Starting phenix.real_space_refine on Wed Apr 10 11:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnm_26014/04_2024/7tnm_26014_updated.pdb" } resolution = 4.74 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12570 2.51 5 N 3144 2.21 5 O 3594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 684": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 1036": "NH1" <-> "NH2" Residue "B ARG 1203": "NH1" <-> "NH2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 1036": "NH1" <-> "NH2" Residue "D ARG 1203": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "B" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "C" Number of atoms: 4831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4831 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "D" Number of atoms: 4835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4835 Classifications: {'peptide': 621} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 604} Chain breaks: 2 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'CYZ': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.48, per 1000 atoms: 0.54 Number of scatterers: 19448 At special positions: 0 Unit cell: (122.01, 117.03, 135.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3594 8.00 N 3144 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 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: 7.57 Conformation dependent library (CDL) restraints added in 3.9 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 20 sheets defined 50.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.56 Creating SS restraints... Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 523 through 544 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 596 through 624 Processing helix chain 'A' and resid 636 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 758 through 769 Processing helix chain 'A' and resid 793 through 819 Processing helix chain 'A' and resid 1005 through 1027 Processing helix chain 'A' and resid 1092 through 1102 Processing helix chain 'A' and resid 1105 through 1122 Processing helix chain 'A' and resid 1133 through 1160 Processing helix chain 'A' and resid 1177 through 1208 Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.715A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 519 Processing helix chain 'B' and resid 523 through 544 Processing helix chain 'B' and resid 564 through 567 No H-bonds generated for 'chain 'B' and resid 564 through 567' Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 616 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 790 through 818 removed outlier: 5.738A pdb=" N GLY B 794 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 798 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 804 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 805 " --> pdb=" O GLY B 802 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 809 " --> pdb=" O ALA B 806 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 813 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 817 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1028 Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1092 through 1102 Processing helix chain 'B' and resid 1105 through 1124 Processing helix chain 'B' and resid 1133 through 1160 removed outlier: 4.542A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1208 Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 516 through 519 Processing helix chain 'C' and resid 523 through 544 Processing helix chain 'C' and resid 565 through 568 No H-bonds generated for 'chain 'C' and resid 565 through 568' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 624 Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 758 through 769 Processing helix chain 'C' and resid 793 through 819 Processing helix chain 'C' and resid 1005 through 1027 Processing helix chain 'C' and resid 1092 through 1102 Processing helix chain 'C' and resid 1105 through 1122 Processing helix chain 'C' and resid 1133 through 1160 Processing helix chain 'C' and resid 1177 through 1208 Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 488 removed outlier: 3.714A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 523 through 544 Processing helix chain 'D' and resid 564 through 567 No H-bonds generated for 'chain 'D' and resid 564 through 567' Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 616 Processing helix chain 'D' and resid 621 through 623 No H-bonds generated for 'chain 'D' and resid 621 through 623' Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 676 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 768 removed outlier: 3.501A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 779 No H-bonds generated for 'chain 'D' and resid 776 through 779' Processing helix chain 'D' and resid 790 through 818 removed outlier: 5.738A pdb=" N GLY D 794 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 798 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 804 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 