Starting phenix.real_space_refine on Tue Dec 12 01:10:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/12_2023/7ola_12975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/12_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_12975/12_2023/7ola_12975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/12_2023/7ola_12975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/12_2023/7ola_12975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/12_2023/7ola_12975_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.38, per 1000 atoms: 0.53 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: 8.08 Conformation dependent library (CDL) restraints added in 3.6 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: 3.92 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: 5.94 Time building geometry restraints manager: 8.63 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: 11882 35.34 - 70.69: 232 70.69 - 106.03: 74 106.03 - 141.38: 1 141.38 - 176.72: 3 Dihedral angle restraints: 12192 sinusoidal: 5161 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 12189 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 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: 2.220 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: 10.780 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 52.440 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 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 : 16.471 176.723 7650 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 % Allowed : 0.32 % Favored : 99.68 % 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: 1.22 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 478 HIS 0.004 0.001 HIS F 402 PHE 0.017 0.001 PHE A 713 TYR 0.020 0.001 TYR B 717 ARG 0.002 0.000 ARG A 597 *********************** 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 : 2.413 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: 0.2886 time to fit residues: 44.5049 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.389 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2222 ------------------------------------------------------------------------------- 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 C 358 ASN C 438 ASN C 519 ASN C 686 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 ASN D 576 ASN F 358 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20126 Z= 0.325 Angle : 0.507 5.733 27205 Z= 0.269 Chirality : 0.043 0.181 2968 Planarity : 0.003 0.033 3480 Dihedral : 10.797 172.076 2700 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.32 % Allowed : 4.97 % Favored : 94.71 % 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: 1.16 (0.18), residues: 2347 helix: 2.08 (0.17), residues: 987 sheet: -0.53 (0.31), residues: 267 loop : -0.04 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 743 HIS 0.005 0.001 HIS F 402 PHE 0.013 0.001 PHE D 545 TYR 0.033 0.001 TYR A 717 ARG 0.004 0.000 ARG A 597 *********************** 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 : 2.187 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: 0.2814 time to fit residues: 37.2050 Evaluate side-chains 76 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1784 time to fit residues: 5.1810 ------------------------------------------------------------------------------- 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: 4.9990 chunk 66 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 191 optimal weight: 0.0040 chunk 212 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 609 ASN C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20126 Z= 0.151 Angle : 0.434 7.519 27205 Z= 0.233 Chirality : 0.041 0.160 2968 Planarity : 0.003 0.035 3480 Dihedral : 9.089 164.566 2700 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.84 % 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: 1.25 (0.18), residues: 2347 helix: 2.11 (0.17), residues: 988 sheet: -0.43 (0.32), residues: 271 loop : 0.04 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 743 HIS 0.004 0.001 HIS F 402 PHE 0.028 0.001 PHE A 713 TYR 0.027 0.001 TYR A 717 ARG 0.002 0.000 ARG B 759 *********************** 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 81 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 2.356 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.2789 time to fit residues: 39.0205 Evaluate side-chains 70 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1726 time to fit residues: 3.5629 ------------------------------------------------------------------------------- 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: 8.9990 chunk 161 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 215 optimal weight: 0.0970 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20126 Z= 0.137 Angle : 0.424 6.519 27205 Z= 0.228 Chirality : 0.041 0.162 2968 Planarity : 0.003 0.036 3480 Dihedral : 8.356 163.012 2700 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.41 % Allowed : 6.98 % Favored : 92.61 % 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: 1.23 (0.18), residues: 2347 helix: 2.17 (0.17), residues: 986 sheet: -0.56 (0.31), residues: 289 loop : 0.01 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 743 HIS 0.004 0.001 HIS F 402 PHE 0.022 0.001 PHE B 735 TYR 0.020 0.001 TYR A 732 ARG 0.008 0.000 ARG B 759 *********************** 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 85 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 2.407 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 9 outliers final: 4 residues processed: 84 average time/residue: 0.2757 time to fit residues: 39.7203 Evaluate side-chains 77 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1631 time to fit residues: 4.1952 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 194 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20126 Z= 0.136 Angle : 0.418 6.630 27205 Z= 0.225 Chirality : 0.040 0.175 2968 Planarity : 0.003 0.037 3480 Dihedral : 8.056 163.460 2700 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.46 % Allowed : 7.44 % Favored : 92.11 % 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: 1.24 (0.18), residues: 2347 helix: 2.18 (0.17), residues: 989 sheet: -0.57 (0.30), residues: 295 loop : 0.00 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.003 0.001 HIS F 402 PHE 0.039 0.001 PHE A 713 TYR 0.017 0.001 TYR A 717 ARG 0.009 0.000 ARG B 759 *********************** 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 87 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 2.481 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 83 average time/residue: 0.2800 time to fit residues: 40.1705 Evaluate side-chains 