Starting phenix.real_space_refine on Thu Jun 12 14:32:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.map" model { file = "/net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ir4_60800/06_2025/9ir4_60800.cif" } resolution = 3.01 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1641 atoms to isotropic. 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 Zn 2 6.06 5 S 82 5.16 5 C 8010 2.51 5 N 2154 2.21 5 O 2356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 12604 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1260, 10150 Classifications: {'peptide': 1260} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1212} Chain breaks: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 557 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 436 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 56} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 484 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 494 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 481 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8787 SG CYS A1236 32.188 23.375 32.854 1.00 65.95 S ATOM 8810 SG CYS A1239 33.186 19.981 34.402 1.00 64.24 S ATOM 8437 SG CYS A1191 52.747 25.744 25.129 1.00 59.93 S ATOM 9982 SG CYS A1429 50.783 26.287 26.901 1.00 72.62 S Time building chain proxies: 7.96, per 1000 atoms: 0.63 Number of scatterers: 12604 At special positions: 0 Unit cell: (100.04, 109.06, 181.22, 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) Zn 2 29.99 S 82 16.00 O 2356 8.00 N 2154 7.00 C 8010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1421 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1239 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1236 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1429 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1191 " Number of angles added : 2 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 63.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.609A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 4.040A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.982A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 167 through 188 Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.575A pdb=" N PHE A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 193 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 194 " --> pdb=" O LYS A 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 194' Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 260 through 273 removed outlier: 4.003A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 289 removed outlier: 3.847A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.896A pdb=" N LEU A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 325 removed outlier: 3.560A pdb=" N HIS A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 removed outlier: 3.686A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.581A pdb=" N PHE A 359 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 360' Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.620A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.782A pdb=" N ILE A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 479 through 486 removed outlier: 3.694A pdb=" N TRP A 483 " --> pdb=" O LYS A 480 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 504 through 511 Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.563A pdb=" N ARG A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.590A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.726A pdb=" N LYS A 757 " --> pdb=" O ASN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.593A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 Processing helix chain 'A' and resid 904 through 911 removed outlier: 3.696A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A 911 " --> pdb=" O LYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 940 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.878A pdb=" N LEU A1037 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1083 removed outlier: 4.007A pdb=" N ASN A1083 " --> pdb=" O THR A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1110 Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'A' and resid 1126 through 1138 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.601A pdb=" N VAL A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 removed outlier: 3.582A pdb=" N ASN A1168 " --> pdb=" O HIS A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1204 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1236 through 1242 Processing helix chain 'A' and resid 1293 through 1308 Processing helix chain 'A' and resid 1311 through 1323 Processing helix chain 'A' and resid 1329 through 1337 Processing helix chain 'A' and resid 1391 through 1407 removed outlier: 3.538A pdb=" N ALA A1395 " --> pdb=" O ILE A1391 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 672 removed outlier: 3.565A pdb=" N ARG C 661 " --> pdb=" O ASP C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 706 Processing helix chain 'D' and resid 520 through 541 removed outlier: 4.007A pdb=" N GLN D 539 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 574 removed outlier: 3.501A pdb=" N ILE D 546 " --> pdb=" O GLU D 542 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 573 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET D 574 " --> pdb=" O HIS D 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 541 removed outlier: 3.551A pdb=" N GLU E 538 " --> pdb=" O ASN E 534 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 578 removed