Starting phenix.real_space_refine on Thu Jun 19 02:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.map" model { file = "/net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uxt_42775/06_2025/8uxt_42775.cif" } resolution = 1.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.047 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 7132 2.51 5 N 1942 2.21 5 O 2169 1.98 5 H 10719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21989 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1414, 21989 Classifications: {'peptide': 1414} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 45, 'TRANS': 1368} Chain breaks: 4 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 11.37, per 1000 atoms: 0.52 Number of scatterers: 21989 At special positions: 0 Unit cell: (91, 96.2, 124.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 2169 8.00 N 1942 7.00 C 7132 6.00 H 10719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 2.1 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2630 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 7 sheets defined 15.1% alpha, 48.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 30 through 48 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.161A pdb=" N SER A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 83 Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.546A pdb=" N GLY A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 131 Proline residue: A 120 - end of helix removed outlier: 4.520A pdb=" N ARG A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.999A pdb=" N MET A 151 " --> pdb=" O HIS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 166 Processing helix chain 'A' and resid 166 through 186 removed outlier: 4.038A pdb=" N SER A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 226 removed outlier: 4.272A pdb=" N LEU A 220 " --> pdb=" O TRP A 216 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 removed outlier: 4.476A pdb=" N SER A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 270 through 286 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.981A pdb=" N ILE A 411 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1334 Processing helix chain 'A' and resid 1371 through 1376 Processing helix chain 'A' and resid 1405 through 1410 removed outlier: 3.891A pdb=" N ALA A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 65 removed outlier: 6.146A pdb=" N ILE A 61 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 215 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A 211 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 344 through 352 removed outlier: 5.538A pdb=" N GLN A 346 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N TYR A 363 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA A 348 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG A 361 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 350 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406 removed outlier: 3.503A pdb=" N MET A 386 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 14.545A pdb=" N ASN A 452 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU A 473 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N TYR A 454 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N TYR A 471 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU A 466 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE A 485 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 468 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 483 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 470 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 12.817A pdb=" N TYR A 479 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N PHE A 498 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 481 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE A 505 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 529 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 528 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 539 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A 549 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE A 573 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 616 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR A 637 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 658 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 679 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 700 " --> pdb=" O TYR A 712 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL A 721 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 742 " --> pdb=" O TRP A 754 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR A 763 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A 788 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 799 " --> pdb=" O HIS A 811 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS A 811 " --> pdb=" O TYR A 799 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 801 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU A 809 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 830 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 841 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 853 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN A 843 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN A 851 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE A 893 " --> pdb=" O PHE A 904 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA A 913 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 939 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL A 959 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE A 988 " --> pdb=" O