Starting phenix.real_space_refine (version: dev) on Fri Mar 17 13:29:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2023/7ola_12975_updated.pdb" } resolution = 3.3 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= 0.001 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 GLU 370": "OE1" <-> "OE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "F PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19719 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3664 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 429} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3676 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 430} Chain breaks: 3 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3542 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 5 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3042 Classifications: {'peptide': 375} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 360} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2833 Classifications: {'peptide': 349} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2835 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.04, per 1000 atoms: 0.56 Number of scatterers: 19719 At special positions: 0 Unit cell: (139.4, 124.64, 126.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 3 11.99 O 3749 8.00 N 3282 7.00 C 12615 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: 8.22 Conformation dependent library (CDL) restraints added in 3.0 seconds 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 23 sheets defined 37.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 317 through 338 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 404 through 417 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 487 through 501 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 575 through 582 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 651 through 663 Processing helix chain 'A' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 707 through 719 removed outlier: 6.054A pdb=" N PHE A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TYR A 714 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS A 715 " --> pdb=" O TYR A 711 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU A 716 " --> pdb=" O ALA A 712 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'B' and resid 317 through 323 Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 388 through 398 Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 521 through 531 Processing helix chain 'B' and resid 542 through 544 No H-bonds generated for 'chain 'B' and resid 542 through 544' Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 651 through 663 Processing helix chain 'B' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'B' and resid 730 through 736 removed outlier: 3.696A pdb=" N GLN B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 337 Processing helix chain 'C' and resid 350 through 360 Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 404 through 417 Processing helix chain 'C' and resid 475 through 482 Processing helix chain 'C' and resid 487 through 501 Processing helix chain 'C' and resid 521 through 531 Processing helix chain 'C' and resid 542 through 544 No H-bonds generated for 'chain 'C' and resid 542 through 544' Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 575 through 581 Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 641 through 645 Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 651 through 663 Processing helix chain 'C' and resid 674 through 686 WARNING: missing atoms! Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 707 through 719 removed outlier: 6.255A pdb=" N PHE C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 714 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASP C 719 " --> pdb=" O LYS C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'D' and resid 317 through 338 Processing helix chain 'D' and resid 350 through 360 Processing helix chain 'D' and resid 388 through 398 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 475 through 483 Processing helix chain 'D' and resid 487 through 501 Processing helix chain 'D' and resid 521 through 532 Processing helix chain 'D' and resid 575 through 582 Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 641 through 645 Processing helix chain 'D' and resid 651 through 663 Processing helix chain 'D' and resid 673 through 686 Processing helix chain 'E' and resid 317 through 337 Processing helix chain 'E' and resid 350 through 360 Processing helix chain 'E' and resid 388 through 398 Processing helix chain 'E' and resid 404 through 417 Processing helix chain 'E' and resid 475 through 482 Processing helix chain 'E' and resid 487 through 501 Processing helix chain 'E' and resid 521 through 531 Processing helix chain 'E' and resid 542 through 544 No H-bonds generated for 'chain 'E' and resid 542 through 544' Processing helix chain 'E' and resid 551 through 554 Processing helix chain 'E' and resid 576 through 581 Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 641 through 644 Processing helix chain 'E' and resid 651 through 663 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 327 through 338 Processing helix chain 'F' and resid 350 through 360 Processing helix chain 'F' and resid 388 through 398 Processing helix chain 'F' and resid 404 through 417 Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 487 through 501 Processing helix