Starting phenix.real_space_refine on Wed Feb 14 00:27:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v0v_21003/02_2024/6v0v_21003.pdb" } resolution = 3.61 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 60 5.49 5 S 51 5.16 5 C 5002 2.51 5 N 1428 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A ASP 573": "OD1" <-> "OD2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A PHE 911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 927": "NH1" <-> "NH2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 977": "NH1" <-> "NH2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8192 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4286 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 617 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "I" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2016 SG CYS A 727 70.241 55.803 61.715 1.00 82.81 S ATOM 2037 SG CYS A 730 72.316 58.531 60.217 1.00 86.87 S Time building chain proxies: 5.09, per 1000 atoms: 0.62 Number of scatterers: 8192 At special positions: 0 Unit cell: (107.06, 95.4, 118.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 51 16.00 P 60 15.00 O 1648 8.00 N 1428 7.00 C 5002 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: 3.57 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " Number of angles added : 2 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 33.8% alpha, 25.0% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.849A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.670A pdb=" N ALA A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.603A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.579A pdb=" N GLU A 716 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 793 through 814 removed outlier: 3.964A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 4.005A pdb=" N MET A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 removed outlier: 3.548A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.769A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.843A pdb=" N CYS A 902 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 924 removed outlier: 5.330A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.904A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 removed outlier: 3.787A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.567A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.815A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'A' and resid 1002 through 1005 Processing helix chain 'B' and resid 11 through 15 removed outlier: 4.008A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 10.087A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 10.087A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.936A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.350A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.650A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.147A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.102A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 124 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.722A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 removed outlier: 4.540A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.809A pdb=" N ILE B 262 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2196 1.33 - 1.45: 2147 1.45 - 1.58: 3960 1.58 - 1.70: 117 1.70 - 1.82: 78 Bond restraints: 8498 Sorted by residual: bond pdb=" O3' DT F 29 " pdb=" P DG F 30 " ideal model delta sigma weight residual 1.607 1.562 0.045 1.50e-02 4.44e+03 9.15e+00 bond pdb=" CA LEU A 735 " pdb=" C LEU A 735 " ideal model delta sigma weight residual 1.522 1.484 0.038 1.37e-02 5.33e+03 7.83e+00 bond pdb=" N MET A 847 " pdb=" CA MET A 847 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.22e+00 bond pdb=" C PRO A 654 " pdb=" N LEU A 655 " ideal model delta sigma weight residual 1.331 1.299 0.033 1.40e-02 5.10e+03 5.47e+00 bond pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.34e+00 ... (remaining 8493 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.77: 291 103.77 - 111.36: 3699 111.36 - 118.95: 3202 118.95 - 126.55: 4287 126.55 - 134.14: 279 Bond angle restraints: 11758 Sorted by residual: angle pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " pdb=" O3' DT F 29 " ideal model delta sigma weight residual 110.00 96.18 13.82 1.50e+00 4.44e-01 8.49e+01 angle pdb=" C2' DC F 26 " pdb=" C1' DC F 26 " pdb=" N1 DC F 26 " ideal model delta sigma weight residual 113.50 120.36 -6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 121.54 130.19 -8.65 1.91e+00 2.74e-01 2.05e+01 angle pdb=" C4' DT F 27 " pdb=" C3' DT F 27 " pdb=" O3' DT F 27 " ideal model delta sigma weight residual 110.00 103.31 6.69 1.50e+00 4.44e-01 1.99e+01 angle pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " pdb=" P DG I 7 " ideal model delta sigma weight residual 120.20 125.96 -5.76 1.50e+00 4.44e-01 1.47e+01 ... (remaining 11753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 4578 35.36 - 70.72: 347 70.72 - 106.09: 9 106.09 - 141.45: 1 141.45 - 176.81: 2 Dihedral angle restraints: 4937 sinusoidal: 2358 harmonic: 2579 Sorted by residual: dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS B 41 " pdb=" C CYS B 41 " pdb=" N PRO B 42 " pdb=" CA PRO B 42 " ideal model delta harmonic sigma weight residual -180.00 -157.91 -22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PRO A 871 " pdb=" C PRO A 871 " pdb=" N SER A 872 " pdb=" CA SER A 872 " ideal model delta harmonic sigma weight residual -180.00 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1013 0.065 - 0.129: 244 0.129 - 0.194: 33 0.194 - 0.259: 6 0.259 - 0.323: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" C1' DC F 26 " pdb=" O4' DC F 26 " pdb=" C2' DC F 26 " pdb=" N1 DC F 26 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB VAL A 943 " pdb=" CA VAL A 943 " pdb=" CG1 VAL A 943 " pdb=" CG2 VAL A 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL B 8 " pdb=" CA VAL B 8 " pdb=" CG1 VAL B 8 " pdb=" CG2 VAL B 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1295 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 26 " 0.095 2.00e-02 2.50e+03 4.30e-02 4.17e+01 pdb=" N1 DC F 26 " -0.043 2.00e-02 2.50e+03 pdb=" C2 DC F 26 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DC F 26 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DC F 26 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC F 26 " 0.009 2.00e-02 2.50e+03 pdb=" N4 DC F 26 " 0.044 2.00e-02 2.50e+03 pdb=" C5 DC F 26 " -0.018 2.00e-02 2.50e+03 pdb=" C6 DC F 26 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C ARG B 212 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG B 212 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 213 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 99 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.042 5.00e-02 4.00e+02 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 83 2.53 - 3.12: 5775 3.12 - 3.71: 13865 3.71 - 4.31: 18150 4.31 - 4.90: 28488 Nonbonded interactions: 66361 Sorted by model distance: nonbonded pdb=" OP1 DC I 17 " pdb="CA CA A1102 " model vdw 1.932 2.510 nonbonded pdb=" OE1 GLU A 962 " pdb="CA CA A1102 " model vdw 2.026 2.510 nonbonded pdb=" OD1 ASP A 600 " pdb="CA CA A1101 " model vdw 2.193 2.510 nonbonded pdb=" OE2 GLU A 803 " pdb=" OH TYR A 928 " model vdw 2.231 2.440 nonbonded pdb=" O SER A 958 " pdb=" OG SER A 958 " model vdw 2.266 2.440 ... (remaining 66356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.000 Extract box with map and model: 4.740 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.310 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.008 0.087 8498 Z= 0.479 Angle : 1.005 13.822 11758 Z= 0.577 Chirality : 0.057 0.323 1298 Planarity : 0.007 0.075 1303 Dihedral : 21.033 176.809 3275 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.28 % Favored : 92.61 % Rotamer: Outliers : 0.40 % Allowed : 6.88 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -3.85 (0.23), residues: 879 helix: -2.89 (0.22), residues: 271 sheet: -1.77 (0.40), residues: 158 loop : -2.63 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 893 HIS 0.008 0.002 HIS B 47 PHE 0.035 0.003 PHE A 804 TYR 0.016 0.002 TYR A 805 ARG 0.006 0.001 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.893 Fit side-chains REVERT: A 576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 753 ASN cc_start: 0.8184 (t0) cc_final: 0.6963 (t0) REVERT: A 857 LEU cc_start: 0.9194 (mt) cc_final: 0.8898 (tt) REVERT: B 24 PHE cc_start: 0.6579 (m-10) cc_final: 0.6234 (m-80) REVERT: B 80 TYR cc_start: 0.7482 (t80) cc_final: 0.6994 (t80) REVERT: B 90 GLN cc_start: 0.8212 (pt0) cc_final: 0.7827 (pt0) REVERT: B 269 ASP cc_start: 0.6285 (t0) cc_final: 0.6067 (t0) REVERT: B 281 ASN cc_start: 0.7903 (p0) cc_final: 0.7451 (p0) REVERT: B 313 HIS cc_start: 0.8340 (t70) cc_final: 0.7986 (t-90) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.2068 time to fit residues: 