outlier: 3.740A pdb=" N ILE E 547 " --> pdb=" O ILE E 543 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 572 " --> pdb=" O GLU E 568 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER E 573 " --> pdb=" O GLY E 569 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 576 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 578 " --> pdb=" O MET E 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 539 removed outlier: 3.524A pdb=" N GLN F 539 " --> pdb=" O HIS F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 574 removed outlier: 3.872A pdb=" N LYS F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 567 " --> pdb=" O ALA F 563 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU F 568 " --> pdb=" O LEU F 564 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY F 569 " --> pdb=" O SER F 565 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER F 573 " --> pdb=" O GLY F 569 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 541 removed outlier: 3.539A pdb=" N GLU G 537 " --> pdb=" O LEU G 533 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN G 539 " --> pdb=" O HIS G 535 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 574 removed outlier: 3.827A pdb=" N ILE G 546 " --> pdb=" O GLU G 542 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE G 547 " --> pdb=" O ILE G 543 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA G 558 " --> pdb=" O ASP G 554 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 563 " --> pdb=" O LYS G 559 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL G 572 " --> pdb=" O GLU G 568 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER G 573 " --> pdb=" O GLY G 569 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET G 574 " --> pdb=" O HIS G 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.577A pdb=" N ILE A 21 " --> pdb=" O LEU A 368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.161A pdb=" N MET A 84 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N TYR A 229 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA5, first strand: chain 'A' and resid 552 through 555 removed outlier: 4.761A pdb=" N VAL A 537 " --> pdb=" O VAL A 763 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 765 " --> pdb=" O VAL A 537 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.013A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 834 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA9, first strand: chain 'A' and resid 1225 through 1231 738 hydrogen bonds defined for protein. 2130 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: 3.93 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4124 1.34 - 1.46: 1601 1.46 - 1.57: 6963 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 12824 Sorted by residual: bond pdb=" CB PRO A 190 " pdb=" CG PRO A 190 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.46e+00 bond pdb=" CG GLU A 325 " pdb=" CD GLU A 325 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB ASN A1374 " pdb=" CG ASN A1374 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 8.92e-01 bond pdb=" CB ASP A1261 " pdb=" CG ASP A1261 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.65e-01 bond pdb=" CG ARG F 555 " pdb=" CD ARG F 555 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.55e-01 ... (remaining 12819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 17085 1.90 - 3.80: 202 3.80 - 5.70: 33 5.70 - 7.60: 10 7.60 - 9.50: 1 Bond angle restraints: 17331 Sorted by residual: angle pdb=" N GLU A 325 " pdb=" CA GLU A 325 " pdb=" CB GLU A 325 " ideal model delta sigma weight residual 110.39 116.29 -5.90 1.75e+00 3.27e-01 1.14e+01 angle pdb=" C ARG A1253 " pdb=" N ASP A1254 " pdb=" CA ASP A1254 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.36e+00 angle pdb=" N MET G 531 " pdb=" CA MET G 531 " pdb=" C MET G 531 " ideal model delta sigma weight residual 111.07 107.86 3.21 1.07e+00 8.73e-01 9.03e+00 angle pdb=" N GLU D 538 " pdb=" CA GLU D 538 " pdb=" CB GLU D 538 " ideal model delta sigma weight residual 110.12 114.30 -4.18 1.47e+00 4.63e-01 8.10e+00 angle pdb=" C ASP F 554 " pdb=" N ARG F 555 " pdb=" CA ARG F 555 " ideal model delta sigma weight residual 121.94 116.35 5.59 2.00e+00 2.50e-01 7.81e+00 ... (remaining 17326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7153 17.96 - 35.91: 611 35.91 - 53.87: 84 53.87 - 71.82: 15 71.82 - 89.78: 4 Dihedral angle restraints: 7867 sinusoidal: 3207 harmonic: 4660 Sorted by residual: dihedral pdb=" CG ARG A 181 " pdb=" CD ARG A 181 " pdb=" NE ARG A 181 " pdb=" CZ ARG A 181 " ideal model delta sinusoidal sigma weight residual -180.00 -136.37 -43.63 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA GLU F 537 " pdb=" C GLU F 537 " pdb=" N GLU F 538 " pdb=" CA GLU F 538 " ideal model delta harmonic sigma weight residual -180.00 -164.29 -15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA MET E 577 " pdb=" C MET E 577 " pdb=" N ILE E 578 " pdb=" CA ILE E 578 " ideal model delta harmonic sigma weight residual 180.00 -164.34 -15.66 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 7864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1369 0.035 - 0.070: 454 0.070 - 0.105: 124 0.105 - 0.140: 44 0.140 - 0.176: 5 Chirality restraints: 1996 Sorted by residual: chirality pdb=" CB ILE G 576 " pdb=" CA ILE G 576 " pdb=" CG1 ILE G 576 " pdb=" CG2 ILE G 576 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB ILE A 828 " pdb=" CA ILE A 828 " pdb=" CG1 ILE A 828 " pdb=" CG2 ILE A 828 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CA ILE A 828 " pdb=" N ILE A 828 " pdb=" C ILE A 828 " pdb=" CB ILE A 828 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1993 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1443 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A1444 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A1444 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1444 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 175 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C THR A 175 " -0.028 2.00e-02 2.50e+03 pdb=" O THR A 175 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 176 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 211 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A 212 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.022 5.00e-02 4.00e+02 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 159 2.68 - 3.24: 12318 3.24 - 3.79: 19260 3.79 - 4.35: 25424 4.35 - 4.90: 42569 Nonbonded interactions: 99730 Sorted by model distance: nonbonded pdb=" OE2 GLU A1223 " pdb="ZN ZN A2302 " model vdw 2.127 2.230 nonbonded pdb=" O VAL E 520 " pdb=" OG SER E 523 " model vdw 2.161 3.040 nonbonded pdb=" O VAL G 520 " pdb=" OG SER G 523 " model vdw 2.198 3.040 nonbonded pdb=" OD1 ASP A1101 " pdb=" OG1 THR A1128 " model vdw 2.205 3.040 nonbonded pdb=" O ALA G 563 " pdb=" OG1 THR G 566 " model vdw 2.215 3.040 ... (remaining 99725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 519 through 522 and (name N or name CA or name C or name \ O or name CB )) or resid 523 through 526 or (resid 527 and (name N or name CA or \ name C or name O or name CB )) or resid 528 through 531 or (resid 532 through 5 \ 33 and (name N or name CA or name C or name O or name CB )) or resid 534 or (res \ id 535 and (name N or name CA or name C or name O or name CB )) or resid 536 thr \ ough 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) \ or resid 542 through 549 or (resid 550 and (name N or name CA or name C or name \ O or name CB )) or resid 551 through 560 or (resid 561 and (name N or name CA or \ name C or name O or name CB )) or resid 562 through 576)) selection = (chain 'E' and (resid 519 or (resid 520 through 522 and (name N or name CA or na \ me C or name O or name CB )) or resid 523 through 525 or (resid 526 through 527 \ and (name N or name CA or name C or name O or name CB )) or resid 528 or (resid \ 529 and (name N or name CA or name C or name O or name CB )) or resid 530 throug \ h 531 or (resid 532 through 533 and (name N or name CA or name C or name O or na \ me CB )) or resid 534 through 540 or (resid 541 and (name N or name CA or name C \ or name O or name CB )) or resid 542 through 548 or (resid 549 through 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 through 576)) selection = (chain 'F' and ((resid 519 through 522 and (name N or name CA or name C or name \ O or name CB )) or resid 523 through 528 or (resid 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 through 531 or (resid 532 through 5 \ 33 and (name N or name CA or name C or name O or name CB )) or resid 534 or (res \ id 535 and (name N or name CA or name C or name O or name CB )) or resid 536 thr \ ough 548 or (resid 549 through 550 and (name N or name CA or name C or name O or \ name CB )) or resid 551 through 560 or (resid 561 and (name N or name CA or nam \ e C or name O or name CB )) or resid 562 through 576)) selection = (chain 'G' and ((resid 519 through 522 and (name N or name CA or name C or name \ O or name CB )) or resid 523 through 524 or (resid 525 through 527 and (name N o \ r name CA or name C or name O or name CB )) or resid 528 or (resid 529 and (name \ N or name CA or name C or name O or name CB )) or resid 530 through 534 or (res \ id 535 and (name N or name CA or name C or name O or name CB )) or resid 536 thr \ ough 540 or (resid 541 and (name N or name CA or name C or name O or name CB )) \ or resid 542 through 560 or (resid 561 and (name N or name CA or name C or name \ O or name CB )) or resid 562 through 576)) } 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.640 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.002 0.060 12830 Z= 0.117 Angle : 0.541 9.499 17333 Z= 0.292 Chirality : 0.040 0.176 1996 Planarity : 0.004 0.046 2203 Dihedral : 13.202 89.780 4833 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.06 (0.22), residues: 1564 helix: 1.60 (0.18), residues: 919 sheet: 0.29 (0.50), residues: 105 loop : -0.73 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1315 HIS 0.004 0.001 HIS A 320 PHE 0.018 0.001 PHE A 965 TYR 0.020 0.001 TYR A 801 ARG 0.010 0.000 ARG A1299 Details of bonding type rmsd hydrogen bonds : bond 0.15212 ( 738) hydrogen bonds : angle 5.87219 ( 2130) metal coordination : bond 0.01271 ( 6) metal coordination : angle 2.82242 ( 2) covalent geometry : bond 0.00243 (12824) covalent geometry : angle 0.54062 (17331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 179 GLU cc_start: 0.7236 (mp0) cc_final: 0.6559 (mp0) REVERT: A 283 ILE cc_start: 0.8025 (tp) cc_final: 0.7743 (tt) REVERT: A 445 LYS cc_start: 0.8060 (mtmt) cc_final: 0.7854 (mttt) REVERT: A 495 THR cc_start: 0.8256 (t) cc_final: 0.8009 (p) REVERT: A 972 THR cc_start: 0.8468 (m) cc_final: 0.7966 (p) REVERT: A 1047 ASP cc_start: 0.6794 (p0) cc_final: 0.6534 (p0) REVERT: A 1121 GLU cc_start: 0.7262 (tp30) cc_final: 0.7032 (tp30) REVERT: G 575 MET cc_start: 0.7725 (mtp) cc_final: 0.7514 (mtm) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2831 time to fit residues: 114.4943 Evaluate side-chains 270 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 