chain 'F' and resid 521 through 531 Processing helix chain 'F' and resid 551 through 554 Processing helix chain 'F' and resid 575 through 581 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 641 through 645 Processing helix chain 'F' and resid 651 through 663 Processing sheet with id= A, first strand: chain 'A' and resid 363 through 365 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 431 Processing sheet with id= C, first strand: chain 'A' and resid 625 through 628 removed outlier: 5.866A pdb=" N ALA A 510 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL A 628 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 512 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 604 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE A 513 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN A 606 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 585 through 588 Processing sheet with id= E, first strand: chain 'B' and resid 363 through 365 Processing sheet with id= F, first strand: chain 'B' and resid 429 through 431 Processing sheet with id= G, first strand: chain 'B' and resid 625 through 629 removed outlier: 5.568A pdb=" N ALA B 510 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B 628 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B 512 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 604 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE B 513 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN B 606 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 585 through 588 Processing sheet with id= I, first strand: chain 'C' and resid 363 through 365 Processing sheet with id= J, first strand: chain 'C' and resid 429 through 431 Processing sheet with id= K, first strand: chain 'C' and resid 625 through 629 removed outlier: 5.900A pdb=" N ALA C 510 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL C 628 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE C 512 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 585 through 588 Processing sheet with id= M, first strand: chain 'D' and resid 363 through 365 Processing sheet with id= N, first strand: chain 'D' and resid 429 through 432 Processing sheet with id= O, first strand: chain 'D' and resid 625 through 630 removed outlier: 5.806A pdb=" N ALA D 510 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 628 " --> pdb=" O ALA D 510 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE D 512 " --> pdb=" O VAL D 628 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE D 630 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 514 " --> pdb=" O PHE D 630 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 560 " --> pdb=" O ILE D 605 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N SER D 607 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY D 562 " --> pdb=" O SER D 607 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 363 through 365 Processing sheet with id= Q, first strand: chain 'E' and resid 429 through 431 Processing sheet with id= R, first strand: chain 'E' and resid 625 through 629 removed outlier: 6.414A pdb=" N ALA E 510 " --> pdb=" O LEU E 626 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL E 628 " --> pdb=" O ALA E 510 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE E 512 " --> pdb=" O VAL E 628 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 586 through 588 Processing sheet with id= T, first strand: chain 'F' and resid 363 through 365 Processing sheet with id= U, first strand: chain 'F' and resid 429 through 432 Processing sheet with id= V, first strand: chain 'F' and resid 625 through 630 removed outlier: 5.866A pdb=" N ALA F 510 " --> pdb=" O LEU F 626 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL F 628 " --> pdb=" O ALA F 510 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE F 512 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE F 630 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL F 514 " --> pdb=" O PHE F 630 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 586 through 588 647 hydrogen bonds defined for protein. 1851 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: 5.53 Time building geometry restraints manager: 8.75 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: 6307 1.34 - 1.46: 3442 1.46 - 1.58: 10262 1.58 - 1.69: 20 1.69 - 1.81: 95 Bond restraints: 20126 Sorted by residual: bond pdb=" N3B ANP A1201 " pdb=" PG ANP A1201 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N3B ANP C1201 " pdb=" PG ANP C1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N3B ANP D1201 " pdb=" PG ANP D1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" N3B ANP B1201 " pdb=" PG ANP B1201 " ideal model delta sigma weight residual 1.795 1.635 0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" O3A ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 20121 not shown) Histogram of bond angle deviations from ideal: 98.05 - 105.29: 331 105.29 - 112.53: 10177 112.53 - 119.78: 6781 119.78 - 127.02: 9724 127.02 - 134.26: 192 Bond angle restraints: 27205 Sorted by residual: angle pdb=" C LEU B 739 " pdb=" CA LEU B 739 " pdb=" CB LEU B 739 " ideal model delta sigma weight residual 117.23 110.55 6.68 1.36e+00 5.41e-01 2.41e+01 angle pdb=" N ILE B 760 " pdb=" CA ILE B 760 " pdb=" C ILE B 760 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.61e+01 angle pdb=" CA LEU B 739 " pdb=" C LEU B 739 " pdb=" N GLU B 740 " ideal model delta sigma weight residual 119.98 116.93 3.05 8.50e-01 1.38e+00 1.28e+01 angle pdb=" CA GLU D 547 " pdb=" C GLU D 547 " pdb=" O GLU D 547 " ideal model delta sigma weight residual 121.38 117.59 3.79 1.06e+00 8.90e-01 1.28e+01 angle pdb=" C VAL B 705 " pdb=" CA VAL B 705 " pdb=" CB VAL B 705 " ideal model delta sigma weight residual 114.35 110.67 3.68 1.06e+00 8.90e-01 1.20e+01 ... (remaining 27200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 11854 35.34 - 70.69: 177 70.69 - 106.03: 45 106.03 - 141.38: 1 141.38 - 176.72: 3 Dihedral angle restraints: 12080 sinusoidal: 5049 harmonic: 7031 Sorted by residual: dihedral pdb=" O1A ANP B1201 " pdb=" O3A ANP B1201 " pdb=" PA ANP B1201 " pdb=" PB ANP B1201 " ideal model delta sinusoidal sigma weight residual 83.11 -93.61 176.