805 " --> pdb=" O GLY D 802 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 809 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 813 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 817 " --> pdb=" O PHE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1028 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1092 through 1102 Processing helix chain 'D' and resid 1105 through 1124 Processing helix chain 'D' and resid 1133 through 1160 removed outlier: 4.542A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1177 through 1208 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.613A pdb=" N ILE A 504 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1033 through 1035 Processing sheet with id= E, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.698A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 4.046A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.592A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1033 through 1037 Processing sheet with id= J, first strand: chain 'B' and resid 1064 through 1066 Processing sheet with id= K, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= L, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= M, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.612A pdb=" N ILE C 504 " --> pdb=" O MET C 721 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 1033 through 1035 Processing sheet with id= O, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.698A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= Q, first strand: chain 'D' and resid 496 through 499 removed outlier: 4.046A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.592A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 1033 through 1037 Processing sheet with id= T, first strand: chain 'D' and resid 1064 through 1066 945 hydrogen bonds defined for protein. 2667 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 8.31 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: 5439 1.34 - 1.46: 4181 1.46 - 1.58: 10034 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19882 Sorted by residual: bond pdb=" N THR D1049 " pdb=" CA THR D1049 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 6.99e+00 bond pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" N LYS D1052 " pdb=" CA LYS D1052 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.15e-02 7.56e+03 5.73e+00 bond pdb=" N LYS B1052 " pdb=" CA LYS B1052 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.15e-02 7.56e+03 5.63e+00 bond pdb=" N SER B1050 " pdb=" CA SER B1050 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.61e+00 ... (remaining 19877 not shown) Histogram of bond angle deviations from ideal: 93.28 - 101.54: 88 101.54 - 109.80: 2825 109.80 - 118.07: 12179 118.07 - 126.33: 11458 126.33 - 134.59: 314 Bond angle restraints: 26864 Sorted by residual: angle pdb=" C ARG A1130 " pdb=" N HIS A1131 " pdb=" CA HIS A1131 " ideal model delta sigma weight residual 121.54 131.98 -10.44 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C ARG C1130 " pdb=" N HIS C1131 " pdb=" CA HIS C1131 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 angle pdb=" C LYS A1051 " pdb=" N LYS A1052 " pdb=" CA LYS A1052 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS C1051 " pdb=" N LYS C1052 " pdb=" CA LYS C1052 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLY D1161 " pdb=" N ASP D1162 " pdb=" CA ASP D1162 " ideal model delta sigma weight residual 123.10 128.13 -5.03 9.60e-01 1.09e+00 2.74e+01 ... (remaining 26859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 11389 24.69 - 49.38: 374 49.38 - 74.07: 20 74.07 - 98.76: 13 98.76 - 123.45: 6 Dihedral angle restraints: 11802 sinusoidal: 4670 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PRO D1083 " pdb=" C PRO D1083 " pdb=" N GLU D1084 " pdb=" CA GLU D1084 " ideal model delta harmonic sigma weight residual 180.00 127.09 52.91 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA PRO B1083 " pdb=" C PRO B1083 " pdb=" N GLU B1084 " pdb=" CA GLU B1084 " ideal model delta harmonic sigma weight residual 180.00 127.11 52.89 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 175.81 -82.81 1 1.00e+01 1.00e-02 8.40e+01 ... (remaining 11799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2619 0.082 - 0.164: 324 0.164 - 0.246: 36 0.246 - 0.328: 13 0.328 - 0.410: 6 Chirality restraints: 2998 Sorted by residual: chirality pdb=" CG LEU C1002 " pdb=" CB LEU C1002 " pdb=" CD1 LEU C1002 " pdb=" CD2 LEU C1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CG LEU A1002 " pdb=" CB LEU A1002 " pdb=" CD1 LEU A1002 " pdb=" CD2 LEU A1002 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CG LEU A1114 " pdb=" CB LEU A1114 " pdb=" CD1 LEU A1114 " pdb=" CD2 LEU A1114 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2995 not shown) Planarity restraints: 3314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 513 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C GLY B 513 