HIS A1000 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A1010 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A1003 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE A1008 " --> pdb=" O TYR A1003 " (cutoff:3.500A) removed outlier: 11.492A pdb=" N HIS A1007 " --> pdb=" O GLN A1022 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N GLN A1022 " --> pdb=" O HIS A1007 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TYR A1009 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A1020 " --> pdb=" O TYR A1009 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE A1011 " --> pdb=" O VAL A1018 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR A1030 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A1038 " --> pdb=" O LEU A1034 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER A1051 " --> pdb=" O TYR A1073 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N SER A1082 " --> pdb=" O TYR A1094 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.639A pdb=" N LYS A 457 " --> pdb=" O HIS A 443 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLN A 445 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU A 455 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 14.545A pdb=" N ASN A 452 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N LEU A 473 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N TYR A 454 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N TYR A 471 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL A 456 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU A 466 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE A 485 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 468 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 483 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 470 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 12.817A pdb=" N TYR A 479 " --> pdb=" O PHE A 498 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N PHE A 498 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 481 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ILE A 505 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 529 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 528 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 539 " --> pdb=" O THR A 552 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR A 549 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE A 573 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 616 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR A 637 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 658 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 679 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N SER A 700 " --> pdb=" O TYR A 712 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL A 721 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE A 742 " --> pdb=" O TRP A 754 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR A 763 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A 788 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR A 799 " --> pdb=" O HIS A 811 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N HIS A 811 " --> pdb=" O TYR A 799 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU A 801 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU A 809 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 830 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 841 " --> pdb=" O LEU A 853 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU A 853 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN A 843 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLN A 851 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N PHE A 893 " --> pdb=" O PHE A 904 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA A 913 " --> pdb=" O PHE A 930 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 939 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL A 959 " --> pdb=" O TYR A 979 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.353A pdb=" N HIS A1146 " --> pdb=" O ILE A1158 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE A1158 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN A1148 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR A1156 " --> pdb=" O LEU A1167 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE A1176 " --> pdb=" O TYR A1187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A1197 " --> pdb=" O GLY A1188 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LEU A1196 " --> pdb=" O PHE A1207 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A1204 " --> pdb=" O PHE A1219 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A1219 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A1206 " --> pdb=" O GLU A1217 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A1217 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY A1208 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N LEU A1213 " --> pdb=" O TYR A1232 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N TYR A1232 " --> pdb=" O LEU A1213 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ILE A1215 " --> pdb=" O TYR A1230 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A1240 " --> pdb=" O TYR A1290 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLN A1299 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A1311 " --> pdb=" O GLN A1299 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET A1301 " --> pdb=" O VAL A1309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1343 through 1344 613 hydrogen bonds defined for protein. 1722 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: 20.26 Time building geometry restraints manager: 6.