HIS A 981 ASN A1376 ASN ** G 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119952 restraints weight = 17971.629| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.10 r_work: 0.3401 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12830 Z= 0.204 Angle : 0.564 12.560 17333 Z= 0.289 Chirality : 0.043 0.157 1996 Planarity : 0.004 0.041 2203 Dihedral : 3.875 16.401 1706 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 0.64 % Allowed : 8.71 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.70 (0.22), residues: 1564 helix: 2.35 (0.17), residues: 917 sheet: 0.00 (0.55), residues: 90 loop : -0.79 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1248 HIS 0.008 0.001 HIS A 792 PHE 0.015 0.002 PHE A 553 TYR 0.013 0.002 TYR A 732 ARG 0.003 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.05769 ( 738) hydrogen bonds : angle 4.24724 ( 2130) metal coordination : bond 0.01127 ( 6) metal coordination : angle 3.66286 ( 2) covalent geometry : bond 0.00479 (12824) covalent geometry : angle 0.56263 (17331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7983 (tp30) cc_final: 0.7770 (tp30) REVERT: A 134 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.8173 (ttp80) REVERT: A 152 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7988 (ttm-80) REVERT: A 193 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7716 (mtt90) REVERT: A 283 ILE cc_start: 0.8313 (tp) cc_final: 0.8050 (tt) REVERT: A 322 GLU cc_start: 0.7542 (tp30) cc_final: 0.7079 (tp30) REVERT: A 325 GLU cc_start: 0.7823 (mp0) cc_final: 0.7123 (mp0) REVERT: A 387 LEU cc_start: 0.8528 (mt) cc_final: 0.8240 (mt) REVERT: A 445 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8157 (mttt) REVERT: A 972 THR cc_start: 0.8537 (m) cc_final: 0.7929 (p) REVERT: A 1047 ASP cc_start: 0.7614 (p0) cc_final: 0.7311 (p0) REVERT: A 1133 GLU cc_start: 0.7667 (tp30) cc_final: 0.7176 (tp30) REVERT: A 1299 ARG cc_start: 0.7543 (tpt90) cc_final: 0.6928 (tpt90) REVERT: A 1302 THR cc_start: 0.8575 (m) cc_final: 0.8357 (t) REVERT: A 1372 ILE cc_start: 0.8740 (mm) cc_final: 0.8451 (mt) REVERT: G 577 MET cc_start: 0.5244 (tpt) cc_final: 0.4967 (tpt) outliers start: 9 outliers final: 6 residues processed: 290 average time/residue: 0.2945 time to fit residues: 117.4995 Evaluate side-chains 282 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 276 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain G residue 531 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 945 ASN A 957 GLN A 981 ASN A1376 ASN E 570 HIS ** G 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.140466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117814 restraints weight = 18073.279| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.08 r_work: 0.3370 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12830 Z= 0.239 Angle : 0.575 10.080 17333 Z= 0.296 Chirality : 0.045 0.274 1996 Planarity : 0.004 0.048 2203 Dihedral : 4.041 17.976 1706 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 1.57 % Allowed : 11.49 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.55 (0.22), residues: 1564 helix: 2.23 (0.17), residues: 926 sheet: 0.03 (0.53), residues: 95 loop : -0.95 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1248 HIS 0.009 0.001 HIS A 792 PHE 0.018 0.002 PHE A 399 TYR 0.017 0.002 TYR A 523 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05933 ( 738) hydrogen bonds : angle 4.16648 ( 2130) metal coordination : bond 0.01170 ( 6) metal coordination : angle 4.05842 ( 2) covalent geometry : bond 0.00568 (12824) covalent geometry : angle 0.57349 (17331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 300 time to evaluate : 1.302 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.7940 (mm) cc_final: 0.7739 (mm) REVERT: A 14 GLU cc_start: 0.7981 (tp30) cc_final: 0.7760 (tp30) REVERT: A 131 ASN cc_start: 0.8287 (t0) cc_final: 0.8065 (t0) REVERT: A 146 ILE cc_start: 0.8465 (mm) cc_final: 0.8231 (mt) REVERT: A 152 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7933 (ttm-80) REVERT: A 179 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: A 193 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7748 (mtt90) REVERT: A 273 ASP cc_start: 0.8217 (m-30) cc_final: 0.7888 (m-30) REVERT: A 283 ILE cc_start: 0.8346 (tp) cc_final: 0.8070 (tt) REVERT: A 375 GLU cc_start: 0.7981 (tp30) cc_final: 0.7775 (tp30) REVERT: A 387 LEU cc_start: 0.8533 (mt) cc_final: 0.8294 (mt) REVERT: A 441 ASP cc_start: 0.7913 (t0) cc_final: 0.7702 (t0) REVERT: A 578 TYR cc_start: 0.8278 (m-10) cc_final: 0.8047 (m-10) REVERT: A 882 THR cc_start: 0.8168 (t) cc_final: 0.7805 (p) REVERT: A 1047 ASP cc_start: 0.7540 (p0) cc_final: 0.7211 (p0) REVERT: A 1093 PHE cc_start: 0.8803 (m-80) cc_final: 0.8538 (m-80) REVERT: A 1133 GLU cc_start: 0.7758 (tp30) cc_final: 0.7387 (tp30) REVERT: A 1299 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7158 (tpt90) REVERT: A 1372 ILE cc_start: 0.8799 (mm) cc_final: 0.8547 (mt) REVERT: A 1396 MET cc_start: 0.7803 (mmt) cc_final: 0.7536 (mmt) REVERT: A 1404 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7767 (mt-10) REVERT: G 577 MET cc_start: 0.5386 (tpt) cc_final: 0.5015 (tpt) outliers start: 22 outliers final: 8 residues processed: 310 average time/residue: 0.2770 time to fit residues: 119.7650 Evaluate side-chains 301 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 292 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 131 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 ASN E 570 HIS G 522 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118548 restraints weight = 17990.549| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.07 r_work: 0.3392 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12830 Z= 0.152 Angle : 0.523 8.367 17333 Z= 0.269 Chirality : 0.042 0.202 1996 Planarity : 0.004 0.048 2203 Dihedral : 3.880 17.240 1706 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 2.28 % Allowed : 12.21 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.68 (0.22), residues: 1564 helix: 2.42 (0.17), residues: 922 sheet: 0.03 (0.51), residues: 104 loop : -1.05 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.005 0.001 HIS A 792 PHE 0.019 0.001 PHE A 965 TYR 0.021 0.001 TYR A 389 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05035 ( 738) hydrogen bonds : angle 3.96269 ( 2130) metal coordination : bond 0.00954 ( 6) metal coordination : angle 4.05448 ( 2) covalent geometry : bond 0.00353 (12824) covalent geometry : angle 0.52152 (17331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7965 (tp30) cc_final: 0.7737 (tp30) REVERT: A 134 ARG cc_start: 0.8325 (ttm-80) cc_final: 0.8084 (ttp80) REVERT: A 146 ILE cc_start: 0.8455 (mm) cc_final: 0.8203 (mt) REVERT: A 152 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7892 (ttm-80) REVERT: A 179 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: A 193 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7737 (mtt90) REVERT: A 195 ASP cc_start: 0.7555 (m-30) cc_final: 0.7270 (m-30) REVERT: A 273 ASP cc_start: 0.8213 (m-30) cc_final: 0.7658 (m-30) REVERT: A 283 ILE cc_start: 0.8298 (tp) cc_final: 0.8043 (tt) REVERT: A 355 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 387 LEU cc_start: 0.8610 (mt) cc_final: 0.8259 (mt) REVERT: A 441 ASP cc_start: 0.7983 (t0) cc_final: 0.7665 (t0) REVERT: A 520 MET cc_start: 0.7907 (mtt) cc_final: 0.7595 (mtm) REVERT: A 557 THR cc_start: 0.7640 (p) cc_final: 0.6812 (t) REVERT: A 578 TYR cc_start: 0.8266 (m-10) cc_final: 0.8033 (m-10) REVERT: A 865 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7926 (tpt170) REVERT: A 882 THR cc_start: 0.8158 (t) cc_final: 0.7732 (p) REVERT: A 1047 ASP cc_start: 0.7558 (p0) cc_final: 0.7212 (p0) REVERT: A 1093 PHE cc_start: 0.8780 (m-80) cc_final: 0.8504 (m-80) REVERT: A 1133 GLU cc_start: 0.7737 (tp30) cc_final: 0.7368 (tp30) REVERT: A 1372 ILE cc_start: 0.8803 (mm) cc_final: 0.8531 (mt) REVERT: G 577 MET cc_start: 0.5347 (tpt) cc_final: 0.4973 (tpt) outliers start: 32 outliers final: 16 residues processed: 309 average time/residue: 0.2825 time to fit residues: 122.3591 Evaluate side-chains 306 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 289 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain G residue 531 MET Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1376 ASN F 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116124 restraints weight = 18007.747| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.07 r_work: 0.3383 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12830 Z= 0.169 Angle : 0.529 8.566 17333 Z= 0.271 Chirality : 0.042 0.199 1996 Planarity : 0.004 0.049 2203 Dihedral : 3.877 17.547 1706 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.06 % Rotamer: Outliers : 2.36 % Allowed : 12.56 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.68 (0.22), residues: 1564 helix: 2.41 (0.17), residues: 927 sheet: 0.02 (0.51), residues: 104 loop : -1.08 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS A 792 PHE 0.021 0.002 PHE A 965 TYR 0.014 0.001 TYR A 523 ARG 0.002 0.000 ARG A 561 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 738) hydrogen bonds : angle 3.93727 ( 2130) metal coordination : bond 0.00947 ( 6) metal coordination : angle 3.83665 ( 2) covalent geometry : bond 0.00399 (12824) covalent geometry : angle 0.52708 (17331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 296 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7954 (tp30) cc_final: 0.7709 (tp30) REVERT: A 146 ILE cc_start: 0.8464 (mm) cc_final: 0.8223 (mt) REVERT: A 152 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: A 179 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 193 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7703 (mtt90) REVERT: A 195 ASP cc_start: 0.7594 (m-30) cc_final: 0.7311 (m-30) REVERT: A 273 ASP cc_start: 0.8206 (m-30) cc_final: 0.7645 (m-30) REVERT: A 283 ILE cc_start: 0.8302 (tp) cc_final: 0.8056 (tt) REVERT: A 355 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7844 (mm-30) REVERT: A 441 ASP cc_start: 0.8057 (t0) cc_final: 0.7814 (t0) REVERT: A 557 THR cc_start: 0.7620 (p) cc_final: 0.6798 (t) REVERT: A 578 TYR cc_start: 0.8277 (m-10) cc_final: 0.8031 (m-10) REVERT: A 723 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7568 (mm) REVERT: A 882 THR cc_start: 0.8172 (t) cc_final: 0.7746 (p) REVERT: A 1047 ASP cc_start: 0.7553 (p0) cc_final: 0.7202 (p0) REVERT: A 1073 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8125 (mmtm) REVERT: A 1093 PHE cc_start: 0.8784 (m-80) cc_final: 0.8528 (m-80) REVERT: A 1133 GLU cc_start: 0.7750 (tp30) cc_final: 0.7342 (tp30) REVERT: A 1203 MET cc_start: 0.7996 (mtm) cc_final: 0.7747 (mtm) REVERT: A 1372 ILE cc_start: 0.8801 (mm) cc_final: 0.8545 (mt) REVERT: E 531 MET cc_start: 0.6047 (mpp) cc_final: 0.5819 (mpp) REVERT: G 577 MET cc_start: 0.5408 (tpt) cc_final: 0.5009 (tpt) outliers start: 33 outliers final: 19 residues processed: 312 average time/residue: 0.2739 time to fit residues: 119.6063 Evaluate side-chains 313 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 292 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 85 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 792 HIS A 858 GLN A1376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.139473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117188 restraints weight = 18181.681| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.08 r_work: 0.3393 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12830 Z= 0.147 Angle : 0.525 8.775 17333 Z= 0.268 Chirality : 0.041 0.163 1996 Planarity : 0.004 0.049 2203 Dihedral : 3.818 17.341 1706 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 2.14 % Allowed : 13.63 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.81 (0.22), residues: 1564 helix: 2.54 (0.17), residues: 923 sheet: 0.07 (0.51), residues: 104 loop : -1.