Starting phenix.real_space_refine (version: dev) on Tue Feb 21 11:25:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhh_24461/02_2023/7rhh_24461_updated.pdb" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 998": "OE1" <-> "OE2" Residue "C ARG 220": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "D GLU 490": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14717 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3561 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 14, 'TRANS': 419} Chain breaks: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.72, per 1000 atoms: 0.59 Number of scatterers: 14717 At special positions: 0 Unit cell: (98.857, 100.491, 120.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 4 15.00 O 2633 8.00 N 2396 7.00 C 9602 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 8 sheets defined 59.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 163 through 188 removed outlier: 3.630A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.130A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.889A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 263 removed outlier: 3.838A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 291 removed outlier: 3.593A pdb=" N LEU A 272 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 387 Processing helix chain 'A' and resid 389 through 403 Processing helix chain 'A' and resid 405 through 423 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.640A pdb=" N ASN A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 476 Processing helix chain 'A' and resid 487 through 494 removed outlier: 4.035A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.830A pdb=" N THR A 593 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 594 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 602 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU A 603 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET A 604 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 679 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 707 Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing helix chain 'B' and resid 725 through 734 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 759 through 767 removed outlier: 3.586A pdb=" N ARG B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 763 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 770 through 782 Processing helix chain 'B' and resid 787 through 816 Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 855 through 886 removed outlier: 3.722A pdb=" N PHE B 870 " --> pdb=" O PHE B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 927 Processing helix chain 'B' and resid 934 through 939 removed outlier: 3.810A pdb=" N GLN B 939 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 959 removed outlier: 5.645A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 removed outlier: 3.804A pdb=" N LYS B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 977 " --> pdb=" O ASP B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1063 through 1066 No H-bonds generated for 'chain 'B' and resid 1063 through 1066' Processing helix chain 'B' and resid 1070 through 1083 Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 3.546A pdb=" N THR C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 220 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 257 through 263 removed outlier: 3.776A pdb=" N LEU C 263 " --> pdb=" O TYR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.452A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 286 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 288 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 290 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 360 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 5.287A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 471 through 474 No H-bonds generated for 'chain 'C' and resid 471 through 474' Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.979A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.993A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 removed outlier: 3.594A pdb=" N MET C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 188 removed outlier: 3.541A pdb=" N CYS D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 3.673A pdb=" N VAL D 183 " --> pdb=" O ASN D 179 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 4.310A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 271 removed outlier: 3.538A pdb=" N ARG D 271 " --> pdb=" O PRO D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 268 through 271' Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 278 through 291 Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 401 removed outlier: 3.730A pdb=" N PHE D 389 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 3.797A pdb=" N LYS D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.867A pdb=" N LYS D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 471 through 475' Processing helix chain 'D' and resid 487 through 491 removed outlier: 3.880A pdb=" N LEU D 491 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 585 removed outlier: 3.601A pdb=" N MET D 582 " --> pdb=" O LYS D 578 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 603 Processing sheet with id= A, first strand: chain 'A' and resid 496 through 500 Processing sheet with id= B, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.706A pdb=" N ASP A 504 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A 565 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 527 " --> pdb=" O ASN A 564 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS A 523 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.809A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.355A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 987 through 990 removed outlier: 3.663A pdb=" N ASP B 987 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B1046 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 496 through 500 removed outlier: 6.478A pdb=" N PHE C 574 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE C 519 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C 576 " --> pdb=" O TYR C 517 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR C 517 