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY B 513 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 514 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 513 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C GLY D 513 " 0.042 2.00e-02 2.50e+03 pdb=" O GLY D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL D 514 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 421 " 0.032 2.00e-02 2.50e+03 1.70e-02 5.76e+00 pdb=" CG TYR A 421 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 421 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 421 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 421 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 421 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 421 " 0.023 2.00e-02 2.50e+03 ... (remaining 3311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2064 2.75 - 3.29: 20484 3.29 - 3.83: 32725 3.83 - 4.36: 37955 4.36 - 4.90: 63575 Nonbonded interactions: 156803 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.214 2.440 nonbonded pdb=" O PHE B1106 " pdb=" OG SER B1147 " model vdw 2.214 2.440 nonbonded pdb=" O PHE C1106 " pdb=" OG SER C1147 " model vdw 2.252 2.440 nonbonded pdb=" O PHE A1106 " pdb=" OG SER A1147 " model vdw 2.253 2.440 nonbonded pdb=" O PRO C1107 " pdb=" OG SER C1110 " model vdw 2.295 2.440 ... (remaining 156798 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 394 through 819 or resid 1002 through 1209 or resid 1302)) \ selection = (chain 'B' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) selection = (chain 'C' and (resid 394 through 819 or resid 1002 through 1209 or resid 1302)) \ selection = (chain 'D' and (resid 394 through 549 or resid 564 through 1209 or resid 1301)) } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.690 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 52.380 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 19882 Z= 0.430 Angle : 1.075 13.326 26864 Z= 0.587 Chirality : 0.060 0.410 2998 Planarity : 0.006 0.049 3314 Dihedral : 12.009 123.452 7218 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 4.74 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -1.48 (0.14), residues: 2460 helix: -0.43 (0.11), residues: 1318 sheet: -0.85 (0.37), residues: 150 loop : -1.65 (0.17), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 767 HIS 0.015 0.003 HIS C1204 PHE 0.036 0.003 PHE D1126 TYR 0.032 0.003 TYR A 421 ARG 0.006 0.001 ARG C1098 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 744 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7143 (tt0) cc_final: 0.6726 (tp30) REVERT: A 463 MET cc_start: 0.3694 (ptm) cc_final: 0.3329 (ttm) REVERT: A 474 ILE cc_start: 0.7564 (tt) cc_final: 0.7097 (mp) REVERT: A 478 PRO cc_start: 0.5095 (Cg_endo) cc_final: 0.4853 (Cg_exo) REVERT: A 489 ILE cc_start: 0.8092 (pt) cc_final: 0.7772 (pt) REVERT: A 500 ILE cc_start: 0.5861 (mt) cc_final: 0.5224 (mt) REVERT: A 503 MET cc_start: 0.4179 (ttt) cc_final: 0.3771 (ttt) REVERT: A 514 VAL cc_start: 0.8271 (m) cc_final: 0.7829 (m) REVERT: A 527 MET cc_start: 0.7095 (mtt) cc_final: 0.6197 (mpp) REVERT: A 528 CYS cc_start: 0.8959 (m) cc_final: 0.8479 (m) REVERT: A 585 MET cc_start: 0.8867 (mmt) cc_final: 0.8592 (mmm) REVERT: A 609 THR cc_start: 0.9321 (m) cc_final: 0.8966 (p) REVERT: A 627 GLU cc_start: 0.3883 (mt-10) cc_final: 0.2837 (pm20) REVERT: A 641 LYS cc_start: 0.5622 (mttp) cc_final: 0.5403 (ttpp) REVERT: A 705 GLU cc_start: 0.5364 (mm-30) cc_final: 0.5164 (mm-30) REVERT: A 721 MET cc_start: 0.5494 (pp-130) cc_final: 0.5078 (mtp) REVERT: A 742 LEU cc_start: 0.5555 (mm) cc_final: 0.5038 (tp) REVERT: A 811 LEU cc_start: 0.8472 (mm) cc_final: 0.8200 (mm) REVERT: A 815 CYS cc_start: 0.7992 (m) cc_final: 0.7643 (p) REVERT: A 1025 ILE cc_start: 0.8010 (mm) cc_final: 0.7741 (tp) REVERT: A 1030 ASP cc_start: 0.7115 (p0) cc_final: 0.6872 (t70) REVERT: A 1059 HIS cc_start: 0.7729 (p-80) cc_final: 0.6431 (p-80) REVERT: A 1169 LYS cc_start: 0.5613 (mtpt) cc_final: 0.5365 (mtmm) REVERT: A 1174 SER cc_start: 0.6071 (p) cc_final: 0.5750 (t) REVERT: A 1191 MET cc_start: 0.8003 (tpp) cc_final: 0.7406 (tpp) REVERT: A 1194 VAL cc_start: 0.7369 (t) cc_final: 0.7038 (t) REVERT: A 1195 LEU cc_start: 0.8277 (mm) cc_final: 0.7909 (mm) REVERT: B 411 ASN cc_start: 0.7286 (p0) cc_final: 0.6181 (m-40) REVERT: B 414 MET cc_start: 0.8154 (mpt) cc_final: 0.7752 (ptt) REVERT: B 442 LEU cc_start: 0.7873 (mt) cc_final: 0.7290 (mt) REVERT: B 463 MET cc_start: 0.2475 (mtm) cc_final: 0.2043 (mtm) REVERT: B 471 LYS cc_start: 0.6421 (tppp) cc_final: 0.5911 (mttp) REVERT: B 496 MET cc_start: 0.7878 (ttp) cc_final: 0.7624 (ttp) REVERT: B 511 LYS cc_start: 0.7316 (mmpt) cc_final: 0.6988 (mttt) REVERT: B 519 ASP cc_start: 0.8306 (t70) cc_final: 0.8078 (t0) REVERT: B 527 MET cc_start: 0.8594 (ttp) cc_final: 0.8241 (mmt) REVERT: B 538 VAL cc_start: 0.9090 (t) cc_final: 0.8864 (m) REVERT: B 546 PHE cc_start: 0.7964 (t80) cc_final: 0.7654 (t80) REVERT: B 586 GLN cc_start: 0.6652 (tp-100) cc_final: 0.5230 (mm110) REVERT: B 594 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7593 (ttp-170) REVERT: B 616 TYR cc_start: 0.8365 (t80) cc_final: 0.8079 (t80) REVERT: B 679 PRO cc_start: 0.5493 (Cg_endo) cc_final: 0.4797 (Cg_exo) REVERT: B 688 GLU cc_start: 0.8130 (tt0) cc_final: 0.7711 (tp30) REVERT: B 704 LEU cc_start: 0.7788 (pt) cc_final: 0.7456 (pt) REVERT: B 708 MET cc_start: 0.8283 (tpp) cc_final: 0.7716 (tpp) REVERT: B 710 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7263 (mp0) REVERT: B 713 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6025 (pt0) REVERT: B 714 GLN cc_start: 0.8018 (mm110) cc_final: 0.7582 (mm-40) REVERT: B 720 THR cc_start: 0.5719 (p) cc_final: 0.4768 (p) REVERT: B 752 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8054 (ptpp) REVERT: B 769 ASP cc_start: 0.6714 (m-30) cc_final: 0.6460 (m-30) REVERT: B 1040 LYS cc_start: 0.4568 (tppt) cc_final: 0.3839 (tppt) REVERT: B 1069 GLU cc_start: 0.6516 (tp30) cc_final: 0.6284 (tp30) REVERT: B 1087 ASP cc_start: 0.5792 (t70) cc_final: 0.4922 (p0) REVERT: B 1116 MET cc_start: 0.8500 (mmt) cc_final: 0.8259 (mmp) REVERT: B 1127 TYR cc_start: 0.5529 (m-10) cc_final: 0.5130 (m-80) REVERT: B 1191 MET cc_start: 0.8574 (mtt) cc_final: 0.8235 (mmm) REVERT: B 1195 LEU cc_start: 0.8830 (mt) cc_final: 0.8608 (mt) REVERT: C 402 GLU cc_start: 0.7965 (tt0) cc_final: 0.7550 (mm-30) REVERT: C 406 VAL cc_start: 0.8613 (t) cc_final: 0.8300 (t) REVERT: C 414 MET cc_start: 0.7152 (mpm) cc_final: 0.6268 (ttp) REVERT: C 474 ILE cc_start: 0.8706 (tt) cc_final: 0.8365 (mp) REVERT: C 498 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.3296 (pp) REVERT: C 517 PHE cc_start: 0.7580 (p90) cc_final: 0.7043 (p90) REVERT: C 528 CYS cc_start: 0.8731 (m) cc_final: 0.8387 (m) REVERT: C 586 GLN cc_start: 0.8101 (mt0) cc_final: 0.7661 (tm-30) REVERT: C 609 THR cc_start: 0.9206 (m) cc_final: 0.8820 (p) REVERT: C 663 LYS cc_start: 0.7864 (mmpt) cc_final: 0.7194 (pttm) REVERT: C 674 MET cc_start: 0.6835 (mtt) cc_final: 0.6348 (mtm) REVERT: C 692 ARG cc_start: 0.8026 (ttt90) cc_final: 0.7812 (ttt180) REVERT: C 721 MET cc_start: 0.6248 (pp-130) cc_final: 0.5356 (mtp) REVERT: C 783 LYS cc_start: 0.3456 (mtpt) cc_final: 0.3044 (mmtm) REVERT: C 1030 ASP cc_start: 0.7944 (p0) cc_final: 0.7593 (t0) REVERT: C 1056 VAL cc_start: 0.7432 (p) cc_final: 0.6971 (t) REVERT: C 1081 HIS cc_start: 0.6638 (m90) cc_final: 0.6384 (m-70) REVERT: C 1190 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8794 (mm-30) REVERT: C 1191 MET cc_start: 0.7951 (tpp) cc_final: 0.7362 (tpp) REVERT: C 1195 LEU cc_start: 0.8260 (mm) cc_final: 0.7666 (mm) REVERT: D 399 THR cc_start: 0.7531 (t) cc_final: 0.7268 (m) REVERT: D 432 ILE cc_start: 0.8017 (mm) cc_final: 0.7759 (tp) REVERT: D 481 ILE cc_start: 0.8343 (mt) cc_final: 0.8135 (mp) REVERT: D 539 VAL cc_start: 0.9105 (t) cc_final: 0.8856 (t) REVERT: D 542 LEU cc_start: 0.8939 (tt) cc_final: 0.8463 (tt) REVERT: D 546 PHE cc_start: 0.7846 (t80) cc_final: 0.7459 (t80) REVERT: D 585 MET cc_start: 0.8553 (mmt) cc_final: 0.8350 (mmt) REVERT: D 586 GLN cc_start: 0.7049 (tp-100) cc_final: 0.6129 (mm110) REVERT: D 625 THR cc_start: 0.6761 (p) cc_final: 0.6363 (t) REVERT: D 661 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7451 (mtt-85) REVERT: D 688 GLU cc_start: 0.8040 (tt0) cc_final: 0.7787 (mm-30) REVERT: D 706 SER cc_start: 0.8132 (p) cc_final: 0.7715 (m) REVERT: D 708 MET cc_start: 0.8279 (tpp) cc_final: 0.7525 (tpp) REVERT: D 713 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6546 (tp30) REVERT: D 714 GLN cc_start: 0.8006 (mm110) cc_final: 0.7630 (mm-40) REVERT: D 767 TRP cc_start: 0.6253 (m-90) cc_final: 0.5621 (m-90) REVERT: D 768 TYR cc_start: 0.6257 (m-80) cc_final: 0.6005 (m-10) REVERT: D 769 ASP cc_start: 0.6730 (m-30) cc_final: 0.6090 (t70) REVERT: D 799 LEU cc_start: 0.8877 (tp) cc_final: 0.8615 (tp) REVERT: D 1040 LYS cc_start: 0.4804 (tppt) cc_final: 0.4080 (tppt) REVERT: D 1058 THR cc_start: 0.3890 (m) cc_final: 0.3538 (m) REVERT: D 1068 LEU cc_start: 0.7384 (pt) cc_final: 0.6974 (pp) REVERT: D 1069 GLU cc_start: 0.6343 (tp30) cc_final: 0.6062 (mp0) REVERT: D 1087 ASP cc_start: 0.5908 (t70) cc_final: 0.5680 (p0) REVERT: D 1116 MET cc_start: 0.8382 (mmt) cc_final: 0.7877 (mmp) REVERT: D 1130 ARG cc_start: 0.6189 (tpm170) cc_final: 0.5783 (mmm160) REVERT: D 1140 PHE cc_start: 0.8056 (m-10) cc_final: 0.7808 (m-10) REVERT: D 1141 PHE cc_start: 0.8144 (m-80) cc_final: 0.7134 (m-80) REVERT: D 1190 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8248 (pt0) outliers start: 18 outliers final: 2 residues processed: 755 average time/residue: 0.3175 time to fit residues: 358.8625 Evaluate side-chains 443 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 440 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 619 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN A1204 HIS ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN B 726 ASN B 791 ASN B1081 HIS B1171 ASN C 412 HIS C 569 