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10711 1.03 - 1.23: 12 1.23 - 1.42: 5014 1.42 - 1.62: 6452 1.62 - 1.81: 46 Bond restraints: 22235 Sorted by residual: bond pdb=" C GLU A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.97e+00 bond pdb=" CB GLU A 758 " pdb=" CG GLU A 758 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.91e-01 bond pdb=" CA GLU A 107 " pdb=" C GLU A 107 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.26e-02 6.30e+03 7.25e-01 bond pdb=" CB GLN A 229 " pdb=" CG GLN A 229 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.94e-01 bond pdb=" CA ASP A 717 " pdb=" CB ASP A 717 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.78e-02 3.16e+03 6.65e-01 ... (remaining 22230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39210 1.43 - 2.87: 654 2.87 - 4.30: 60 4.30 - 5.73: 2 5.73 - 7.17: 2 Bond angle restraints: 39928 Sorted by residual: angle pdb=" C GLY A1405 " pdb=" N ILE A1406 " pdb=" CA ILE A1406 " ideal model delta sigma weight residual 120.24 122.71 -2.47 6.30e-01 2.52e+00 1.54e+01 angle pdb=" C ILE A1406 " pdb=" CA ILE A1406 " pdb=" CB ILE A1406 " ideal model delta sigma weight residual 114.35 111.68 2.67 1.06e+00 8.90e-01 6.37e+00 angle pdb=" N ARG A1338 " pdb=" CA ARG A1338 " pdb=" C ARG A1338 " ideal model delta sigma weight residual 110.80 105.58 5.22 2.13e+00 2.20e-01 6.00e+00 angle pdb=" CA GLU A 107 " pdb=" C GLU A 107 " pdb=" N PRO A 108 " ideal model delta sigma weight residual 118.44 121.96 -3.52 1.59e+00 3.96e-01 4.90e+00 angle pdb=" CA GLU A 758 " pdb=" CB GLU A 758 " pdb=" CG GLU A 758 " ideal model delta sigma weight residual 114.10 118.47 -4.37 2.00e+00 2.50e-01 4.78e+00 ... (remaining 39923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9531 17.81 - 35.63: 713 35.63 - 53.44: 203 53.44 - 71.26: 61 71.26 - 89.07: 33 Dihedral angle restraints: 10541 sinusoidal: 5608 harmonic: 4933 Sorted by residual: dihedral pdb=" CA TYR A1422 " pdb=" C TYR A1422 " pdb=" N GLU A1423 " pdb=" CA GLU A1423 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA MET A 459 " pdb=" C MET A 459 " pdb=" N ASN A 460 " pdb=" CA ASN A 460 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU A1430 " pdb=" C GLU A1430 " pdb=" N LEU A1431 " pdb=" CA LEU A1431 " ideal model delta harmonic sigma weight residual 180.00 163.32 16.68 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 10538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1021 0.028 - 0.056: 459 0.056 - 0.083: 74 0.083 - 0.111: 73 0.111 - 0.139: 34 Chirality restraints: 1661 Sorted by residual: chirality pdb=" CA ILE A 467 " pdb=" N ILE A 467 " pdb=" C ILE A 467 " pdb=" CB ILE A 467 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 967 " pdb=" N ILE A 967 " pdb=" C ILE A 967 " pdb=" CB ILE A 967 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1658 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 251 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C ALA A 251 " -0.023 2.00e-02 2.50e+03 pdb=" O ALA A 251 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 252 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1097 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A1098 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1098 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1098 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 717 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ASP A 717 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 717 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN A 718 " -0.007 2.00e-02 2.50e+03 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 448 2.06 - 2.70: 35263 2.70 - 3.33: 65543 3.33 - 3.97: 89703 3.97 - 4.60: 135721 Nonbonded interactions: 326678 Sorted by model distance: nonbonded pdb=" OE1 GLU A 758 " pdb=" H GLU A 758 " model vdw 1.426 2.450 nonbonded pdb=" OE1 GLN A1328 " pdb=" H GLN A1328 " model vdw 1.527 2.450 nonbonded pdb=" O LEU A 871 " pdb=" HH TYR A 886 " model vdw 1.584 2.450 nonbonded pdb=" OD2 ASP A 994 " pdb=" HE2 HIS A1229 " model vdw 1.591 2.450 nonbonded pdb=" OH TYR A 608 " pdb="HH21 ARG A 619 " model vdw 1.595 2.450 ... (remaining 326673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.110 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: 0.390 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 62.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:21.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.003 0.033 11516 Z= 0.118 Angle : 0.480 7.169 15600 Z= 0.261 Chirality : 0.039 0.139 1661 Planarity : 0.003 0.029 2054 Dihedral : 16.631 89.069 4221 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.49 % Favored : 95.01 % Rotamer: Outliers : 1.45 % Allowed : 15.08 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1404 helix: 3.33 (0.40), residues: 165 sheet: 1.54 (0.25), residues: 400 loop : -0.15 (0.23), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A1291 PHE 0.008 0.001 PHE A 350 TYR 0.010 0.001 TYR A 601 ARG 0.002 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.18679 ( 443) hydrogen bonds : angle 8.64849 ( 1722) covalent geometry : bond 0.00250 (11516) covalent geometry : angle 0.48010 (15600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 104 average time/residue: 2.7711 time to fit residues: 312.5910 Evaluate side-chains 101 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 1068 GLN Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 SER Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.150486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106208 restraints weight = 36880.914| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.92 r_work: 0.3392 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11516 Z= 0.168 Angle : 0.540 6.998 15600 Z= 0.299 Chirality : 0.042 0.149 1661 Planarity : 0.004 0.047 2054 Dihedral : 5.468 42.594 1575 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.50 % Allowed : 4.99 % Favored : 94.52 % Rotamer: Outliers : 1.79 % Allowed : 14.65 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1404 helix: 3.07 (0.40), residues: 166 sheet: 1.29 (0.24), residues: 415 loop : -0.23 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1317 HIS 0.003 0.001 HIS A1229 PHE 0.009 0.001 PHE A 350 TYR 0.013 0.001 TYR A 965 ARG 0.003 0.000 ARG A 538 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 443) hydrogen bonds : angle 6.19751 ( 1722) covalent geometry : bond 0.00345 (11516) covalent geometry : angle 0.54012 (15600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 MET cc_start: 0.7618 (mmm) cc_final: 0.7406 (mmm) REVERT: A 971 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8441 (ttpp) REVERT: A 1328 GLN cc_start: 0.8000 (mp10) cc_final: 0.7798 (mp10) REVERT: A 1346 ARG cc_start: 0.8356 (ptt90) cc_final: 0.8127 (ptt90) REVERT: A 1359 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8064 (tm-30) outliers start: 21 outliers final: 9 residues processed: 101 average time/residue: 3.3189 time to fit residues: 366.4198 Evaluate side-chains 95 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 971 LYS Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1377 MET Chi-restraints excluded: chain A residue 1434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 72 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 594 GLN A1327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105901 restraints weight = 36855.635| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.90 r_work: 0.3389 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11516 Z= 0.183 Angle : 0.530 6.971 15600 Z= 0.292 Chirality : 0.041 0.140 1661 Planarity : 0.004 0.038 2054 Dihedral : 4.884 38.030 1560 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.48 % Favored : 94.02 % Rotamer: Outliers : 1.62 % Allowed : 14.99 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1404 helix: 2.99 (0.40), residues: 166 sheet: 1.10 (0.24), residues: 409 loop : -0.34 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1317 HIS 0.004 0.001 HIS A1291 PHE 0.009 0.001 PHE A 350 TYR 0.012 0.001 TYR A 792 ARG 0.003 0.000 ARG A1305 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 443) hydrogen bonds : angle 5.89094 ( 1722) covalent geometry : bond 0.00378 (11516) covalent geometry : angle 0.53007 (15600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.5899 (tm130) REVERT: A 459 MET cc_start: 0.7724 (mmm) cc_final: 0.7475 (mmm) REVERT: A 971 LYS cc_start: 0.8665 (pmmt) cc_final: 0.8399 (ttpp) REVERT: A 1328 GLN cc_start: 0.8054 (mp10) cc_final: 0.7843 (mp10) REVERT: A 1346 ARG cc_start: 0.8406 (ptt90) cc_final: 0.8178 (ptt90) REVERT: A 1359 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8115 (tm-30) outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 2.8707 time to fit residues: 307.8965 Evaluate side-chains 97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1377 MET Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 20.0000 chunk 82 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.149928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105610 restraints weight = 37396.575| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.89 r_work: 0.3384 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11516 Z= 0.192 Angle : 0.531 6.937 15600 Z= 0.293 Chirality : 0.041 0.139 1661 Planarity : 0.004 0.054 2054 Dihedral : 4.673 18.563 1555 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.56 % Favored : 93.87 % Rotamer: Outliers : 1.62 % Allowed : 14.99 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1404 helix: 2.95 (0.40), residues: 166 sheet: 0.99 (0.24), residues: 415 loop : -0.39 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1169 HIS 0.004 0.001 HIS A1291 PHE 0.009 0.001 PHE A 350 TYR 0.013 0.001 TYR A 792 ARG 0.003 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 443) hydrogen bonds : angle 5.75442 ( 1722) covalent geometry : bond 0.00398 (11516) covalent geometry : angle 0.53149 (15600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: A 459 MET cc_start: 0.7692 (mmm) cc_final: 0.7487 (mmm) REVERT: A 1328 GLN cc_start: 0.8101 (mp10) cc_final: 0.7879 (mp10) REVERT: A 1346 ARG cc_start: 0.8415 (ptt90) cc_final: 0.8187 (ptt90) REVERT: A 1359 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8034 (tm-30) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 2.9669 time to fit residues: 334.7399 Evaluate side-chains 98 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1377 MET Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.148321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103474 restraints weight = 37257.645| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.94 r_work: 0.3349 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11516 Z= 0.276 Angle : 0.578 6.920 15600 Z= 0.320 Chirality : 0.043 0.141 1661 Planarity : 0.004 0.041 2054 Dihedral : 4.898 19.860 1555 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.56 % Favored : 93.95 % Rotamer: Outliers : 1.87 % Allowed : 14.74 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1404 helix: 2.74 (0.40), residues: 166 sheet: 1.00 (0.24), residues: 407 loop : -0.47 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1169 HIS 0.006 0.001 HIS A1291 PHE 0.010 0.001 PHE