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1248 HIS 0.006 0.001 HIS A 875 PHE 0.020 0.001 PHE A 965 TYR 0.013 0.001 TYR A 523 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 738) hydrogen bonds : angle 3.85553 ( 2130) metal coordination : bond 0.01002 ( 6) metal coordination : angle 3.81355 ( 2) covalent geometry : bond 0.00342 (12824) covalent geometry : angle 0.52348 (17331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 290 time to evaluate : 2.234 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7946 (tp30) cc_final: 0.7705 (tp30) REVERT: A 146 ILE cc_start: 0.8444 (mm) cc_final: 0.8198 (mt) REVERT: A 152 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7910 (ttm-80) REVERT: A 179 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: A 193 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7658 (mtt90) REVERT: A 195 ASP cc_start: 0.7571 (m-30) cc_final: 0.7288 (m-30) REVERT: A 240 ASP cc_start: 0.7555 (m-30) cc_final: 0.7270 (m-30) REVERT: A 273 ASP cc_start: 0.8222 (m-30) cc_final: 0.7656 (m-30) REVERT: A 283 ILE cc_start: 0.8271 (tp) cc_final: 0.8039 (tt) REVERT: A 355 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 387 LEU cc_start: 0.8638 (mt) cc_final: 0.8329 (mt) REVERT: A 441 ASP cc_start: 0.8080 (t0) cc_final: 0.7795 (t0) REVERT: A 774 ASN cc_start: 0.8245 (t0) cc_final: 0.7972 (t0) REVERT: A 882 THR cc_start: 0.8159 (t) cc_final: 0.7758 (p) REVERT: A 1047 ASP cc_start: 0.7540 (p0) cc_final: 0.7184 (p0) REVERT: A 1093 PHE cc_start: 0.8771 (m-80) cc_final: 0.8516 (m-80) REVERT: A 1133 GLU cc_start: 0.7733 (tp30) cc_final: 0.7234 (tp30) REVERT: A 1203 MET cc_start: 0.7963 (mtm) cc_final: 0.7713 (mtm) REVERT: A 1372 ILE cc_start: 0.8801 (mm) cc_final: 0.8547 (mt) REVERT: G 577 MET cc_start: 0.5346 (tpt) cc_final: 0.4950 (tpt) outliers start: 30 outliers final: 20 residues processed: 305 average time/residue: 0.4207 time to fit residues: 181.2488 Evaluate side-chains 309 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 288 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 151 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118539 restraints weight = 17992.406| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.08 r_work: 0.3393 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12830 Z= 0.154 Angle : 0.528 9.043 17333 Z= 0.270 Chirality : 0.041 0.166 1996 Planarity : 0.004 0.048 2203 Dihedral : 3.813 17.534 1706 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % Rotamer: Outliers : 2.07 % Allowed : 14.06 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.82 (0.22), residues: 1564 helix: 2.57 (0.17), residues: 923 sheet: 0.02 (0.50), residues: 104 loop : -1.07 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS A 875 PHE 0.020 0.001 PHE A 914 TYR 0.013 0.001 TYR A 523 ARG 0.004 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04785 ( 738) hydrogen bonds : angle 3.84918 ( 2130) metal coordination : bond 0.00923 ( 6) metal coordination : angle 3.75846 ( 2) covalent geometry : bond 0.00362 (12824) covalent geometry : angle 0.52691 (17331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 1.294 Fit side-chains REVERT: A 14 GLU cc_start: 0.7928 (tp30) cc_final: 0.7688 (tp30) REVERT: A 107 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6893 (mm) REVERT: A 146 ILE cc_start: 0.8456 (mm) cc_final: 0.8214 (mt) REVERT: A 152 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: A 179 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: A 193 ARG cc_start: 0.7904 (mtt90) cc_final: 0.7657 (mtt90) REVERT: A 195 ASP cc_start: 0.7583 (m-30) cc_final: 0.7308 (m-30) REVERT: A 240 ASP cc_start: 0.7581 (m-30) cc_final: 0.7282 (m-30) REVERT: A 273 ASP cc_start: 0.8226 (m-30) cc_final: 0.7639 (m-30) REVERT: A 283 ILE cc_start: 0.8268 (tp) cc_final: 0.8049 (tt) REVERT: A 355 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 387 LEU cc_start: 0.8650 (mt) cc_final: 0.8319 (mp) REVERT: A 441 ASP cc_start: 0.8079 (t0) cc_final: 0.7771 (t0) REVERT: A 774 ASN cc_start: 0.8282 (t0) cc_final: 0.8037 (t0) REVERT: A 882 THR cc_start: 0.8161 (t) cc_final: 0.7769 (p) REVERT: A 1047 ASP cc_start: 0.7532 (p0) cc_final: 0.7176 (p0) REVERT: A 1093 PHE cc_start: 0.8751 (m-80) cc_final: 0.8510 (m-80) REVERT: A 1133 GLU cc_start: 0.7746 (tp30) cc_final: 0.7238 (tp30) REVERT: A 1203 MET cc_start: 0.7959 (mtm) cc_final: 0.7700 (mtm) REVERT: A 1295 ARG cc_start: 0.7188 (mtm110) cc_final: 0.6881 (mtm180) REVERT: A 1372 ILE cc_start: 0.8807 (mm) cc_final: 0.8566 (mt) REVERT: G 577 MET cc_start: 0.5348 (tpt) cc_final: 0.4928 (tpt) outliers start: 29 outliers final: 21 residues processed: 302 average time/residue: 0.2776 time to fit residues: 117.3614 Evaluate side-chains 307 