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 495 through 500 removed outlier: 3.616A pdb=" N GLN D 496 " --> pdb=" O CYS D 575 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 524 through 527 removed outlier: 4.731A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 6.97 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: 4538 1.34 - 1.46: 3283 1.46 - 1.58: 7109 1.58 - 1.70: 8 1.70 - 1.81: 138 Bond restraints: 15076 Sorted by residual: bond pdb=" C3' PCG C 701 " pdb=" C4' PCG C 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C3' PCG A 701 " pdb=" C4' PCG A 701 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG B1301 " pdb=" C4' PCG B1301 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C3' PCG D 701 " pdb=" C4' PCG D 701 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C2' PCG D 701 " pdb=" C3' PCG D 701 " ideal model delta sigma weight residual 1.200 1.504 -0.304 2.00e-02 2.50e+03 2.31e+02 ... (remaining 15071 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.34: 251 105.34 - 112.58: 7734 112.58 - 119.83: 5194 119.83 - 127.07: 7109 127.07 - 134.32: 158 Bond angle restraints: 20446 Sorted by residual: angle pdb=" N ILE C 363 " pdb=" CA ILE C 363 " pdb=" C ILE C 363 " ideal model delta sigma weight residual 113.53 108.67 4.86 9.80e-01 1.04e+00 2.46e+01 angle pdb=" C ASP B 649 " pdb=" N PRO B 650 " pdb=" CA PRO B 650 " ideal model delta sigma weight residual 119.05 124.16 -5.11 1.11e+00 8.12e-01 2.12e+01 angle pdb=" N PHE B 709 " pdb=" CA PHE B 709 " pdb=" C PHE B 709 " ideal model delta sigma weight residual 112.04 117.74 -5.70 1.44e+00 4.82e-01 1.57e+01 angle pdb=" N ASN D 468 " pdb=" CA ASN D 468 " pdb=" C ASN D 468 " ideal model delta sigma weight residual 111.28 115.56 -4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N TYR B 656 " pdb=" CA TYR B 656 " pdb=" C TYR B 656 " ideal model delta sigma weight residual 111.36 107.13 4.23 1.09e+00 8.42e-01 1.50e+01 ... (remaining 20441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 8103 18.19 - 36.38: 692 36.38 - 54.57: 80 54.57 - 72.76: 8 72.76 - 90.95: 9 Dihedral angle restraints: 8892 sinusoidal: 3628 harmonic: 5264 Sorted by residual: dihedral pdb=" CA ASP C 572 " pdb=" CB ASP C 572 " pdb=" CG ASP C 572 " pdb=" OD1 ASP C 572 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASN A 314 " pdb=" CB ASN A 314 " pdb=" CG ASN A 314 " pdb=" OD1 ASN A 314 " ideal model delta sinusoidal sigma weight residual -90.00 -163.21 73.21 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB GLU B 998 " pdb=" CG GLU B 998 " pdb=" CD GLU B 998 " pdb=" OE1 GLU B 998 " ideal model delta sinusoidal sigma weight residual 0.00 90.95 -90.95 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 8889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2179 0.094 - 0.188: 95 0.188 - 0.282: 0 0.282 - 0.376: 3 0.376 - 0.470: 5 Chirality restraints: 2282 Sorted by residual: chirality pdb=" C3' PCG C 701 " pdb=" C2' PCG C 701 " pdb=" C4' PCG C 701 " pdb=" O3' PCG C 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.57 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C3' PCG A 701 " pdb=" C2' PCG A 701 " pdb=" C4' PCG A 701 " pdb=" O3' PCG A 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" C3' PCG D 701 " pdb=" C2' PCG D 701 " pdb=" C4' PCG D 701 " pdb=" O3' PCG D 701 " both_signs ideal model delta sigma weight residual False -2.10 -2.56 0.46 2.00e-01 2.50e+01 5.26e+00 ... (remaining 2279 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO B 764 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 496 " -0.046 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO A 497 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 497 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 497 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 588 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO A 589 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.027 5.00e-02 4.00e+02 ... (remaining 2515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2530 2.76 - 3.30: 14630 3.30 - 3.83: 25822 3.83 - 4.37: 29942 4.37 - 4.90: 50850 Nonbonded interactions: 123774 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.231 2.440 nonbonded pdb=" O PHE B 703 " pdb=" OG1 THR B 707 " model vdw 2.262 2.440 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.263 2.440 nonbonded pdb=" OG SER B 647 " pdb=" OE1 GLN B 714 " model vdw 2.274 2.440 nonbonded pdb=" OD1 ASN B 776 " pdb=" OH TYR B 789 " model vdw 2.292 2.440 ... (remaining 123769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 82 5.16 5 C 9602 2.51 5 N 2396 2.21 5 O 2633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.400 Check model and map are aligned: 0.210 Process input model: 39.860 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.012 0.314 15076 Z= 0.800 Angle : 0.655 10.509 20446 Z= 0.327 Chirality : 0.050 0.470 2282 Planarity : 0.005 0.069 2518 Dihedral : 13.018 90.946 5520 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1774 helix: 0.89 (0.15), residues: 1098 sheet: 0.25 (0.58), residues: 62 loop : -0.11 (0.25), residues: 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.764 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2350 time to fit residues: 64.1825 Evaluate side-chains 135 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN B1040 ASN D 468 ASN D 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15076 Z= 0.143 Angle : 0.437 5.378 20446 Z= 0.228 Chirality : 0.037 0.169 2282 Planarity : 0.004 0.059 2518 Dihedral : 3.594 15.709 1991 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1774 helix: 1.46 (0.15), residues: 1109 sheet: 0.37 (0.57), residues: 62 loop : 0.03 (0.26), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.846 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 153 average time/residue: 0.2231 time to fit residues: 54.9565 Evaluate side-chains 144 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1338 time to fit residues: 4.7558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1053 ASN D 601 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 15076 Z= 0.280 Angle : 0.491 6.309 20446 Z= 0.257 Chirality : 0.040 0.166 2282 Planarity : 0.004 0.055 2518 Dihedral : 3.687 16.827 1991 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1774 helix: 1.38 (0.15), residues: 1114 sheet: 0.10 (0.63), residues: 53 loop : -0.07 (0.26), residues: 607 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.881 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 145 average time/residue: 0.2385 time to fit residues: 56.2378 Evaluate side-chains 140 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1346 time to fit residues: 5.6364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 731 ASN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 15076 Z= 0.306 Angle : 0.496 7.061 20446 Z= 0.260 Chirality : 0.040 0.173 2282 Planarity : 0.004 0.054 2518 Dihedral : 3.788 17.401 1991 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1774 helix: 1.29 (0.15), residues: 1114 sheet: 0.25 (0.64), residues: 59 loop : -0.15 (0.26), residues: 601 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.899 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 141 average time/residue: 0.2432 time to fit residues: 54.9180 Evaluate side-chains 132 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 125 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1394 time to fit residues: 4.4051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 411 GLN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15076 Z= 0.144 Angle : 0.428 7.113 20446 Z= 0.225 Chirality : 0.037 0.197 2282 Planarity : 0.003 0.053 2518 Dihedral : 3.591 16.656 1991 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1774 helix: 1.63 (0.15), residues: 1101 sheet: 0.15 (0.66), residues: 60 loop : -0.15 (0.26), residues: 613 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.809 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 155 average time/residue: 0.2251 time to fit residues: 56.1951 Evaluate side-chains 137 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1459 time to fit residues: 4.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0060 chunk 34 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 166 optimal weight: 0.0970 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15076 Z= 0.122 Angle : 0.418 8.414 20446 Z= 0.217 Chirality : 0.037 0.166 2282 Planarity : 0.003 0.050 2518 Dihedral : 3.474 16.809 1991 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.20), residues: 1774 helix: 1.85 (0.16), residues: 1093 sheet: 0.14 (0.66), residues: 60 loop : -0.08 (0.26), residues: 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.801 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 149 average time/residue: 0.2373 time to fit residues: 56.2159 Evaluate side-chains 135 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1319 time to fit residues: 4.4868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 15076 Z= 0.139 Angle : 0.422 6.424 20446 Z= 0.220 Chirality : 0.037 0.153 2282 Planarity : 0.003 0.047 2518 Dihedral : 3.428 16.112 1991 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1774 helix: 1.90 (0.16), residues: 1094 sheet: 0.13 (0.66), residues: 60 loop : -0.06 (0.26), residues: 620 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.746 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.2350 time to fit residues: 53.4975 Evaluate side-chains 135 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.949 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1371 time to fit residues: 3.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 314 ASN ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 601 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15076 Z= 0.181 Angle : 0.441 6.940 20446 Z= 0.229 Chirality : 0.038 0.149 2282 Planarity : 0.003 0.046 2518 Dihedral : 3.462 15.992 1991 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1774 helix: 1.87 (0.16), residues: 1095 sheet: 0.05 (0.65), residues: 60 loop : -0.10 (0.26), residues: 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.827 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 135 average time/residue: 0.2358 time to fit residues: 51.3502 Evaluate side-chains 133 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1386 time to fit residues: 4.0608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 551 ASN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 HIS C 551 ASN D 601 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 15076 Z= 0.362 Angle : 0.541 7.300 20446 Z= 0.282 Chirality : 0.041 0.168 2282 Planarity : 0.004 0.047 2518 Dihedral : 3.781 16.378 1991 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1774 helix: 1.41 (0.15), residues: 1105 sheet: -0.05 (0.67), residues: 60 loop : -0.30 (0.26), residues: 609 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.900 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 133 average time/residue: 0.2332 time to fit residues: 50.0508 Evaluate side-chains 131 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1414 time to fit residues: 4.6527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 564 ASN ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15076 Z= 0.146 Angle : 0.452 9.045 20446 Z= 0.235 Chirality : 0.038 0.150 2282 Planarity : 0.003 0.047 2518 Dihedral : 3.597 15.716 1991 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1774 helix: 1.68 (0.15), residues: 1099 sheet: -0.08 (0.66), residues: 60 loop : -0.19 (0.26), residues: 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.794 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.2377 time to fit residues: 49.1719 Evaluate side-chains 125 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1401 time to fit residues: 2.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087878 restraints weight = 25097.352| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.46 r_work: 0.3034 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15076 Z= 0.147 Angle : 0.442 7.124 20446 Z= 0.230 Chirality : 0.037 0.145 2282 Planarity : 0.003 0.046 2518 Dihedral : 3.523 15.916 1991 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1774 helix: 1.77 (0.16), residues: 1099 sheet: -0.14 (0.66), residues: 60 loop : -0.15 (0.26), residues: 615 =============================================================================== Job complete usr+sys time: 2567.05 seconds wall clock time: 47 minutes 52.18 seconds (2872.18 seconds total)