A 22 TYR 0.015 0.002 TYR A 792 ARG 0.003 0.000 ARG A1305 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 443) hydrogen bonds : angle 5.95201 ( 1722) covalent geometry : bond 0.00579 (11516) covalent geometry : angle 0.57805 (15600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.723 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6247 (tm-30) REVERT: A 459 MET cc_start: 0.7739 (mmm) cc_final: 0.7530 (mmm) REVERT: A 487 LEU cc_start: 0.8618 (mp) cc_final: 0.8308 (mp) REVERT: A 1328 GLN cc_start: 0.8144 (mp10) cc_final: 0.7923 (mp10) REVERT: A 1346 ARG cc_start: 0.8463 (ptt90) cc_final: 0.8239 (ptt90) REVERT: A 1359 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8110 (tm-30) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 2.6807 time to fit residues: 303.7933 Evaluate side-chains 99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1377 MET Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 122 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 140 optimal weight: 20.0000 chunk 113 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 HIS A 594 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.150638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106535 restraints weight = 36996.649| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.00 r_work: 0.3400 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11516 Z= 0.146 Angle : 0.516 6.838 15600 Z= 0.284 Chirality : 0.041 0.142 1661 Planarity : 0.004 0.052 2054 Dihedral : 4.656 18.366 1555 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.27 % Favored : 94.16 % Rotamer: Outliers : 1.28 % Allowed : 15.76 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1404 helix: 2.93 (0.41), residues: 166 sheet: 0.86 (0.24), residues: 411 loop : -0.43 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A1291 PHE 0.008 0.001 PHE A 22 TYR 0.012 0.001 TYR A 792 ARG 0.005 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 443) hydrogen bonds : angle 5.58822 ( 1722) covalent geometry : bond 0.00301 (11516) covalent geometry : angle 0.51585 (15600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6269 (tm-30) REVERT: A 487 LEU cc_start: 0.8581 (mp) cc_final: 0.8280 (mp) REVERT: A 1328 GLN cc_start: 0.8146 (mp10) cc_final: 0.7921 (mp10) REVERT: A 1346 ARG cc_start: 0.8404 (ptt90) cc_final: 0.8176 (ptt90) REVERT: A 1359 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8091 (tm-30) outliers start: 15 outliers final: 8 residues processed: 99 average time/residue: 2.9913 time to fit residues: 323.4365 Evaluate side-chains 97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1434 ILE Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 132 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 14 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106667 restraints weight = 37129.629| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.93 r_work: 0.3400 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11516 Z= 0.142 Angle : 0.515 6.793 15600 Z= 0.282 Chirality : 0.041 0.139 1661 Planarity : 0.004 0.097 2054 Dihedral : 4.592 18.231 1555 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.70 % Favored : 93.80 % Rotamer: Outliers : 1.28 % Allowed : 15.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1404 helix: 2.97 (0.40), residues: 166 sheet: 0.76 (0.24), residues: 414 loop : -0.41 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1317 HIS 0.003 0.001 HIS A1291 PHE 0.007 0.001 PHE A 350 TYR 0.010 0.001 TYR A 792 ARG 0.012 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 443) hydrogen bonds : angle 5.47778 ( 1722) covalent geometry : bond 0.00296 (11516) covalent geometry : angle 0.51512 (15600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6296 (tm-30) REVERT: A 1328 GLN cc_start: 0.8145 (mp10) cc_final: 0.7917 (mp10) REVERT: A 1346 ARG cc_start: 0.8381 (ptt90) cc_final: 0.8148 (ptt90) REVERT: A 1359 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8099 (tm-30) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 2.7649 time to fit residues: 294.7441 Evaluate side-chains 92 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 45 optimal weight: 0.7980 chunk 137 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 105 optimal weight: 0.8980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107944 restraints weight = 37199.542| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.90 r_work: 0.3424 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11516 Z= 0.116 Angle : 0.500 6.747 15600 Z= 0.272 Chirality : 0.041 0.138 1661 Planarity : 0.004 0.090 2054 Dihedral : 4.460 17.421 1555 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.56 % Favored : 93.95 % Rotamer: Outliers : 1.11 % Allowed : 16.01 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1404 helix: 3.09 (0.40), residues: 166 sheet: 0.61 (0.24), residues: 429 loop : -0.38 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.002 0.001 HIS A 443 PHE 0.007 0.001 PHE A 904 TYR 0.009 0.001 TYR A 965 ARG 0.011 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 443) hydrogen bonds : angle 5.29796 ( 1722) covalent geometry : bond 0.00242 (11516) covalent geometry : angle 0.50009 (15600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: A 1328 GLN cc_start: 0.8159 (mp10) cc_final: 0.7928 (mp10) REVERT: A 1346 ARG cc_start: 0.8350 (ptt90) cc_final: 0.8127 (ptt90) REVERT: A 1359 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8047 (tm-30) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 2.8508 time to fit residues: 309.7680 Evaluate side-chains 96 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 1 