Starting phenix.real_space_refine (version: dev) on Tue Apr 5 06:31:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fd9_31537/04_2022/7fd9_31537_updated.pdb" } resolution = 4.0 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 220": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 357": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 11476 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 5698 Classifications: {'peptide': 767} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 32, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.73, per 1000 atoms: 0.59 Number of scatterers: 11476 At special positions: 0 Unit cell: (79.21, 112.14, 178.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 2066 8.00 N 1916 7.00 C 7384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.05 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.04 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.04 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.05 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.04 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.04 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 14 sheets defined 45.5% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.419A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.818A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.405A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.509A pdb=" N GLN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 434 through 442 Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 578 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 617 through 635 Processing helix chain 'A' and resid 641 through 672 removed outlier: 3.914A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 693 through 714 removed outlier: 3.573A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 761 Proline residue: A 743 - end of helix removed outlier: 3.985A pdb=" N LYS A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 769 No H-bonds generated for 'chain 'A' and resid 766 through 769' Processing helix chain 'A' and resid 771 through 793 Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 798 through 817 Processing helix chain 'A' and resid 819 through 825 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 102 through 119 Processing helix chain 'B' and resid 152 through 165 removed outlier: 4.419A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.817A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.405A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.509A pdb=" N GLN B 360 " --> pdb=" O GLN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 578 through 603 Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 617 through 635 Processing helix chain 'B' and resid 641 through 672 removed outlier: 3.913A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 693 through 714 removed outlier: 3.573A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 761 Proline residue: B 743 - end of helix removed outlier: 3.986A pdb=" N LYS B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 769 No H-bonds generated for 'chain 'B' and resid 766 through 769' Processing helix chain 'B' and resid 771 through 793 Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 798 through 817 Processing helix chain 'B' and resid 819 through 825 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.392A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 38 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 146 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 40 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 245 through 248 removed outlier: 7.016A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.627A pdb=" N GLY A 485 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 469 through 472 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 558 Processing sheet with id= G, first strand: chain 'A' and resid 720 through 722 Processing sheet with id= H, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.393A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY B 38 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 146 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 40 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 245 through 248 removed outlier: 7.017A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.626A pdb=" N GLY B 485 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.838A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 469 through 472 Processing sheet with id= M, first strand: chain 'B' and resid 556 through 558 Processing sheet with id= N, first strand: chain 'B' and resid 720 through 722 532 hydrogen bonds defined for protein. 1464 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: 4.02 Time building geometry restraints manager: 4.67 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: 3604 1.34 - 1.47: 2964 1.47 - 1.59: 5018 1.59 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 11742 Sorted by residual: bond pdb=" CAN Z99 A 902 " pdb=" CAW Z99 A 902 " ideal model delta sigma weight residual 1.621 1.489 0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " ideal model delta sigma weight residual 1.621 1.489 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CAT Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAS Z99 A 902 " pdb=" OAP Z99 A 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CAT Z99 B 902 " pdb=" OAP Z99 B 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 11737 not shown) Histogram of bond angle deviations from ideal: 59.32 - 74.35: 6 74.35 - 89.38: 0 89.38 - 104.41: 213 104.41 - 119.43: 9429 119.43 - 134.46: 6356 Bond angle restraints: 16004 Sorted by residual: angle pdb=" CAN Z99 A 902 " pdb=" CAW Z99 A 902 " pdb=" CAV Z99 A 902 " ideal model delta sigma weight residual 107.34 130.06 -22.72 3.00e+00 1.11e-01 5.73e+01 angle pdb=" CAN Z99 B 902 " pdb=" CAW Z99 B 902 " pdb=" CAV Z99 B 902 " ideal model delta sigma weight residual 107.34 130.05 -22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAY Z99 B 902 " ideal model delta sigma weight residual 109.52 131.39 -21.87 3.00e+00 1.11e-01 5.31e+01 angle pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAY Z99 A 902 " ideal