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A ANP D1201 " pdb=" O3A ANP D1201 " pdb=" PA ANP D1201 " pdb=" PB ANP D1201 " ideal model delta sinusoidal sigma weight residual 83.11 -77.29 160.40 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A ANP A1201 " pdb=" O3A ANP A1201 " pdb=" PA ANP A1201 " pdb=" PB ANP A1201 " ideal model delta sinusoidal sigma weight residual 83.11 -68.37 151.48 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 12077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2682 0.073 - 0.146: 272 0.146 - 0.219: 8 0.219 - 0.292: 3 0.292 - 0.365: 3 Chirality restraints: 2968 Sorted by residual: chirality pdb=" C3' ANP C1201 " pdb=" C2' ANP C1201 " pdb=" C4' ANP C1201 " pdb=" O3' ANP C1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C3' ANP A1201 " pdb=" C2' ANP A1201 " pdb=" C4' ANP A1201 " pdb=" O3' ANP A1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C3' ANP D1201 " pdb=" C2' ANP D1201 " pdb=" C4' ANP D1201 " pdb=" O3' ANP D1201 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2965 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 611 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO E 612 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 612 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 612 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 322 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" CD GLN A 322 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN A 322 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN A 322 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ANP B1201 " 0.016 2.00e-02 2.50e+03 7.97e-03 1.75e+00 pdb=" C2 ANP B1201 " -0.001 2.00e-02 2.50e+03 pdb=" C4 ANP B1201 " -0.004 2.00e-02 2.50e+03 pdb=" C5 ANP B1201 " -0.003 2.00e-02 2.50e+03 pdb=" C6 ANP B1201 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ANP B1201 " 0.006 2.00e-02 2.50e+03 pdb=" N1 ANP B1201 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ANP B1201 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ANP B1201 " 0.009 2.00e-02 2.50e+03 pdb=" N7 ANP B1201 " -0.007 2.00e-02 2.50e+03 pdb=" N9 ANP B1201 " -0.015 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 177 2.60 - 3.17: 17366 3.17 - 3.75: 31271 3.75 - 4.32: 43827 4.32 - 4.90: 70030 Nonbonded interactions: 162671 Sorted by model distance: nonbonded pdb=" O2B ANP B1201 " pdb="MG MG B1202 " model vdw 2.023 2.170 nonbonded pdb=" O1B ANP D1201 " pdb="MG MG D1202 " model vdw 2.090 2.170 nonbonded pdb=" NH1 ARG F 328 " pdb=" OE1 GLU F 399 " model vdw 2.205 2.520 nonbonded pdb=" OG SER C 579 " pdb=" OD2 ASP D 563 " model vdw 2.210 2.440 nonbonded pdb=" OD1 ASP C 563 " pdb=" N ASP C 564 " model vdw 2.237 2.520 ... (remaining 162666 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' and (resid 316 through 697 or resid 703 through 736 or (resid 737 and \ (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2)) or resid 741 through 742 or (resid 743 and (name N or name \ CA or name C or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 745 through 747 o \ r (resid 748 and (name N or name CA or name C or name CB or name CG or name CD o \ r name OE1 or name NE2)) or resid 749 or resid 759 through 762 or resid 766 or r \ esid 1201)) selection = (chain 'B' and (resid 316 through 697 or resid 703 through 736 or (resid 737 and \ (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or n \ ame CE1 or name NE2)) or resid 741 through 742 or (resid 743 and (name N or name \ CA or name C or name CB or name CG or name CD1 or name CD2 or name NE1 or name \ CE2 or name CE3 or name CZ2 or name CZ3 or name CH2)) or resid 745 through 750 o \ r resid 759 through 762 or resid 766 or resid 1201)) selection = (chain 'C' and (resid 316 through 747 or (resid 748 and (name N or name CA or na \ me C or name CB or name CG or name CD or name OE1 or name NE2)) or resid 749 or \ resid 759 through 764 or resid 1201)) } ncs_group { reference = (chain 'D' and (resid 316 through 514 or (resid 515 and (name N or name CA or na \ me C )) or resid 519 through 563 or resid 565 or (resid 566 and (name N or name \ CA or name C or name CB or name CG or name CD )) or resid 574 or resid 576 throu \ gh 633 or (resid 634 and (name N or name CA or name C or name CB or name CG or n \ ame CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 635 and (nam \ e N or name CA or name C or name CB or name CG or name OD1 or name ND2)) or resi \ d 641 through 671 or (resid 672 and (name N or name CA or name C or name CB or n \ ame CG or name CD )))) selection = (chain 'E' and (resid 316 through 544 or (resid 545 and (name N or name CA or na \ me C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ )) or resid 546 through 565 or (resid 566 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 575 through 585 or resid 587 throu \ gh 588 or (resid 589 and (name N or name CA or name C or name CB or name CG or n \ ame CD or name OE1 or name OE2)) or resid 590 through 591 or (resid 592 and (nam \ e N or name CA or name C or name O or name CB )) or resid 593 through 634 or (re \ sid 640 and (name N or name CA or name C or name CB or name CG or name OD1 or na \ me ND2)) or resid 641 through 671 or (resid 672 and (name N or name CA or name C \ or name CB or name CG or name CD )))) selection = (chain 'F' and (resid 316 through 514 or (resid 515 and (name N or name CA or na \ me C )) or resid 519 through 544 or (resid 545 and (name N or name CA or name C \ or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ \ )) or resid 546 through 563 or resid 565 through 574 or resid 576 through 585 o \ r resid 587 through 588 or (resid 589 and (name N or name CA or name C or name C \ B or name CG or name CD or name OE1 or name OE2)) or resid 590 through 591 or (r \ esid 592 and (name N or name CA or name C or name O or name CB )) or resid 593 t \ hrough 633 or (resid 634 and (name N or name CA or name C or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 635 or re \ sid 641 through 672)) } 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 3 5.21 5 S 58 5.16 5 C 12615 2.51 5 N 3282 2.21 5 O 3749 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: 2.590 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: 0.020 Extract box with map and model: 11.490 Check model and map are aligned: 0.280 Process input model: 50.010 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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 : 0.004 0.161 20126 Z= 0.272 Angle : 0.585 9.638 27205 Z= 0.324 Chirality : 0.044 0.365 2968 Planarity : 0.003 0.039 3480 Dihedral : 15.066 176.723 7538 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 1.22 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 987 sheet: -0.33 (0.30), residues: 287 loop : -0.05 (0.19), residues: 1073 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.503 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2958 time to fit residues: 46.1257 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 ASN B 609 ASN C 358 ASN C 438 ASN C 519 ASN C 686 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN F 358 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 20126 Z= 0.324 Angle : 0.502 5.048 27205 Z= 0.270 Chirality : 0.043 0.179 2968 Planarity : 0.003 0.032 3480 Dihedral : 7.736 171.634 2588 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.32 % 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: 1.14 (0.18), residues: 2347 helix: 2.05 (0.17), residues: 988 sheet: -0.53 (0.31), residues: 267 loop : -0.04 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 2.550 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2812 time to fit residues: 36.8121 Evaluate side-chains 75 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 2.512 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1790 time to fit residues: 5.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN E 321 ASN F 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 20126 Z= 0.264 Angle : 0.464 7.268 27205 Z= 0.250 Chirality : 0.042 0.165 2968 Planarity : 0.003 0.035 3480 Dihedral : 7.476 163.945 2588 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: 1.14 (0.18), residues: 2347 helix: 2.02 (0.17), residues: 988 sheet: -0.53 (0.32), residues: 267 loop : -0.02 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 2.649 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 0.3015 time to fit residues: 42.4689 Evaluate side-chains 79 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2014 time to fit residues: 4.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 729 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20126 Z= 0.233 Angle : 0.453 6.827 27205 Z= 0.245 Chirality : 0.041 0.176 2968 Planarity : 0.003 0.036 3480 Dihedral : 7.293 160.721 2588 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.68 % 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: 1.19 (0.18), residues: 2347 helix: 2.06 (0.17), residues: 987 sheet: -0.48 (0.31), residues: 277 loop : 0.03 (0.20), residues: 1083 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 2.550 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 0.2862 time to fit residues: 41.6551 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1835 time to fit residues: 5.9156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN F 358 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 20126 Z= 0.369 Angle : 0.516 6.261 27205 Z= 0.277 Chirality : 0.043 0.158 2968 Planarity : 0.003 0.039 3480 Dihedral : 7.294 159.741 2588 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 1.08 (0.18), residues: 2347 helix: 1.94 (0.17), residues: 985 sheet: -0.57 (0.32), residues: 265 loop : -0.00 (0.20), residues: 1097 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 2.585 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.2986 time to fit residues: 44.6166 Evaluate side-chains 76 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1774 time to fit residues: 4.8621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.9144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1258 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: