Starting phenix.real_space_refine on Mon Mar 18 02:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2024/7ola_12975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2024/7ola_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_2024/7ola_12975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2024/7ola_12975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2024/7ola_12975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ola_12975/03_2024/7ola_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.36, 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: 8.35 Conformation dependent library (CDL) restraints added in 3.5 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: 4.00 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: 6.06 Time building geometry restraints manager: 8.98 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: 2.690 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: 10.820 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 54.110 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.820 ------------------------------------------------------------------------------- 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 : 2.425 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7929 (t80) cc_final: 0.7258 (t80) REVERT: A 743 TRP cc_start: 0.4233 (t-100) cc_final: 0.3460 (t-100) REVERT: B 709 ILE cc_start: 0.9172 (pt) cc_final: 0.8832 (pt) REVERT: C 692 PHE cc_start: 0.8205 (t80) cc_final: 0.7923 (t80) REVERT: E 611 MET cc_start: 0.7897 (mmm) cc_final: 0.7070 (ttm) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2894 time to fit residues: 44.5333 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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: 0.8515 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20126 Z= 0.320 Angle : 0.506 5.731 27205 Z= 0.269 Chirality : 0.043 0.161 2968 Planarity : 0.003 0.034 3480 Dihedral : 10.647 171.572 2700 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.65 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: -0.52 (0.31), residues: 267 loop : -0.04 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.005 0.001 HIS F 402 PHE 0.011 0.001 PHE D 545 TYR 0.029 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 : 2.606 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8011 (t80) cc_final: 0.7261 (t80) REVERT: A 743 TRP cc_start: 0.4113 (t-100) cc_final: 0.3327 (t-100) REVERT: E 331 MET cc_start: 0.8507 (mtp) cc_final: 0.8259 (mtp) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2790 time to fit residues: 36.4413 Evaluate side-chains 74 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain F residue 484 CYS 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: 3.9990 chunk 178 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 609 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: 0.8501 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20126 Z= 0.225 Angle : 0.456 7.895 27205 Z= 0.244 Chirality : 0.041 0.167 2968 Planarity : 0.003 0.036 3480 Dihedral : 9.109 162.314 2700 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.46 % Allowed : 6.25 % Favored : 93.29 % 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: 1.20 (0.18), residues: 2347 helix: 2.09 (0.17), residues: 987 sheet: -0.50 (0.31), residues: 278 loop : 0.01 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.005 0.001 HIS F 402 PHE 0.029 0.001 PHE A 713 TYR 0.035 0.001 TYR A 717 ARG 0.003 0.000 ARG A 597 *********************** 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: 10 poor density : 74 time to evaluate : 2.522 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8030 (t80) cc_final: 0.7261 (t80) REVERT: A 743 TRP cc_start: 0.4039 (t-100) cc_final: 0.3221 (t-100) REVERT: E 331 MET cc_start: 0.8507 (mtp) cc_final: 0.8193 (mtp) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.2887 time to fit residues: 39.5597 Evaluate side-chains 78 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL 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: 4.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 144 optimal weight: 0.0040 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 112 optimal weight: 0.0040 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN C 729 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20126 Z= 0.210 Angle : 0.446 6.649 27205 Z= 0.239 Chirality : 0.041 0.163 2968 Planarity : 0.003 0.038 3480 Dihedral : 8.380 161.735 2700 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.82 % Allowed : 6.80 % Favored : 92.38 % 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: 2.12 (0.17), residues: 988 sheet: -0.48 (0.31), residues: 277 loop : 0.04 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.022 0.001 PHE B 735 TYR 0.026 0.001 TYR A 717 ARG 0.003 0.000 ARG A 597 *********************** 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 93 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 2.421 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 611 MET cc_start: 0.8227 (mmm) cc_final: 0.8011 (tmm) REVERT: A 732 TYR cc_start: 0.8017 (t80) cc_final: 0.7253 (t80) REVERT: A 743 TRP cc_start: 0.4121 (t-100) cc_final: 0.3245 (t-100) REVERT: E 331 MET cc_start: 0.8528 (mtp) cc_final: 0.8200 (mtp) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.2718 time to fit residues: 41.5335 Evaluate side-chains 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL 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: 7.9990 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** E 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20126 Z= 0.247 Angle : 0.459 6.190 27205 Z= 0.246 Chirality : 0.041 0.164 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.245 161.911 2700 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.82 % Allowed : 7.62 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.18), residues: 2347 helix: 2.11 (0.17), residues: 987 sheet: -0.51 (0.31), residues: 277 loop : 0.06 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.038 0.001 PHE A 713 TYR 0.013 0.001 TYR C 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 91 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 2.463 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 716 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 732 TYR cc_start: 0.8019 (t80) cc_final: 0.7256 (t80) REVERT: A 743 TRP cc_start: 0.4115 (t-100) cc_final: 0.3221 (t-100) REVERT: E 331 MET cc_start: 0.8540 (mtp) cc_final: 0.8198 (mtp) outliers start: 18 outliers final: 13 residues processed: 87 average time/residue: 0.2678 time to fit residues: 40.4476 Evaluate side-chains 83 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** E 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20126 Z= 0.158 Angle : 0.434 7.108 27205 Z= 0.233 Chirality : 0.041 0.147 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.072 163.193 2700 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.78 % Allowed : 8.71 % Favored : 90.51 % 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: 2.15 (0.17), residues: 985 sheet: -0.55 (0.31), residues: 283 loop : 0.04 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 478 HIS 0.004 0.001 HIS F 402 PHE 0.027 0.001 PHE D 666 TYR 0.011 0.001 TYR C 732 ARG 0.011 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 91 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 2.866 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.8001 (t80) cc_final: 0.7234 (t80) REVERT: A 743 TRP cc_start: 0.4217 (t-100) cc_final: 0.3287 (t-100) REVERT: D 563 ASP cc_start: 0.7290 (p0) cc_final: 0.6933 (p0) REVERT: E 331 MET cc_start: 0.8530 (mtp) cc_final: 0.8279 (mtp) REVERT: E 611 MET cc_start: 0.8128 (mmm) cc_final: 0.7784 (tpp) REVERT: E 658 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9269 (tp) outliers start: 17 outliers final: 13 residues processed: 86 average time/residue: 0.2732 time to fit residues: 41.1558 Evaluate side-chains 82 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 658 LEU Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** B 766 ASN C 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN E 321 ASN F 358 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20126 Z= 0.442 Angle : 0.570 7.304 27205 Z= 0.304 Chirality : 0.044 0.142 2968 Planarity : 0.003 0.037 3480 Dihedral : 8.457 167.070 2700 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.96 % Allowed : 9.53 % Favored : 89.51 % 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: 1.01 (0.18), residues: 2347 helix: 1.88 (0.17), residues: 987 sheet: -0.63 (0.32), residues: 265 loop : -0.04 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 335 HIS 0.005 0.001 HIS F 402 PHE 0.052 0.001 PHE A 713 TYR 0.015 0.001 TYR A 717 ARG 0.008 0.000 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 94 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 73 time to evaluate : 2.570 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7995 (t80) cc_final: 0.7552 (t80) REVERT: A 743 TRP cc_start: 0.4396 (t-100) cc_final: 0.3398 (t-100) REVERT: B 759 ARG cc_start: 0.7667 (mpp-170) cc_final: 0.7174 (mpp-170) outliers start: 21 outliers final: 16 residues processed: 91 average time/residue: 0.2729 time to fit residues: 42.3998 Evaluate side-chains 84 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain D residue 487 ASN Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- 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 358 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 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: 0.8489 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20126 Z= 0.136 Angle : 0.454 9.292 27205 Z= 0.245 Chirality : 0.041 0.139 2968 Planarity : 0.003 0.038 3480 Dihedral : 8.049 170.327 2700 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.50 % Allowed : 10.36 % Favored : 89.14 % 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: 1.12 (0.18), residues: 2347 helix: 2.07 (0.17), residues: 986 sheet: -0.67 (0.31), residues: 282 loop : -0.04 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 