model delta sigma weight residual 109.52 131.35 -21.83 3.00e+00 1.11e-01 5.29e+01 angle pdb=" CAT Z99 A 902 " pdb=" CAV Z99 A 902 " pdb=" CAW Z99 A 902 " ideal model delta sigma weight residual 119.76 106.06 13.70 3.00e+00 1.11e-01 2.09e+01 ... (remaining 15999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.62: 6530 19.62 - 39.24: 364 39.24 - 58.86: 54 58.86 - 78.48: 6 78.48 - 98.10: 8 Dihedral angle restraints: 6962 sinusoidal: 2502 harmonic: 4460 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.80 78.80 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -164.77 78.77 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 155.70 -62.70 1 1.00e+01 1.00e-02 5.20e+01 ... (remaining 6959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.548: 1846 0.548 - 1.097: 0 1.097 - 1.645: 0 1.645 - 2.194: 0 2.194 - 2.742: 2 Chirality restraints: 1848 Sorted by residual: chirality pdb=" CAW Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAU Z99 B 902 " pdb=" CAV Z99 B 902 " both_signs ideal model delta sigma weight residual False 2.67 -0.07 2.74 2.00e-01 2.50e+01 1.88e+02 chirality pdb=" CAW Z99 A 902 " pdb=" CAN Z99 A 902 " pdb=" CAU Z99 A 902 " pdb=" CAV Z99 A 902 " both_signs ideal model delta sigma weight residual False 2.67 -0.06 2.74 2.00e-01 2.50e+01 1.87e+02 chirality pdb=" CAY Z99 B 902 " pdb=" CAN Z99 B 902 " pdb=" CAR Z99 B 902 " pdb=" CAZ Z99 B 902 " both_signs ideal model delta sigma weight residual False -2.77 -2.38 -0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 1845 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAG Z99 A 902 " 0.016 2.00e-02 2.50e+03 2.32e-02 1.08e+01 pdb=" CAI Z99 A 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 A 902 " 0.006 2.00e-02 2.50e+03 pdb=" CAM Z99 A 902 " -0.023 2.00e-02 2.50e+03 pdb=" CAT Z99 A 902 " 0.002 2.00e-02 2.50e+03 pdb=" CAV Z99 A 902 " -0.035 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.043 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAG Z99 B 902 " 0.016 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CAI Z99 B 902 " 0.008 2.00e-02 2.50e+03 pdb=" CAK Z99 B 902 " 0.005 2.00e-02 2.50e+03 pdb=" CAM Z99 B 902 " -0.022 2.00e-02 2.50e+03 pdb=" CAT Z99 B 902 " 0.003 2.00e-02 2.50e+03 pdb=" CAV Z99 B 902 " -0.034 2.00e-02 2.50e+03 pdb=" CAW Z99 B 902 " 0.042 2.00e-02 2.50e+03 pdb=" OAP Z99 B 902 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAF Z99 A 902 " 0.000 2.00e-02 2.50e+03 1.22e-02 3.00e+00 pdb=" CAH Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAJ Z99 A 902 " 0.000 2.00e-02 2.50e+03 pdb=" CAL Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" CAS Z99 A 902 " 0.007 2.00e-02 2.50e+03 pdb=" CAU Z99 A 902 " -0.030 2.00e-02 2.50e+03 pdb=" CAW Z99 A 902 " 0.011 2.00e-02 2.50e+03 pdb=" OAP Z99 A 902 " 0.001 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1891 2.79 - 3.32: 12126 3.32 - 3.85: 19164 3.85 - 4.37: 20848 4.37 - 4.90: 35974 Nonbonded interactions: 90003 Sorted by model distance: nonbonded pdb=" OE1 GLN A 198 " pdb=" OG SER A 304 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLN B 198 " pdb=" OG SER B 304 " model vdw 2.266 2.440 nonbonded pdb=" O SER A 116 " pdb=" OG SER A 119 " model vdw 2.288 2.440 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.288 2.440 nonbonded pdb=" NH2 ARG B 648 " pdb=" OD1 ASN B 734 " model vdw 2.320 2.520 ... (remaining 89998 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 'B' } 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 7384 2.51 5 N 1916 2.21 5 O 2066 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 group one per residue 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: 1.000 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: 6.510 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 32.800 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 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 : 0.007 0.132 11742 Z= 0.487 Angle : 1.288 22.718 16004 Z= 0.843 Chirality : 0.127 2.742 1848 Planarity : 0.003 0.023 2026 Dihedral : 12.169 98.101 4038 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.00 % 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: -0.84 (0.21), residues: 1522 helix: 0.96 (0.19), residues: 700 sheet: -0.60 (0.47), residues: 124 loop : -2.22 (0.21), residues: 698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1902 time to fit residues: 23.9511 Evaluate side-chains 60 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0970 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 11742 Z= 0.150 Angle : 0.549 9.944 16004 Z= 0.273 Chirality : 0.042 0.320 1848 Planarity : 0.003 0.026 2026 Dihedral : 7.397 100.418 1670 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.80 % 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: -0.42 (0.21), residues: 1522 helix: 1.26 (0.20), residues: 710 sheet: -0.44 (0.44), residues: 130 loop : -2.00 (0.22), residues: 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 68 average time/residue: 0.1848 time to fit residues: 20.6654 Evaluate side-chains 66 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0932 time to fit residues: 1.7870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 30.0000 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 40.0000 chunk 110 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11742 Z= 0.222 Angle : 0.538 8.446 16004 Z= 0.271 Chirality : 0.042 0.249 1848 Planarity : 0.003 0.026 2026 Dihedral : 7.339 99.973 1670 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 0.71 % 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: -0.35 (0.21), residues: 1522 helix: 1.38 (0.19), residues: 710 sheet: -0.83 (0.45), residues: 138 loop : -1.95 (0.22), residues: 674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 1.304 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 66 average time/residue: 0.1987 time to fit residues: 21.5981 Evaluate side-chains 60 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1320 time to fit residues: 2.0496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 0.1980 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 138 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 11742 Z= 0.416 Angle : 0.668 9.072 16004 Z= 0.337 Chirality : 0.044 0.254 1848 Planarity : 0.004 0.033 2026 Dihedral : 7.610 100.808 1670 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 1.77 % 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: -0.59 (0.21), residues: 1522 helix: 1.12 (0.19), residues: 708 sheet: -0.93 (0.44), residues: 140 loop : -1.99 (0.22), residues: 674 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 77 average time/residue: 0.1840 time to fit residues: 23.6866 Evaluate side-chains 67 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0995 time to fit residues: 2.9400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0870 chunk 83 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 3.