38.5600 Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 85 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS ** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A 820 ASN A 908 GLN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 HIS ** B 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8498 Z= 0.209 Angle : 0.629 8.078 11758 Z= 0.341 Chirality : 0.042 0.158 1298 Planarity : 0.005 0.057 1303 Dihedral : 23.573 175.599 1618 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 1.85 % Allowed : 15.08 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -2.32 (0.26), residues: 879 helix: -1.05 (0.29), residues: 270 sheet: -1.09 (0.39), residues: 183 loop : -2.04 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 317 HIS 0.003 0.001 HIS A 937 PHE 0.033 0.002 PHE A 804 TYR 0.013 0.001 TYR A 757 ARG 0.006 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.929 Fit side-chains REVERT: A 568 MET cc_start: 0.8019 (mtm) cc_final: 0.7610 (ttm) REVERT: A 576 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 919 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8166 (tt) REVERT: B 80 TYR cc_start: 0.7595 (t80) cc_final: 0.7365 (t80) REVERT: B 90 GLN cc_start: 0.8100 (pt0) cc_final: 0.7743 (pt0) REVERT: B 313 HIS cc_start: 0.8343 (t70) cc_final: 0.8055 (t-90) outliers start: 14 outliers final: 6 residues processed: 110 average time/residue: 0.1776 time to fit residues: 28.0603 Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 272 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8498 Z= 0.206 Angle : 0.612 9.213 11758 Z= 0.327 Chirality : 0.041 0.165 1298 Planarity : 0.004 0.053 1303 Dihedral : 23.366 174.966 1618 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 3.17 % Allowed : 16.53 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.46 (0.28), residues: 879 helix: -0.22 (0.31), residues: 270 sheet: -0.52 (0.40), residues: 183 loop : -1.65 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 317 HIS 0.003 0.001 HIS A 515 PHE 0.029 0.002 PHE A 804 TYR 0.010 0.001 TYR A 805 ARG 0.007 0.001 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.815 Fit side-chains REVERT: A 576 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8024 (tm-30) REVERT: A 657 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8621 (pp) REVERT: A 760 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.8703 (t-100) REVERT: A 849 MET cc_start: 0.7454 (ttm) cc_final: 0.7156 (mtm) REVERT: A 887 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9059 (mp) REVERT: A 919 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (tt) REVERT: B 80 TYR cc_start: 0.7694 (t80) cc_final: 0.7484 (t80) REVERT: B 298 GLU cc_start: 0.8494 (mp0) cc_final: 0.8226 (mp0) REVERT: B 313 HIS cc_start: 0.8365 (t70) cc_final: 0.8148 (t-90) outliers start: 24 outliers final: 10 residues processed: 100 average time/residue: 0.1697 time to fit residues: 24.6598 Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 760 TRP Chi-restraints excluded: chain A residue 841 MET Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN B 89 HIS B 181 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8498 Z= 0.322 Angle : 0.694 10.329 11758 Z= 0.365 Chirality : 0.043 0.184 1298 Planarity : 0.004 0.055 1303 Dihedral : 23.580 174.980 1618 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.89 % Favored : 94.99 % Rotamer: Outliers : 4.63 % Allowed : 18.39 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 (0.28), residues: 879 helix: -0.05 (0.32), residues: 269 sheet: 0.08 (0.42), residues: 157 loop : -1.60 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 317 HIS 0.007 0.001 HIS A 515 PHE 0.031 0.002 PHE A 804 TYR 0.015 0.002 TYR A 805 ARG 0.007 0.001 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 70 time to evaluate : 0.867 Fit side-chains REVERT: A 576 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 627 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7473 (ttp) REVERT: A 844 LYS cc_start: 0.6665 (mmtt) cc_final: 0.5887 (tttp) REVERT: A 919 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8245 (tt) REVERT: B 298 GLU cc_start: 0.8505 (mp0) cc_final: 0.8147 (mp0) REVERT: B 302 MET cc_start: 0.7423 (mmm) cc_final: 0.7220 (mmm) REVERT: B 322 MET cc_start: 0.8722 (mtm) cc_final: 0.8106 (mpp) outliers start: 35 outliers final: 19 residues processed: 97 average time/residue: 0.1759 time to fit residues: 24.8009 Evaluate side-chains 86 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 77 optimal weight: 0.0980 chunk 62 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 HIS ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8498 Z= 0.168 Angle : 0.593 11.096 11758 Z= 0.314 Chirality : 0.041 0.182 1298 Planarity : 0.004 0.055 1303 Dihedral : 23.247 178.051 1618 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.13 % Rotamer: Outliers : 2.38 % Allowed : 19.84 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.77 (0.28), residues: 879 helix: 0.28 (0.33), residues: 268 sheet: 0.22 (0.42), residues: 163 loop : -1.29 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 836 PHE 0.031 0.001 PHE A 804 TYR 0.011 0.001 TYR A 757 ARG 0.004 0.000 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 576 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 844 LYS cc_start: 0.6550 (mmtt) cc_final: 0.5583 (tttp) REVERT: A 919 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8314 (tt) REVERT: B 280 GLU cc_start: 0.8156 (pm20) cc_final: 0.7753 (pm20) REVERT: B 302 MET cc_start: 0.7588 (mmm) cc_final: 0.7350 (mmm) REVERT: B 322 MET cc_start: 0.8576 (mtm) cc_final: 0.8070 (mpp) outliers start: 18 outliers final: 9 residues processed: 88 average time/residue: 0.1825 time to fit residues: 23.2017 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 87 optimal weight: 9.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8498 Z= 0.181 Angle : 0.615 13.619 11758 Z= 0.321 Chirality : 0.041 0.178 1298 Planarity : 0.004 0.052 1303 Dihedral : 23.144 176.921 1618 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 1.98 % Allowed : 21.56 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.55 (0.28), residues: 879 helix: 0.38 (0.33), residues: 268 sheet: 0.58 (0.42), residues: 158 loop : -1.17 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 317 HIS 0.003 0.001 HIS A 501 PHE 0.029 0.001 PHE A 804 TYR 0.016 0.001 TYR A 485 ARG 0.003 0.000 ARG A 848 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 2.264 Fit side-chains REVERT: A 576 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 844 LYS cc_start: 0.6682 (mmtt) cc_final: 0.5702 (tttp) REVERT: A 919 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8342 (tt) REVERT: B 280 GLU cc_start: 0.8098 (pm20) cc_final: 0.7740 (pm20) REVERT: B 302 MET cc_start: 0.7756 (mmm) cc_final: 0.7549 (mmm) REVERT: B 322 MET cc_start: 0.8608 (mtm) cc_final: 0.8074 (mpp) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.2353 time to fit residues: 31.4861 Evaluate side-chains 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 983 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8498 Z= 0.209 Angle : 0.626 12.095 11758 Z= 0.324 Chirality : 0.041 0.192 1298 Planarity : 0.004 0.052 1303 Dihedral : 23.155 177.207 1618 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 2.65 % Allowed : 21.96 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.49 (0.28), residues: 879 helix: 0.33 (0.33), residues: 269 sheet: 0.71 (0.42), residues: 156 loop : -1.10 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 317 HIS 0.003 0.001 HIS A 501 PHE 0.024 0.002 PHE B 48 TYR 0.018 0.001 TYR A 485 ARG 0.006 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.891 Fit side-chains REVERT: A 576 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 844 LYS cc_start: 0.6719 (mmtt) cc_final: 0.5737 (tttp) REVERT: A 858 MET cc_start: 0.7802 (mmm) cc_final: 0.7533 (mmm) REVERT: A 919 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8318 (tt) REVERT: B 280 GLU cc_start: 0.8015 (pm20) cc_final: 0.7685 (pm20) REVERT: B 302 MET cc_start: 0.7943 (mmm) cc_final: 0.7714 (mmm) REVERT: B 322 MET cc_start: 0.8623 (mtm) cc_final: 0.8067 (mpp) outliers start: 20 outliers final: 12 residues processed: 87 average time/residue: 0.1852 time to fit residues: 23.0485 Evaluate side-chains 77 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 983 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8498 Z= 0.188 Angle : 0.596 10.434 11758 Z= 0.313 Chirality : 0.040 0.175 1298 Planarity : 0.004 0.052 1303 Dihedral : 23.111 178.187 1618 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.02 % Rotamer: Outliers : 2.51 % Allowed : 21.56 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.38 (0.29), residues: 879 helix: 0.41 (0.33), residues: 269 sheet: 0.71 (0.42), residues: 158 loop : -1.01 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 317 HIS 0.003 0.001 HIS A 501 PHE 0.022 0.001 PHE B 48 TYR 0.019 0.001 TYR A 485 