76 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1965 time to fit residues: 4.6938 ------------------------------------------------------------------------------- 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: 7.9990 chunk 205 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 525 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20126 Z= 0.156 Angle : 0.435 8.210 27205 Z= 0.233 Chirality : 0.041 0.136 2968 Planarity : 0.003 0.051 3480 Dihedral : 7.962 164.816 2700 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % 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: 1.25 (0.18), residues: 2347 helix: 2.19 (0.17), residues: 989 sheet: -0.56 (0.30), residues: 295 loop : 0.00 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS F 402 PHE 0.020 0.001 PHE B 763 TYR 0.013 0.001 TYR B 717 ARG 0.006 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 6 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 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 2.383 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 0.2889 time to fit residues: 39.7773 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1753 time to fit residues: 3.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 766 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN E 321 ASN F 358 ASN F 530 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 20126 Z= 0.537 Angle : 0.613 7.621 27205 Z= 0.327 Chirality : 0.046 0.143 2968 Planarity : 0.003 0.041 3480 Dihedral : 8.564 165.625 2700 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.59 % Allowed : 9.08 % Favored : 90.33 % 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: 0.93 (0.18), residues: 2347 helix: 1.79 (0.17), residues: 986 sheet: -0.62 (0.32), residues: 270 loop : -0.07 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 335 HIS 0.006 0.001 HIS F 402 PHE 0.048 0.002 PHE A 713 TYR 0.029 0.002 TYR A 717 ARG 0.007 0.001 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 7 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 86 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 2.689 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 0.2987 time to fit residues: 42.0528 Evaluate side-chains 76 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 2.503 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2091 time to fit residues: 5.0789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.5980 chunk 90 optimal weight: 0.0670 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 0.0170 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN E 321 ASN F 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20126 Z= 0.120 Angle : 0.456 8.549 27205 Z= 0.246 Chirality : 0.041 0.156 2968 Planarity : 0.003 0.036 3480 Dihedral : 8.039 167.867 2700 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.23 % Allowed : 9.76 % Favored : 90.01 % 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: 984 sheet: -0.56 (0.31), residues: 275 loop : -0.02 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 478 HIS 0.003 0.001 HIS F 402 PHE 0.017 0.001 PHE B 735 TYR 0.017 0.001 TYR C 717 ARG 0.005 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 8 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 80 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 2.261 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 1 residues processed: 79 average time/residue: 0.2810 time to fit residues: 38.6516 Evaluate side-chains 69 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1785 time to fit residues: 3.6067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.0570 chunk 198 optimal weight: 0.6980 chunk 211 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20126 Z= 0.125 Angle : 0.437 7.726 27205 Z= 0.237 Chirality : 0.041 0.159 2968 Planarity : 0.003 0.033 3480 Dihedral : 7.893 174.207 2700 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.18 % Allowed : 10.17 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2347 helix: 2.12 (0.17), residues: 985 sheet: -0.69 (0.30), residues: 287 loop : -0.03 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 473 HIS 0.003 0.001 HIS F 402 PHE 0.067 0.001 PHE A 713 TYR 0.016 0.001 TYR C 717 ARG 0.004 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 9 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 77 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 2.409 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.2977 time to fit residues: 38.2389 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1751 time to fit residues: 3.7074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 766 ASN C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 ASN E 321 ASN E 498 ASN F 358 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20126 Z= 0.330 Angle : 0.511 12.537 27205 Z= 0.273 Chirality : 0.042 0.145 2968 Planarity : 0.003 0.034 3480 Dihedral : 8.185 175.701 2700 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.09 % Allowed : 10.26 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2347 helix: 2.05 (0.17), residues: 988 sheet: -0.60 (0.32), residues: 269 loop : -0.01 (0.20), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 335 HIS 0.004 0.001 HIS F 402 PHE 0.033 0.001 PHE D 600 TYR 0.021 0.001 TYR A 717 ARG 0.004 0.000 ARG B 759 ********************** REFINEMENT MACRO_CYCLE 10 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 73 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 2.261 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.3033 time to fit residues: 38.1580 Evaluate side-chains 70 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1869 time to fit residues: 3.5041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** E 321 ASN F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.072010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.049888 restraints weight = 72462.378| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.64 r_work: 0.2704 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20126 Z= 0.182 Angle : 0.451 7.066 27205 Z= 0.244 Chirality : 0.041 0.146 2968 Planarity : 0.003 0.033 3480 Dihedral : 8.082 177.526 2700 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.09 % Allowed : 10.26 % Favored : 89.64 % 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: 2.08 (0.17), residues: 988 sheet: -0.64 (0.31), residues: 286 loop : -0.03 (0.20), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 743 HIS 0.004 0.001 HIS F 402 PHE 0.028 0.001 PHE D 600 TYR 0.017 0.001 TYR A 717 ARG 0.004 0.000 ARG B 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.66 seconds wall clock time: 61 minutes 29.06 seconds (3689.06 seconds total)