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 284 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 555 ARG Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 564 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 858 GLN A1376 ASN F 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118011 restraints weight = 18143.049| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.08 r_work: 0.3373 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12830 Z= 0.205 Angle : 0.559 8.632 17333 Z= 0.287 Chirality : 0.043 0.196 1996 Planarity : 0.004 0.047 2203 Dihedral : 3.935 18.871 1706 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 2.43 % Allowed : 14.13 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.71 (0.22), residues: 1564 helix: 2.46 (0.17), residues: 926 sheet: -0.03 (0.53), residues: 95 loop : -1.06 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS A 200 PHE 0.026 0.002 PHE A 914 TYR 0.015 0.002 TYR A 523 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05354 ( 738) hydrogen bonds : angle 3.93598 ( 2130) metal coordination : bond 0.01004 ( 6) metal coordination : angle 3.85552 ( 2) covalent geometry : bond 0.00491 (12824) covalent geometry : angle 0.55782 (17331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 294 time to evaluate : 1.297 Fit side-chains REVERT: A 14 GLU cc_start: 0.7940 (tp30) cc_final: 0.7695 (tp30) REVERT: A 146 ILE cc_start: 0.8481 (mm) cc_final: 0.8248 (mt) REVERT: A 152 ARG cc_start: 0.8257 (ttm-80) cc_final: 0.7936 (ttm-80) REVERT: A 179 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: A 193 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7692 (mtt90) REVERT: A 195 ASP cc_start: 0.7611 (m-30) cc_final: 0.7346 (m-30) REVERT: A 230 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8562 (mt) REVERT: A 240 ASP cc_start: 0.7640 (m-30) cc_final: 0.7316 (m-30) REVERT: A 273 ASP cc_start: 0.8222 (m-30) cc_final: 0.7631 (m-30) REVERT: A 283 ILE cc_start: 0.8314 (tp) cc_final: 0.8088 (tt) REVERT: A 355 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7824 (mm-30) REVERT: A 387 LEU cc_start: 0.8585 (mt) cc_final: 0.8298 (mt) REVERT: A 441 ASP cc_start: 0.8030 (t0) cc_final: 0.7724 (t0) REVERT: A 557 THR cc_start: 0.7647 (p) cc_final: 0.6884 (t) REVERT: A 774 ASN cc_start: 0.8274 (t0) cc_final: 0.8025 (t0) REVERT: A 882 THR cc_start: 0.8148 (t) cc_final: 0.7625 (m) REVERT: A 903 SER cc_start: 0.8820 (p) cc_final: 0.8409 (m) REVERT: A 965 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: A 1047 ASP cc_start: 0.7533 (p0) cc_final: 0.7161 (p0) REVERT: A 1093 PHE cc_start: 0.8769 (m-80) cc_final: 0.8551 (m-80) REVERT: A 1133 GLU cc_start: 0.7755 (tp30) cc_final: 0.7237 (tp30) REVERT: A 1203 MET cc_start: 0.8009 (mtm) cc_final: 0.7767 (mtm) REVERT: A 1225 MET cc_start: 0.8318 (mtt) cc_final: 0.8114 (mtt) REVERT: A 1295 ARG cc_start: 0.7266 (mtm110) cc_final: 0.6947 (mtm180) REVERT: A 1372 ILE cc_start: 0.8831 (mm) cc_final: 0.8605 (mt) REVERT: E 531 MET cc_start: 0.6096 (mpp) cc_final: 0.5748 (mpp) REVERT: G 577 MET cc_start: 0.5400 (tpt) cc_final: 0.4976 (tpt) outliers start: 34 outliers final: 24 residues processed: 315 average time/residue: 0.2854 time to fit residues: 125.0158 Evaluate side-chains 320 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 555 ARG Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 576 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 95 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN A 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118869 restraints weight = 18067.169| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.08 r_work: 0.3387 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12830 Z= 0.163 Angle : 0.546 8.129 17333 Z= 0.278 Chirality : 0.042 0.168 1996 Planarity : 0.004 0.046 2203 Dihedral : 3.888 18.578 1706 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.81 % Favored : 97.12 % Rotamer: Outliers : 2.00 % Allowed : 14.63 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.80 (0.22), residues: 1564 helix: 2.53 (0.17), residues: 926 sheet: -0.01 (0.50), residues: 104 loop : -1.04 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1248 HIS 0.006 0.001 HIS A 875 PHE 0.019 0.001 PHE A 914 TYR 0.013 0.001 TYR A 523 ARG 0.003 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 738) hydrogen bonds : angle 3.88178 ( 2130) metal coordination : bond 0.00973 ( 6) metal coordination : angle 3.91254 ( 2) covalent geometry : bond 0.00384 (12824) covalent geometry : angle 0.54449 (17331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 291 time to evaluate : 1.566 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7937 (tp30) cc_final: 0.7691 (tp30) REVERT: A 146 ILE cc_start: 0.8461 (mm) cc_final: 0.8224 (mt) REVERT: A 152 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7932 (ttm-80) REVERT: A 179 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 193 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7670 (mtt90) REVERT: A 195 ASP cc_start: 0.7593 (m-30) cc_final: 0.7331 (m-30) REVERT: A 240 ASP cc_start: 0.7625 (m-30) cc_final: 0.7320 (m-30) REVERT: A 273 ASP cc_start: 0.8212 (m-30) cc_final: 0.7627 (m-30) REVERT: A 283 ILE cc_start: 0.8284 (tp) cc_final: 0.8059 (tt) REVERT: A 291 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: A 355 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 387 LEU cc_start: 0.8588 (mt) cc_final: 0.8297 (mt) REVERT: A 441 ASP cc_start: 0.8036 (t0) cc_final: 0.7722 (t0) REVERT: A 557 THR cc_start: 0.7628 (p) cc_final: 0.6843 (t) REVERT: A 865 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7948 (tpt170) REVERT: A 882 THR cc_start: 0.8142 (t) cc_final: 0.7625 (m) REVERT: A 903 SER cc_start: 0.8802 (p) cc_final: 0.8429 (m) REVERT: A 965 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7565 (m-80) REVERT: A 1047 ASP cc_start: 0.7529 (p0) cc_final: 0.7175 (p0) REVERT: A 1093 PHE cc_start: 0.8751 (m-80) cc_final: 0.8520 (m-80) REVERT: A 1133 GLU cc_start: 0.7714 (tp30) cc_final: 0.7197 (tp30) REVERT: A 1203 MET cc_start: 0.7981 (mtm) cc_final: 0.7722 (mtm) REVERT: A 1295 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6944 (mtm180) REVERT: A 1310 ASP cc_start: 0.7924 (t0) cc_final: 0.7702 (t0) REVERT: A 1372 ILE cc_start: 0.8815 (mm) cc_final: 0.8570 (mt) REVERT: E 531 MET cc_start: 0.6111 (mpp) cc_final: 0.5744 (mpp) REVERT: G 577 MET cc_start: 0.5353 (tpt) cc_final: 0.4936 (tpt) outliers start: 28 outliers final: 23 residues processed: 307 average time/residue: 0.3355 time to fit residues: 142.5989 Evaluate side-chains 317 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 555 ARG Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 576 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 16 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 0.0070 chunk 134 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 858 GLN A1376 ASN F 570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.120526 restraints weight = 17960.616| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.08 r_work: 0.3417 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12830 Z= 0.121 Angle : 0.525 8.022 17333 Z= 0.267 Chirality : 0.040 0.156 1996 Planarity : 0.003 0.045 2203 Dihedral : 3.755 17.550 1706 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 1.28 % Allowed : 15.56 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.97 (0.22), residues: 1564 helix: 2.70 (0.17), residues: 923 sheet: 0.04 (0.51), residues: 104 loop : -1.03 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1248 HIS 0.005 0.001 HIS A 875 PHE 0.016 0.001 PHE A 914 TYR 0.011 0.001 TYR A 523 ARG 0.004 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 738) hydrogen bonds : angle 3.75195 ( 2130) metal coordination : bond 0.00967 ( 6) metal coordination : angle 3.94457 ( 2) covalent geometry : bond 0.00276 (12824) covalent geometry : angle 0.52315 (17331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 288 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7939 (tp30) cc_final: 0.7702 (tp30) REVERT: A 146 ILE cc_start: 0.8433 (mm) cc_final: 0.8179 (mt) REVERT: A 152 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7917 (ttm-80) REVERT: A 179 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: A 193 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7644 (mtt90) REVERT: A 195 ASP cc_start: 0.7557 (m-30) cc_final: 0.7307 (m-30) REVERT: A 240 ASP cc_start: 0.7624 (m-30) cc_final: 0.7305 (m-30) REVERT: A 273 ASP cc_start: 0.8239 (m-30) cc_final: 0.7645 (m-30) REVERT: A 355 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 387 LEU cc_start: 0.8581 (mt) cc_final: 0.8264 (mt) REVERT: A 441 ASP cc_start: 0.7981 (t0) cc_final: 0.7686 (t0) REVERT: A 445 LYS cc_start: 0.8479 (mtpt) cc_final: 0.8274 (mttt) REVERT: A 882 THR cc_start: 0.8129 (t) cc_final: 0.7758 (p) REVERT: A 965 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: A 1047 ASP cc_start: 0.7528 (p0) cc_final: 0.7169 (p0) REVERT: A 1133 GLU cc_start: 0.7711 (tp30) cc_final: 0.7194 (tp30) REVERT: A 1203 MET cc_start: 0.7953 (mtm) cc_final: 0.7696 (mtm) REVERT: A 1225 MET cc_start: 0.8265 (mtt) cc_final: 0.8030 (mtt) REVERT: A 1295 ARG cc_start: 0.7263 (mtm110) cc_final: 0.6958 (mtm180) REVERT: A 1372 ILE cc_start: 0.8784 (mm) cc_final: 0.8538 (mt) REVERT: E 531 MET cc_start: 0.6193 (mpp) cc_final: 0.5838 (mpp) REVERT: G 577 MET cc_start: 0.5386 (tpt) cc_final: 0.5015 (tpt) outliers start: 18 outliers final: 15 residues processed: 295 average time/residue: 0.2972 time to fit residues: 122.3472 Evaluate side-chains 298 residues out of total 1431 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 281 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1068 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain F residue 555 ARG Chi-restraints excluded: chain G residue 576 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 56 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1376 ASN F 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118121 restraints weight = 18047.902| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.07 r_work: 0.3376 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12830 Z= 0.215 Angle : 0.577 7.726 17333 Z= 0.296 Chirality : 0.044 0.162 1996 Planarity : 0.004 0.047 2203 Dihedral : 3.957 19.634 1706 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 1.78 % Allowed : 15.06 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1.78 (0.22), residues: 1564 helix: 2.55 (0.17), residues: 920 sheet: 0.03 (0.54), residues: 95 loop : -1.07 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1248 HIS 0.007 0.001 HIS A 875 PHE 0.025 0.002 PHE A 914 TYR 0.015 0.002 TYR A1246 ARG 0.004 0.000 ARG A1161 Details of bonding type rmsd hydrogen bonds : bond 0.05320 ( 738) hydrogen bonds : angle 3.90686 ( 2130) metal coordination : bond 0.01034 ( 6) metal coordination : angle 3.81614 ( 2) covalent geometry : bond 0.00518 (12824) covalent geometry : angle 0.57578 (17331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8521.87 seconds wall clock time: 150 minutes 18.79 seconds (9018.79 seconds total)