/residue: 0.3252 time to fit residues: 84.6544 Evaluate side-chains 227 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 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 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE 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 593 MET Chi-restraints excluded: chain A residue 599 PHE Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 710 TYR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1028 TRP 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 87 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 731 ASN ** B 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 ASN B1203 ASN A 731 ASN A 868 GLN A1153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.132208 restraints weight = 15650.458| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.89 r_work: 0.3463 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12958 Z= 0.194 Angle : 0.669 12.092 17672 Z= 0.344 Chirality : 0.046 0.175 2062 Planarity : 0.004 0.044 2216 Dihedral : 4.758 24.119 1880 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.48 % Allowed : 19.34 % Favored : 76.18 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1730 helix: 1.46 (0.16), residues: 980 sheet: -0.78 (0.47), residues: 114 loop : -2.16 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1069 TYR 0.021 0.002 TYR A 746 PHE 0.018 0.002 PHE A 449 TRP 0.029 0.002 TRP B1028 HIS 0.007 0.001 HIS B 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (12954) covalent geometry : angle 0.66893 / 0.34 (17664) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 0.59780 / 0.34 ( 8) hydrogen bonds : bond 0.04533 / 3.11 ( 820) hydrogen bonds : angle 4.56273 / 3.34 ( 2382) *********************** 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 253 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.337 Fit side-chains REVERT: B 242 SER cc_start: 0.7688 (t) cc_final: 0.7275 (m) REVERT: B 492 GLU cc_start: 0.8201 (tm-30) cc_final: 0.6844 (mt-10) REVERT: B 543 CYS cc_start: 0.8149 (t) cc_final: 0.6904 (m) REVERT: B 752 LYS cc_start: 0.7016 (tptt) cc_final: 0.6705 (tttp) REVERT: B 762 THR cc_start: 0.8847 (m) cc_final: 0.8430 (p) REVERT: B 784 VAL cc_start: 0.8617 (t) cc_final: 0.8391 (t) REVERT: B 834 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 242 SER cc_start: 0.7827 (t) cc_final: 0.7419 (m) REVERT: A 485 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 492 GLU cc_start: 0.8165 (tm-30) cc_final: 0.6817 (mt-10) REVERT: A 543 CYS cc_start: 0.8246 (t) cc_final: 0.7208 (m) REVERT: A 752 LYS cc_start: 0.6998 (tptt) cc_final: 0.6686 (tttp) REVERT: A 762 THR cc_start: 0.8846 (m) cc_final: 0.8433 (p) REVERT: A 834 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 1154 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7236 (tp30) outliers start: 53 outliers final: 37 residues processed: 233 average time/residue: 0.3332 time to fit residues: 88.3407 Evaluate side-chains 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 710 TYR Chi-restraints excluded: chain B residue 712 ASN Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 1028 TRP Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE 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 599 PHE 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 793 VAL Chi-restraints excluded: chain A residue 834 GLU Chi-restraints excluded: chain A residue 1028 TRP Chi-restraints excluded: chain A residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 0.0010 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 114 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 731 ASN B1203 ASN A 731 ASN A 790 GLN A1203 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.169879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136986 restraints weight = 15542.950| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.88 r_work: 0.3527 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12958 Z= 0.135 Angle : 0.617 9.559 17672 Z= 0.319 Chirality : 0.043 0.149 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.570 23.211 1880 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.72 % Allowed : 20.44 % Favored : 75.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1730 helix: 1.59 (0.16), residues: 976 sheet: -0.12 (0.52), residues: 98 loop : -2.16 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1069 TYR 0.018 0.001 TYR B 746 PHE 0.022 0.001 PHE A 449 TRP 0.023 0.001 TRP B1028 HIS 0.004 0.001 HIS B 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12954) covalent geometry : angle 0.61669 / 0.32 (17664) SS BOND : bond 0.00166 / 0.08 ( 4) SS BOND : angle 0.53898 / 0.31 ( 8) hydrogen bonds : bond 0.04106 / 2.82 ( 820) hydrogen bonds : angle 4.43113 / 3.24 ( 2382) ********************** 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 230 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.297 Fit side-chains REVERT: B 492 GLU cc_start: 0.8108 (tm-30) cc_final: 0.6804 (mt-10) REVERT: B 752 LYS cc_start: 0.6994 (tptt) cc_final: 0.6692 (tttp) REVERT: B 784 VAL cc_start: 0.8612 (t) cc_final: 0.8358 (t) REVERT: B 834 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: A 242 SER cc_start: 0.7780 (t) cc_final: 0.7374 (m) REVERT: A 440 VAL cc_start: 0.8243 (t) cc_final: 0.7972 (t) REVERT: A 485 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8163 (mm-30) REVERT: A 492 GLU cc_start: 0.8125 (tm-30) cc_final: 0.6687 (mt-10) REVERT: A 543 CYS cc_start: 0.8272 (t) cc_final: 0.7289 (m) REVERT: A 752 LYS cc_start: 0.6976 (tptt) cc_final: 0.6667 (tttp) REVERT: A 834 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: A 1154 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7334 (tp30) outliers start: 44 outliers final: 37 residues processed: 218 average time/residue: 0.3347 time to fit residues: 82.7821 Evaluate side-chains 220 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 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 392 VAL Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 419 ILE 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 599 PHE 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 1028 TRP 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 29 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4014 r_free = 0.4014 target = 0.169314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.136595 restraints weight = 15594.958| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.86 r_work: 0.3517 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12958 Z= 0.147 Angle : 0.629 10.259 17672 Z= 0.325 Chirality : 0.044 0.154 2062 Planarity : 0.004 0.043 2216 Dihedral : 4.561 23.897 1880 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.89 % Allowed : 20.27 % Favored : 75.84 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1730 helix: 1.56 (0.16), residues: 976 sheet: -0.50 (0.49), residues: 114 loop : -2.15 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1069 TYR 0.015 0.001 TYR B 746 PHE 0.015 0.001 PHE A 907 TRP 0.024 0.001 TRP B1028 HIS 0.005 0.001 HIS B 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12954) covalent geometry : angle 0.62919 / 0.32 (17664) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 0.54548 / 0.31 ( 8) hydrogen bonds : bond 0.04155 / 2.85 ( 820) hydrogen bonds : angle 4.43339 / 3.24 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4179.68 seconds wall clock time: 71 minutes 54.34 seconds (4314.34 seconds total)