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.150567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105805 restraints weight = 37310.713| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.00 r_work: 0.3389 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11516 Z= 0.172 Angle : 0.530 6.744 15600 Z= 0.290 Chirality : 0.041 0.137 1661 Planarity : 0.004 0.093 2054 Dihedral : 4.563 17.959 1555 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.48 % Favored : 94.09 % Rotamer: Outliers : 1.11 % Allowed : 15.93 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1404 helix: 3.02 (0.40), residues: 166 sheet: 0.88 (0.24), residues: 408 loop : -0.40 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1169 HIS 0.003 0.001 HIS A1291 PHE 0.008 0.001 PHE A 350 TYR 0.011 0.001 TYR A 792 ARG 0.012 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 443) hydrogen bonds : angle 5.42587 ( 1722) covalent geometry : bond 0.00360 (11516) covalent geometry : angle 0.53040 (15600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6369 (tm-30) REVERT: A 1328 GLN cc_start: 0.8166 (mp10) cc_final: 0.7924 (mp10) REVERT: A 1346 ARG cc_start: 0.8416 (ptt90) cc_final: 0.8187 (ptt90) REVERT: A 1359 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8097 (tm-30) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 2.7448 time to fit residues: 292.7045 Evaluate side-chains 97 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106360 restraints weight = 37108.879| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.93 r_work: 0.3397 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11516 Z= 0.159 Angle : 0.526 6.715 15600 Z= 0.287 Chirality : 0.041 0.138 1661 Planarity : 0.004 0.088 2054 Dihedral : 4.559 17.851 1555 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.27 % Favored : 94.23 % Rotamer: Outliers : 1.11 % Allowed : 16.01 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1404 helix: 3.03 (0.40), residues: 166 sheet: 0.83 (0.24), residues: 410 loop : -0.41 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1216 HIS 0.003 0.001 HIS A1291 PHE 0.008 0.001 PHE A 22 TYR 0.011 0.001 TYR A 792 ARG 0.011 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 443) hydrogen bonds : angle 5.41295 ( 1722) covalent geometry : bond 0.00331 (11516) covalent geometry : angle 0.52572 (15600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue ILE 240 is missing expected H atoms. Skipping. Residue THR 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 244 is missing expected H atoms. Skipping. Residue LYS 306 is missing expected H atoms. Skipping. Residue LEU 1414 is missing expected H atoms. Skipping. Residue TYR 1416 is missing expected H atoms. Skipping. Residue TYR 1422 is missing expected H atoms. Skipping. Residue TYR 1425 is missing expected H atoms. Skipping. Residue LYS 1433 is missing expected H atoms. Skipping. Residue LYS 1435 is missing expected H atoms. Skipping. Residue TYR 1442 is missing expected H atoms. Skipping. Residue VAL 1443 is missing expected H atoms. Skipping. Residue ALA 1444 is missing expected H atoms. Skipping. Residue SER 1446 is missing expected H atoms. Skipping. Residue LEU 1450 is missing expected H atoms. Skipping. Residue ILE 1452 is missing expected H atoms. Skipping. Residue VAL 1457 is missing expected H atoms. Skipping. Residue LYS 1458 is missing expected H atoms. Skipping. Residue TYR 1465 is missing expected H atoms. Skipping. Residue ILE 1467 is missing expected H atoms. Skipping. Residue LYS 1471 is missing expected H atoms. Skipping. Residue LEU 1474 is missing expected H atoms. Skipping. Residue LEU 1475 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Residue VAL 1478 is missing expected H atoms. Skipping. Residue LYS 1480 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.758 Fit side-chains revert: symmetry clash REVERT: A 229 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: A 1328 GLN cc_start: 0.8169 (mp10) cc_final: 0.7933 (mp10) REVERT: A 1346 ARG cc_start: 0.8375 (ptt90) cc_final: 0.8144 (ptt90) REVERT: A 1359 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8080 (tm-30) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 2.8568 time to fit residues: 310.4141 Evaluate side-chains 99 residues out of total 1222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 569 LYS Chi-restraints excluded: chain A residue 610 ASP Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1359 GLU Chi-restraints excluded: chain A residue 1473 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 129 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106477 restraints weight = 37143.892| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.92 r_work: 0.3398 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11516 Z= 0.157 Angle : 0.530 7.431 15600 Z= 0.289 Chirality : 0.041 0.140 1661 Planarity : 0.004 0.095 2054 Dihedral : 4.546 17.820 1555 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.70 % Favored : 93.87 % Rotamer: Outliers : 1.19 % Allowed : 15.84 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1404 helix: 3.03 (0.40), residues: 166 sheet: 0.83 (0.24), residues: 410 loop : -0.40 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1317 HIS 0.003 0.001 HIS A1291 PHE 0.008 0.001 PHE A 22 TYR 0.011 0.001 TYR A 792 ARG 0.012 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 443) hydrogen bonds : angle 5.39385 ( 1722) covalent geometry : bond 0.00329 (11516) covalent geometry : angle 0.52987 (15600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30720.84 seconds wall clock time: 531 minutes 51.31 seconds (31911.31 seconds total)