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 11742 Z= 0.296 Angle : 0.594 9.791 16004 Z= 0.295 Chirality : 0.042 0.246 1848 Planarity : 0.003 0.028 2026 Dihedral : 7.423 99.824 1670 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 0.71 % 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: -0.44 (0.21), residues: 1522 helix: 1.17 (0.19), residues: 718 sheet: -0.72 (0.45), residues: 138 loop : -1.91 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 68 average time/residue: 0.1947 time to fit residues: 21.7842 Evaluate side-chains 62 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1013 time to fit residues: 2.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 29 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 147 optimal weight: 40.0000 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 30.0000 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 159 GLN B 393 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 11742 Z= 0.137 Angle : 0.532 10.293 16004 Z= 0.261 Chirality : 0.041 0.235 1848 Planarity : 0.003 0.028 2026 Dihedral : 7.086 98.542 1670 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 0.35 % 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: -0.25 (0.21), residues: 1522 helix: 1.38 (0.19), residues: 716 sheet: -0.57 (0.45), residues: 138 loop : -1.87 (0.22), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 65 average time/residue: 0.2004 time to fit residues: 21.3991 Evaluate side-chains 61 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1073 time to fit residues: 2.0873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 11742 Z= 0.386 Angle : 0.650 10.210 16004 Z= 0.325 Chirality : 0.044 0.226 1848 Planarity : 0.004 0.031 2026 Dihedral : 7.271 99.855 1670 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 1.06 % 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: -0.40 (0.22), residues: 1522 helix: 1.23 (0.20), residues: 710 sheet: -0.69 (0.44), residues: 138 loop : -1.88 (0.23), residues: 674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 66 average time/residue: 0.2187 time to fit residues: 22.9096 Evaluate side-chains 65 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2765 time to fit residues: 4.2418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 140 optimal weight: 40.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 11742 Z= 0.192 Angle : 0.572 11.187 16004 Z= 0.279 Chirality : 0.042 0.229 1848 Planarity : 0.003 0.028 2026 Dihedral : 7.116 98.321 1670 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.27 % 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: -0.26 (0.21), residues: 1522 helix: 1.35 (0.19), residues: 714 sheet: -0.57 (0.44), residues: 138 loop : -1.84 (0.23), residues: 670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.1923 time to fit residues: 19.8363 Evaluate side-chains 61 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0987 time to fit residues: 2.1815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 30.0000 chunk 136 optimal weight: 10.0000 chunk 140 optimal weight: 40.0000 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 11742 Z= 0.447 Angle : 0.716 11.827 16004 Z= 0.357 Chirality : 0.044 0.225 1848 Planarity : 0.004 0.028 2026 Dihedral : 7.387 99.958 1670 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1522 helix: 1.00 (0.20), residues: 724 sheet: -0.93 (0.45), residues: 128 loop : -1.87 (0.23), residues: 670 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 62 average time/residue: 0.2010 time to fit residues: 20.7954 Evaluate side-chains 61 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1116 time to fit residues: 2.1894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 100 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 50.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 11742 Z= 0.164 Angle : 0.594 12.688 16004 Z= 0.286 Chirality : 0.042 0.236 1848 Planarity : 0.003 0.029 2026 Dihedral : 7.129 98.545 1670 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.00 % 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: -0.28 (0.21), residues: 1522 helix: 1.29 (0.19), residues: 716 sheet: -0.57 (0.44), residues: 138 loop : -1.80 (0.23), residues: 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3044 Ramachandran restraints generated. 1522 Oldfield, 0 Emsley, 1522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2045 time to fit residues: 20.2927 Evaluate side-chains 59 residues out of total 1328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.378 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.0170 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.071239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050490 restraints weight = 72920.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051847 restraints weight = 36789.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052706 restraints weight = 23305.242| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 11742 Z= 0.196 Angle : 0.583 12.506 16004 Z= 0.283 Chirality : 0.041 0.221 1848 Planarity : 0.003 0.029 2026 Dihedral : 7.090 99.514 1670 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.09 % 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: -0.25 (0.21), residues: 1522 helix: 1.28 (0.19), residues: 720 sheet: -0.56 (0.44), residues: 138 loop : -1.76 (0.23), residues: 664 =============================================================================== Job complete usr+sys time: 1681.84 seconds wall clock time: 32 minutes 1.07 seconds (1921.07 seconds total)