478 HIS 0.010 0.001 HIS B 737 PHE 0.017 0.001 PHE D 600 TYR 0.015 0.001 TYR C 732 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 85 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 2.630 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7970 (t80) cc_final: 0.7223 (t80) REVERT: A 743 TRP cc_start: 0.4369 (t-100) cc_final: 0.3356 (t-100) REVERT: B 759 ARG cc_start: 0.7526 (mpp-170) cc_final: 0.7090 (mpp-170) REVERT: C 692 PHE cc_start: 0.8289 (t80) cc_final: 0.7935 (t80) REVERT: D 563 ASP cc_start: 0.7299 (p0) cc_final: 0.6943 (p0) outliers start: 11 outliers final: 11 residues processed: 83 average time/residue: 0.2649 time to fit residues: 38.7212 Evaluate side-chains 84 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 211 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** E 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20126 Z= 0.165 Angle : 0.456 9.147 27205 Z= 0.244 Chirality : 0.041 0.136 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.006 175.414 2700 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.87 % Allowed : 10.36 % Favored : 88.78 % 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: -0.68 (0.31), residues: 282 loop : -0.03 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 335 HIS 0.007 0.001 HIS B 737 PHE 0.070 0.001 PHE A 713 TYR 0.015 0.001 TYR C 732 ARG 0.005 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 95 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 2.023 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7957 (t80) cc_final: 0.7208 (t80) REVERT: A 743 TRP cc_start: 0.4374 (t-100) cc_final: 0.3353 (t-100) REVERT: B 759 ARG cc_start: 0.7554 (mpp-170) cc_final: 0.7148 (mpp-170) REVERT: C 692 PHE cc_start: 0.8259 (t80) cc_final: 0.7909 (t80) REVERT: D 563 ASP cc_start: 0.7286 (p0) cc_final: 0.6921 (p0) REVERT: E 611 MET cc_start: 0.7908 (mmm) cc_final: 0.7199 (ttm) outliers start: 19 outliers final: 16 residues processed: 92 average time/residue: 0.2674 time to fit residues: 42.6300 Evaluate side-chains 89 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 721 ASN ** C 734 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN E 498 ASN F 530 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 20126 Z= 0.405 Angle : 0.547 9.118 27205 Z= 0.293 Chirality : 0.043 0.151 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.398 177.501 2700 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.78 % Allowed : 10.68 % Favored : 88.55 % 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: 1.03 (0.18), residues: 2347 helix: 1.98 (0.17), residues: 985 sheet: -0.84 (0.31), residues: 277 loop : -0.04 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 335 HIS 0.006 0.001 HIS B 737 PHE 0.035 0.001 PHE D 600 TYR 0.014 0.001 TYR A 717 ARG 0.005 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 85 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 2.309 Fit side-chains TARDY: cannot create tardy model for: "HIS C 737 " (corrupted residue). Skipping it. REVERT: A 732 TYR cc_start: 0.7984 (t80) cc_final: 0.7524 (t80) REVERT: A 743 TRP cc_start: 0.4472 (t-100) cc_final: 0.3422 (t-100) REVERT: B 759 ARG cc_start: 0.7640 (mpp-170) cc_final: 0.7183 (mpp-170) REVERT: D 563 ASP cc_start: 0.7465 (p0) cc_final: 0.7070 (p0) outliers start: 17 outliers final: 16 residues processed: 84 average time/residue: 0.2742 time to fit residues: 40.0889 Evaluate side-chains 83 residues out of total 2196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 67 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 616 ASP Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 761 TYR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 596 TYR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain F residue 320 LEU Chi-restraints excluded: chain F residue 484 CYS Chi-restraints excluded: chain F residue 563 ASP Chi-restraints excluded: chain F residue 604 VAL 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: 6.9990 chunk 52 optimal weight: 0.5980 chunk 187 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** C 762 ASN E 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.049744 restraints weight = 72379.373| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.65 r_work: 0.2697 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1478 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= 0.161 Angle : 0.460 9.534 27205 Z= 0.248 Chirality : 0.041 0.152 2968 Planarity : 0.003 0.039 3480 Dihedral : 8.177 179.897 2700 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.64 % Allowed : 10.86 % Favored : 88.50 % 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: 1.10 (0.18), residues: 2347 helix: 2.05 (0.17), residues: 987 sheet: -0.74 (0.31), residues: 283 loop : -0.03 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 478 HIS 0.005 0.001 HIS B 737 PHE 0.067 0.001 PHE A 713 TYR 0.017 0.001 TYR C 732 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: 3262.89 seconds wall clock time: 61 minutes 0.43 seconds (3660.43 seconds total)