ARG 0.005 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.756 Fit side-chains REVERT: A 576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 658 MET cc_start: 0.8201 (ptp) cc_final: 0.7883 (ptp) REVERT: A 844 LYS cc_start: 0.6847 (mmtt) cc_final: 0.5889 (tttp) REVERT: A 858 MET cc_start: 0.7750 (mmm) cc_final: 0.7001 (mmm) REVERT: A 919 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (tt) REVERT: B 280 GLU cc_start: 0.8056 (pm20) cc_final: 0.7740 (pm20) REVERT: B 322 MET cc_start: 0.8597 (mtm) cc_final: 0.8060 (mpp) outliers start: 19 outliers final: 14 residues processed: 83 average time/residue: 0.2534 time to fit residues: 31.4008 Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8498 Z= 0.253 Angle : 0.643 12.876 11758 Z= 0.335 Chirality : 0.042 0.191 1298 Planarity : 0.004 0.052 1303 Dihedral : 23.221 177.780 1618 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 2.12 % Allowed : 22.49 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.41 (0.29), residues: 879 helix: 0.37 (0.33), residues: 269 sheet: 0.72 (0.42), residues: 156 loop : -1.02 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 317 HIS 0.003 0.001 HIS A 515 PHE 0.023 0.002 PHE B 48 TYR 0.019 0.001 TYR A 485 ARG 0.004 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.821 Fit side-chains REVERT: A 576 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8028 (tm-30) REVERT: A 844 LYS cc_start: 0.6960 (mmtt) cc_final: 0.5975 (tttp) REVERT: A 858 MET cc_start: 0.7945 (mmm) cc_final: 0.7301 (mmm) REVERT: A 919 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8358 (tt) REVERT: B 263 LEU cc_start: 0.8410 (tp) cc_final: 0.8004 (pt) REVERT: B 280 GLU cc_start: 0.8027 (pm20) cc_final: 0.7689 (pm20) REVERT: B 302 MET cc_start: 0.7698 (mmm) cc_final: 0.7446 (mmm) REVERT: B 322 MET cc_start: 0.8694 (mtm) cc_final: 0.8127 (mpp) outliers start: 16 outliers final: 13 residues processed: 75 average time/residue: 0.1678 time to fit residues: 18.6230 Evaluate side-chains 77 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8498 Z= 0.186 Angle : 0.604 12.617 11758 Z= 0.316 Chirality : 0.040 0.182 1298 Planarity : 0.004 0.053 1303 Dihedral : 23.126 179.241 1618 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 1.85 % Allowed : 22.49 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.31 (0.29), residues: 879 helix: 0.48 (0.33), residues: 269 sheet: 0.58 (0.41), residues: 160 loop : -0.90 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 501 PHE 0.030 0.001 PHE A 804 TYR 0.020 0.001 TYR A 485 ARG 0.004 0.000 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.841 Fit side-chains REVERT: A 576 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 658 MET cc_start: 0.8193 (ptp) cc_final: 0.7853 (ptp) REVERT: A 844 LYS cc_start: 0.6891 (mmtt) cc_final: 0.5868 (tttp) REVERT: A 858 MET cc_start: 0.7570 (mmm) cc_final: 0.7102 (mmm) REVERT: A 919 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (tt) REVERT: B 110 MET cc_start: 0.8388 (mmm) cc_final: 0.7770 (mmp) REVERT: B 280 GLU cc_start: 0.8067 (pm20) cc_final: 0.7732 (pm20) REVERT: B 302 MET cc_start: 0.7736 (mmm) cc_final: 0.7486 (mmm) REVERT: B 322 MET cc_start: 0.8596 (mtm) cc_final: 0.8062 (mpp) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.1797 time to fit residues: 20.7135 Evaluate side-chains 80 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 350 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.083991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062157 restraints weight = 24617.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063823 restraints weight = 13931.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064908 restraints weight = 9852.834| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8498 Z= 0.197 Angle : 0.602 11.015 11758 Z= 0.317 Chirality : 0.040 0.182 1298 Planarity : 0.004 0.053 1303 Dihedral : 23.092 178.673 1618 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.66 % Favored : 95.22 % Rotamer: Outliers : 1.98 % Allowed : 22.22 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.29), residues: 879 helix: 0.60 (0.33), residues: 266 sheet: 0.61 (0.41), residues: 160 loop : -0.91 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 317 HIS 0.003 0.001 HIS A 501 PHE 0.030 0.002 PHE A 804 TYR 0.021 0.001 TYR A 485 ARG 0.004 0.000 ARG A 838 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.15 seconds wall clock time: 32 minutes 27.43 seconds (1947.43 seconds total)