ASN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C1148 ASN C1204 HIS ** D 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN D 791 ASN D1081 HIS D1171 ASN D1198 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19882 Z= 0.220 Angle : 0.631 6.872 26864 Z= 0.336 Chirality : 0.042 0.170 2998 Planarity : 0.005 0.045 3314 Dihedral : 9.167 114.695 2790 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.25 % Favored : 96.42 % Rotamer: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: 0.29 (0.16), residues: 2460 helix: 1.35 (0.13), residues: 1320 sheet: -0.80 (0.37), residues: 150 loop : -1.26 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 460 HIS 0.007 0.002 HIS A1204 PHE 0.036 0.002 PHE B 658 TYR 0.031 0.002 TYR C 440 ARG 0.014 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 554 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7202 (tt0) cc_final: 0.6719 (tp30) REVERT: A 463 MET cc_start: 0.3335 (ptm) cc_final: 0.2243 (ttp) REVERT: A 466 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 474 ILE cc_start: 0.7666 (tt) cc_final: 0.7153 (mp) REVERT: A 478 PRO cc_start: 0.4740 (Cg_endo) cc_final: 0.4512 (Cg_exo) REVERT: A 496 MET cc_start: 0.8437 (ttp) cc_final: 0.7464 (tmm) REVERT: A 514 VAL cc_start: 0.8011 (m) cc_final: 0.7716 (m) REVERT: A 527 MET cc_start: 0.6581 (mtt) cc_final: 0.6352 (mtt) REVERT: A 528 CYS cc_start: 0.8921 (m) cc_final: 0.8648 (m) REVERT: A 573 ILE cc_start: 0.8278 (tt) cc_final: 0.8057 (tt) REVERT: A 609 THR cc_start: 0.9209 (m) cc_final: 0.8964 (p) REVERT: A 619 ASN cc_start: 0.6704 (t0) cc_final: 0.6160 (t0) REVERT: A 627 GLU cc_start: 0.3683 (mt-10) cc_final: 0.2656 (pm20) REVERT: A 742 LEU cc_start: 0.5781 (mm) cc_final: 0.5227 (tp) REVERT: A 811 LEU cc_start: 0.8527 (mm) cc_final: 0.8194 (mm) REVERT: A 1025 ILE cc_start: 0.7887 (mm) cc_final: 0.7620 (tp) REVERT: A 1059 HIS cc_start: 0.6600 (p-80) cc_final: 0.5554 (p90) REVERT: A 1141 PHE cc_start: 0.8212 (m-80) cc_final: 0.7755 (m-10) REVERT: A 1169 LYS cc_start: 0.5468 (mtpt) cc_final: 0.5209 (mtmm) REVERT: A 1174 SER cc_start: 0.5976 (p) cc_final: 0.5628 (t) REVERT: A 1194 VAL cc_start: 0.7373 (t) cc_final: 0.7150 (t) REVERT: A 1195 LEU cc_start: 0.8200 (mm) cc_final: 0.7909 (mm) REVERT: A 1199 MET cc_start: 0.8597 (mtm) cc_final: 0.8299 (mtt) REVERT: B 408 MET cc_start: 0.6058 (mtt) cc_final: 0.3599 (tmm) REVERT: B 414 MET cc_start: 0.7777 (mpp) cc_final: 0.7382 (ptt) REVERT: B 442 LEU cc_start: 0.7900 (mt) cc_final: 0.7469 (mt) REVERT: B 471 LYS cc_start: 0.6503 (tppp) cc_final: 0.6061 (mttp) REVERT: B 504 ILE cc_start: 0.7830 (pt) cc_final: 0.7358 (pt) REVERT: B 511 LYS cc_start: 0.7241 (mmpt) cc_final: 0.6843 (mttm) REVERT: B 519 ASP cc_start: 0.8383 (t70) cc_final: 0.8094 (t0) REVERT: B 546 PHE cc_start: 0.7947 (t80) cc_final: 0.7602 (t80) REVERT: B 586 GLN cc_start: 0.5636 (tp-100) cc_final: 0.4973 (mm110) REVERT: B 594 ARG cc_start: 0.7865 (ttp-170) cc_final: 0.7564 (ttp-170) REVERT: B 688 GLU cc_start: 0.8080 (tt0) cc_final: 0.7683 (tp30) REVERT: B 708 MET cc_start: 0.7943 (tpp) cc_final: 0.7736 (tpp) REVERT: B 723 VAL cc_start: 0.7068 (OUTLIER) cc_final: 0.6770 (m) REVERT: B 752 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8119 (ptpp) REVERT: B 1069 GLU cc_start: 0.6475 (tp30) cc_final: 0.6213 (mm-30) REVERT: B 1082 PHE cc_start: 0.7203 (m-80) cc_final: 0.6789 (m-80) REVERT: B 1116 MET cc_start: 0.8414 (mmt) cc_final: 0.8054 (mmp) REVERT: B 1187 ILE cc_start: 0.8742 (mt) cc_final: 0.8430 (mt) REVERT: B 1191 MET cc_start: 0.8564 (mtt) cc_final: 0.8310 (mmm) REVERT: C 405 TYR cc_start: 0.7962 (m-80) cc_final: 0.7728 (m-80) REVERT: C 474 ILE cc_start: 0.8680 (tt) cc_final: 0.8286 (mp) REVERT: C 517 PHE cc_start: 0.7576 (p90) cc_final: 0.6916 (p90) REVERT: C 521 LEU cc_start: 0.8803 (mp) cc_final: 0.8572 (mp) REVERT: C 528 CYS cc_start: 0.9039 (m) cc_final: 0.8708 (m) REVERT: C 586 GLN cc_start: 0.8122 (mt0) cc_final: 0.7808 (tm-30) REVERT: C 609 THR cc_start: 0.9166 (m) cc_final: 0.8815 (p) REVERT: C 619 ASN cc_start: 0.7123 (t0) cc_final: 0.6861 (t0) REVERT: C 663 LYS cc_start: 0.7747 (mmpt) cc_final: 0.7102 (pttm) REVERT: C 670 MET cc_start: 0.7332 (mmp) cc_final: 0.6840 (mmp) REVERT: C 673 TYR cc_start: 0.6858 (m-80) cc_final: 0.6389 (m-80) REVERT: C 674 MET cc_start: 0.7191 (mtt) cc_final: 0.6268 (mtt) REVERT: C 692 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7803 (ttt180) REVERT: C 705 GLU cc_start: 0.6467 (mp0) cc_final: 0.5272 (pm20) REVERT: C 708 MET cc_start: 0.6870 (tpt) cc_final: 0.5807 (tpt) REVERT: C 728 ASP cc_start: 0.6113 (p0) cc_final: 0.5856 (p0) REVERT: C 783 LYS cc_start: 0.3492 (mtpt) cc_final: 0.3076 (mmtm) REVERT: C 1023 MET cc_start: 0.8778 (mmm) cc_final: 0.8473 (mmm) REVERT: C 1025 ILE cc_start: 0.8328 (mm) cc_final: 0.8084 (pt) REVERT: C 1030 ASP cc_start: 0.7768 (p0) cc_final: 0.7391 (t0) REVERT: C 1068 LEU cc_start: 0.8621 (mt) cc_final: 0.8385 (mt) REVERT: C 1116 MET cc_start: 0.8962 (mtm) cc_final: 0.8682 (mtt) REVERT: C 1141 PHE cc_start: 0.7961 (m-10) cc_final: 0.7717 (m-10) REVERT: C 1190 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8629 (mm-30) REVERT: C 1191 MET cc_start: 0.7762 (tpp) cc_final: 0.7427 (tpp) REVERT: D 408 MET cc_start: 0.5603 (mtt) cc_final: 0.3718 (tmm) REVERT: D 432 ILE cc_start: 0.8113 (mm) cc_final: 0.7901 (tp) REVERT: D 463 MET cc_start: 0.3612 (pmm) cc_final: 0.1696 (mtt) REVERT: D 496 MET cc_start: 0.7758 (ttp) cc_final: 0.7533 (ttp) REVERT: D 504 ILE cc_start: 0.7958 (pt) cc_final: 0.7445 (pt) REVERT: D 505 LYS cc_start: 0.6655 (tttm) cc_final: 0.6441 (tptt) REVERT: D 546 PHE cc_start: 0.7723 (t80) cc_final: 0.7394 (t80) REVERT: D 585 MET cc_start: 0.8627 (mmt) cc_final: 0.8412 (mmt) REVERT: D 605 TRP cc_start: 0.8636 (t-100) cc_final: 0.8425 (t-100) REVERT: D 625 THR cc_start: 0.6731 (p) cc_final: 0.6289 (t) REVERT: D 661 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7647 (mtt-85) REVERT: D 688 GLU cc_start: 0.8021 (tt0) cc_final: 0.7739 (mm-30) REVERT: D 713 GLU cc_start: 0.6317 (mt-10) cc_final: 0.5929 (tp30) REVERT: D 723 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6432 (m) REVERT: D 769 ASP cc_start: 0.6824 (m-30) cc_final: 0.6621 (m-30) REVERT: D 799 LEU cc_start: 0.8808 (tp) cc_final: 0.8560 (tp) REVERT: D 1023 MET cc_start: 0.8499 (tpt) cc_final: 0.8051 (tpt) REVERT: D 1069 GLU cc_start: 0.6629 (tp30) cc_final: 0.6249 (mp0) REVERT: D 1121 ILE cc_start: 0.8257 (mm) cc_final: 0.8052 (pt) REVERT: D 1130 ARG cc_start: 0.6245 (tpm170) cc_final: 0.5844 (mmm160) REVERT: D 1140 PHE cc_start: 0.8166 (m-10) cc_final: 0.7928 (m-10) REVERT: D 1141 PHE cc_start: 0.8123 (m-80) cc_final: 0.7165 (m-80) REVERT: D 1201 ILE cc_start: 0.9005 (pt) cc_final: 0.8743 (mt) outliers start: 5 outliers final: 0 residues processed: 556 average time/residue: 0.3069 time to fit residues: 268.7130 Evaluate side-chains 389 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 0.1980 chunk 243 optimal weight: 0.0370 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B1008 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 HIS ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1198 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19882 Z= 0.173 Angle : 0.583 7.450 26864 Z= 0.306 Chirality : 0.041 0.170 2998 Planarity : 0.004 0.050 3314 Dihedral : 8.474 105.480 2790 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.74 % Favored : 96.02 % Rotamer: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.51 (0.17), residues: 2460 helix: 1.70 (0.14), residues: 1324 sheet: -1.31 (0.34), residues: 176 loop : -1.31 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 767 HIS 0.007 0.001 HIS B1131 PHE 0.033 0.002 PHE D 658 TYR 0.024 0.002 TYR D 647 ARG 0.005 0.000 ARG C1098 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 504 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.6996 (tt0) cc_final: 0.6528 (mm-30) REVERT: A 408 MET cc_start: 0.6539 (mmp) cc_final: 0.6267 (mmm) REVERT: A 427 ASP cc_start: 0.8068 (t0) cc_final: 0.7597 (m-30) REVERT: A 463 MET cc_start: 0.3463 (ptm) cc_final: 0.2412 (ttp) REVERT: A 474 ILE cc_start: 0.7572 (tt) cc_final: 0.7038 (mp) REVERT: A 496 MET cc_start: 0.8532 (ttp) cc_final: 0.7612 (tmm) REVERT: A 527 MET cc_start: 0.6521 (mtt) cc_final: 0.6310 (mtt) REVERT: A 534 ILE cc_start: 0.8281 (mm) cc_final: 0.8077 (mm) REVERT: A 538 VAL cc_start: 0.8745 (t) cc_final: 0.8498 (m) REVERT: A 627 GLU cc_start: 0.3812 (mt-10) cc_final: 0.3147 (pm20) REVERT: A 742 LEU cc_start: 0.5933 (mm) cc_final: 0.5366 (tp) REVERT: A 765 LYS cc_start: 0.5660 (pttt) cc_final: 0.5164 (mtmm) REVERT: A 1025 ILE cc_start: 0.7965 (mm) cc_final: 0.7702 (tp) REVERT: A 1141 PHE cc_start: 0.8200 (m-80) cc_final: 0.7736 (m-10) REVERT: A 1169 LYS cc_start: 0.5400 (mtpt) cc_final: 0.5105 (mtmm) REVERT: A 1174 SER cc_start: 0.5990 (p) cc_final: 0.5644 (t) REVERT: A 1191 MET cc_start: 0.8009 (tpp) cc_final: 0.7387 (tpp) REVERT: A 1195 LEU cc_start: 0.8275 (mm) cc_final: 0.7866 (mm) REVERT: A 1200 PHE cc_start: 0.8479 (t80) cc_final: 0.8258 (t80) REVERT: B 408 MET cc_start: 0.6020 (mtt) cc_final: 0.3405 (tmm) REVERT: B 414 MET cc_start: 0.7742 (mpp) cc_final: 0.7360 (ptt) REVERT: B 463 MET cc_start: 0.2982 (mtt) cc_final: 0.2396 (mtm) REVERT: B 471 LYS cc_start: 0.6573 (tppp) cc_final: 0.6039 (mttp) REVERT: B 496 MET cc_start: 0.7445 (ttp) cc_final: 0.7220 (ttp) REVERT: B 504 ILE cc_start: 0.7585 (pt) cc_final: 0.7127 (pt) REVERT: B 511 LYS cc_start: 0.7118 (mmpt) cc_final: 0.6710 (mttm) REVERT: B 519 ASP cc_start: 0.8344 (t70) cc_final: 0.8029 (t0) REVERT: B 546 PHE cc_start: 0.7900 (t80) cc_final: 0.7516 (t80) REVERT: B 586 GLN cc_start: 0.6094 (tp-100) cc_final: 0.5819 (mm110) REVERT: B 594 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7543 (ttp-170) REVERT: B 688 GLU cc_start: 0.8111 (tt0) cc_final: 0.7703 (tp30) REVERT: B 704 LEU cc_start: 0.7828 (pp) cc_final: 0.7581 (pp) REVERT: B 708 MET cc_start: 0.8120 (tpp) cc_final: 0.7835 (tpp) REVERT: B 1068 LEU cc_start: 0.7461 (pp) cc_final: 0.6854 (pp) REVERT: B 1069 GLU cc_start: 0.6359 (tp30) cc_final: 0.5944 (mp0) REVERT: B 1080 ASP cc_start: 0.7804 (m-30) cc_final: 0.7566 (m-30) REVERT: B 1191 MET cc_start: 0.8552 (mtt) cc_final: 0.8319 (mmm) REVERT: C 405 TYR cc_start: 0.8242 (m-80) cc_final: 0.8019 (m-80) REVERT: C 474 ILE cc_start: 0.8584 (tt) cc_final: 0.8203 (mp) REVERT: C 517 PHE cc_start: 0.7739 (p90) cc_final: 0.7070 (p90) REVERT: C 521 LEU cc_start: 0.8782 (mp) cc_final: 0.8549 (mp) REVERT: C 528 CYS cc_start: 0.8983 (m) cc_final: 0.8667 (m) REVERT: C 586 GLN cc_start: 0.8152 (mt0) cc_final: 0.7624 (tm-30) REVERT: C 609 THR cc_start: 0.9221 (m) cc_final: 0.8900 (p) REVERT: C 619 ASN cc_start: 0.7157 (t0) cc_final: 0.6817 (t0) REVERT: C 663 LYS cc_start: 0.7751 (mmpt) cc_final: 0.7177 (pttm) REVERT: C 670 MET cc_start: 0.7577 (mmp) cc_final: 0.7241 (mmp) REVERT: C 692 ARG cc_start: 0.7934 (ttt90) cc_final: 0.7729 (ttt180) REVERT: C 708 MET cc_start: 0.6497 (tpt) cc_final: 0.6287 (tpt) REVERT: C 728 ASP cc_start: 0.6248 (p0) cc_final: 0.5937 (p0) REVERT: C 783 LYS cc_start: 0.3448 (mtpt) cc_final: 0.3035 (mmtm) REVERT: C 1023 MET cc_start: 0.8778 (mmm) cc_final: 0.8501 (mmm) REVERT: C 1025 ILE cc_start: 0.8319 (mm) cc_final: 0.8026 (pt) REVERT: C 1030 ASP cc_start: 0.7988 (p0) cc_final: 0.7456 (t0) REVERT: C 1116 MET cc_start: 0.8955 (mtm) cc_final: 0.8680 (mtt) REVERT: C 1180 TYR cc_start: 0.8421 (m-10) cc_final: 0.8196 (m-80) REVERT: C 1190 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8579 (mm-30) REVERT: C 1191 MET cc_start: 0.7743 (tpp) cc_final: 0.7390 (tpp) REVERT: D 408 MET cc_start: 0.5529 (mtt) cc_final: 0.4302 (ttt) REVERT: D 432 ILE cc_start: 0.8227 (mm) cc_final: 0.7993 (tp) REVERT: D 463 MET cc_start: 0.3278 (pmm) cc_final: 0.1567 (ttm) REVERT: D 486 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6596 (mm-30) REVERT: D 496 MET cc_start: 0.7634 (ttp) cc_final: 0.7359 (ttp) REVERT: D 504 ILE cc_start: 0.7805 (pt) cc_final: 0.7460 (pt) REVERT: D 505 LYS cc_start: 0.6560 (tttm) cc_final: 0.6269 (ttpt) REVERT: D 546 PHE cc_start: 0.7608 (t80) cc_final: 0.7385 (t80) REVERT: D 573 ILE cc_start: 0.8331 (tp) cc_final: 0.8125 (tp) REVERT: D 661 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7615 (mtt-85) REVERT: D 688 GLU cc_start: 0.8069 (tt0) cc_final: 0.7724 (mm-30) REVERT: D 1141 PHE cc_start: 0.8202 (m-80) cc_final: 0.7296 (m-80) REVERT: D 1202 ASP cc_start: 0.9032 (m-30) cc_final: 0.8831 (m-30) outliers start: 1 outliers final: 0 residues processed: 504 average time/residue: 0.2894 time to fit residues: 228.4388 Evaluate side-chains 372 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 0.1980 chunk 151 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 791 ASN B1008 GLN ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN D1081 HIS D1198 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19882 Z= 0.205 Angle : 0.597 6.984 26864 Z= 0.311 Chirality : 0.041 0.176 2998 Planarity : 0.004 0.050 3314 Dihedral : 8.011 98.414 2790 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.24 % Rotamer: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2460 helix: 1.68 (0.14), residues: 1336 sheet: -1.43 (0.36), residues: 156 loop : -1.18 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 767 HIS 0.006 0.002 HIS C1059 PHE 0.027 0.002 PHE D 658 TYR 0.025 0.002 TYR C 440 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 463 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7009 (tt0) cc_final: 0.6566 (mm-30) REVERT: A 408 MET cc_start: 0.6698 (mmp) cc_final: 0.6289 (mmm) REVERT: A 427 ASP cc_start: 0.8008 (t0) cc_final: 0.7525 (m-30) REVERT: A 463 MET cc_start: 0.3312 (ptm) cc_final: 0.2403 (ttp) REVERT: A 496 MET cc_start: 0.8402 (ttp) cc_final: 0.8057 (ttp) REVERT: A 527 MET cc_start: 0.6643 (mtt) cc_final: 0.6432 (mtt) REVERT: A 534 ILE cc_start: 0.8389 (mm) cc_final: 0.8145 (mm) REVERT: A 538 VAL cc_start: 0.8796 (t) cc_final: 0.8506 (m) REVERT: A 606 TRP cc_start: 0.7229 (m-10) cc_final: 0.7029 (m-10) REVERT: A 609 THR cc_start: 0.9189 (m) cc_final: 0.8888 (p) REVERT: A 619 ASN cc_start: 0.7013 (t0) cc_final: 0.6681 (t0) REVERT: A 627 GLU cc_start: 0.3635 (mt-10) cc_final: 0.2892 (mp0) REVERT: A 742 LEU cc_start: 0.5986 (mm) cc_final: 0.5440 (tp) REVERT: A 765 LYS cc_start: 0.5585 (pttt) cc_final: 0.5020 (mtmm) REVERT: A 783 LYS cc_start: 0.1869 (tttm) cc_final: 0.1188 (ptmm) REVERT: A 1023 MET cc_start: 0.8521 (mmm) cc_final: 0.8280 (mmm) REVERT: A 1025 ILE cc_start: 0.7968 (mm) cc_final: 0.7728 (tp) REVERT: A 1174 SER cc_start: 0.6175 (p) cc_final: 0.5739 (t) REVERT: A 1195 LEU cc_start: 0.8337 (mm) cc_final: 0.7735 (mm) REVERT: B 404 PRO cc_start: 0.2631 (Cg_endo) cc_final: 0.1109 (Cg_exo) REVERT: B 408 MET cc_start: 0.6252 (mtt) cc_final: 0.3733 (tmm) REVERT: B 414 MET cc_start: 0.7722 (mpp) cc_final: 0.7385 (ptt) REVERT: B 463 MET cc_start: 0.2781 (mtt) cc_final: 0.2310 (mtm) REVERT: B 496 MET cc_start: 0.7431 (ttp) cc_final: 0.7140 (ttp) REVERT: B 504 ILE cc_start: 0.7575 (pt) cc_final: 0.7347 (pt) REVERT: B 511 LYS cc_start: 0.7095 (mmpt) cc_final: 0.6685 (mttm) REVERT: B 519 ASP cc_start: 0.8303 (t70) cc_final: 0.8014 (t0) REVERT: B 539 VAL cc_start: 0.9221 (t) cc_final: 0.8990 (p) REVERT: B 546 PHE cc_start: 0.8016 (t80) cc_final: 0.7588 (t80) REVERT: B 586 GLN cc_start: 0.5999 (tp-100) cc_final: 0.5713 (mm110) REVERT: B 594 ARG cc_start: 0.7788 (ttp-170) cc_final: 0.7548 (ttp-170) REVERT: B 688 GLU cc_start: 0.8117 (tt0) cc_final: 0.7709 (tp30) REVERT: B 708 MET cc_start: 0.8102 (tpp) cc_final: 0.7878 (tpp) REVERT: B 1068 LEU cc_start: 0.7465 (pp) cc_final: 0.6930 (pp) REVERT: B 1069 GLU cc_start: 0.6460 (tp30) cc_final: 0.6116 (mp0) REVERT: B 1191 MET cc_start: 0.8659 (mtt) cc_final: 0.8370 (mmm) REVERT: B 1202 ASP cc_start: 0.8759 (m-30) cc_final: 0.8546 (m-30) REVERT: C 405 TYR cc_start: 0.8263 (m-80) cc_final: 0.7845 (m-80) REVERT: C 474 ILE cc_start: 0.8520 (tt) cc_final: 0.8114 (mp) REVERT: C 496 MET cc_start: 0.7146 (ppp) cc_final: 0.6944 (ppp) REVERT: C 517 PHE cc_start: 0.7910 (p90) cc_final: 0.7201 (p90) REVERT: C 521 LEU cc_start: 0.8766 (mp) cc_final: 0.8535 (mp) REVERT: C 528 CYS cc_start: 0.8976 (m) cc_final: 0.8639 (m) REVERT: C 586 GLN cc_start: 0.8120 (mt0) cc_final: 0.7708 (tm-30) REVERT: C 609 THR cc_start: 0.9243 (m) cc_final: 0.8969 (p) REVERT: C 619 ASN cc_start: 0.7339 (t0) cc_final: 0.7054 (t0) REVERT: C 663 LYS cc_start: 0.7756 (mmpt) cc_final: 0.7169 (pttm) REVERT: C 670 MET cc_start: 0.7753 (mmp) cc_final: 0.7289 (mmp) REVERT: C 783 LYS cc_start: 0.3298 (mtpt) cc_final: 0.2850 (mmtm) REVERT: C 807 MET cc_start: 0.8563 (mtp) cc_final: 0.8276 (tmm) REVERT: C 1023 MET cc_start: 0.8827 (mmm) cc_final: 0.8512 (mmm) REVERT: C 1025 ILE cc_start: 0.8236 (mm) cc_final: 0.7925 (pt) REVERT: C 1030 ASP cc_start: 0.7945 (p0) cc_final: 0.7277 (t0) REVERT: C 1097 LEU cc_start: 0.8672 (pp) cc_final: 0.8455 (pp) REVERT: C 1116 MET cc_start: 0.8949 (mtm) cc_final: 0.8658 (mtt) REVERT: C 1190 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8621 (mm-30) REVERT: C 1191 MET cc_start: 0.7766 (tpp) cc_final: 0.7387 (tpp) REVERT: D 404 PRO cc_start: 0.3113 (Cg_endo) cc_final: 0.2882 (Cg_exo) REVERT: D 408 MET cc_start: 0.5755 (mtt) cc_final: 0.3719 (tmm) REVERT: D 432 ILE cc_start: 0.8165 (mm) cc_final: 0.7917 (tp) REVERT: D 463 MET cc_start: 0.3630 (pmm) cc_final: 0.1884 (mtt) REVERT: D 504 ILE cc_start: 0.7783 (pt) cc_final: 0.7446 (pt) REVERT: D 505 LYS cc_start: 0.6456 (tttm) cc_final: 0.6167 (tptt) REVERT: D 585 MET cc_start: 0.8673 (mmt) cc_final: 0.8278 (mmt) REVERT: D 661 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7619 (mtt-85) REVERT: D 688 GLU cc_start: 0.8131 (tt0) cc_final: 0.7759 (mm-30) REVERT: D 769 ASP cc_start: 0.6815 (m-30) cc_final: 0.6379 (t0) REVERT: D 1141 PHE cc_start: 0.8217 (m-80) cc_final: 0.7351 (m-80) REVERT: D 1153 ILE cc_start: 0.8665 (mm) cc_final: 0.8177 (mm) outliers start: 3 outliers final: 0 residues processed: 465 average time/residue: 0.2844 time to fit residues: 209.0705 Evaluate side-chains 359 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 204 optimal weight: 0.6980 chunk 165 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1204 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C1148 ASN C1204 HIS D 586 GLN D 791 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19882 Z= 0.218 Angle : 0.606 9.953 26864 Z= 0.317 Chirality : 0.041 0.193 2998 Planarity : 0.004 0.040 3314 Dihedral : 7.622 92.180 2790 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.47 (0.17), residues: 2460 helix: 1.67 (0.14), residues: 1324 sheet: -1.58 (0.35), residues: 170 loop : -1.28 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 605 HIS 0.009 0.002 HIS A1204 PHE 0.021 0.002 PHE D 658 TYR 0.020 0.002 TYR C 440 ARG 0.004 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 GLU cc_start: 0.7027 (tt0) cc_final: 0.6557 (mm-30) REVERT: A 408 MET cc_start: 0.6743 (mmp) cc_final: 0.6414 (mmm) REVERT: A 427 ASP cc_start: 0.8034 (t0) cc_final: 0.7621 (m-30) REVERT: A 463 MET cc_start: 0.3490 (ptm) cc_final: 0.2642 (ttp) REVERT: A 496 MET cc_start: 0.8369 (ttp) cc_final: 0.7561 (tmm) REVERT: A 538 VAL cc_start: 0.8758 (t) cc_final: 0.8447 (m) REVERT: A 609 THR cc_start: 0.9192 (m) cc_final: 0.8925 (p) REVERT: A 673 TYR cc_start: 0.6642 (m-80) cc_final: 0.6111 (m-80) REVERT: A 783 LYS cc_start: 0.2639 (tttt) cc_final: 0.2281 (mmtm) REVERT: A 811 LEU cc_start: 0.8493 (mm) cc_final: 0.8279 (mm) REVERT: A 1025 ILE cc_start: 0.7997 (mm) cc_final: 0.7780 (tp) REVERT: A 1059 HIS cc_start: 0.6858 (p90) cc_final: 0.6390 (p-80) REVERT: A 1174 SER cc_start: 0.6195 (p) cc_final: 0.5799 (t) REVERT: A 1191 MET cc_start: 0.7948 (tpp) cc_final: 0.7235 (tpp) REVERT: A 1195 LEU cc_start: 0.8327 (mm) cc_final: 0.7701 (mm) REVERT: B 404 PRO cc_start: 0.2915 (Cg_endo) cc_final: 0.1420 (Cg_exo) REVERT: B 408 MET cc_start: 0.6147 (mtt) cc_final: 0.4159 (tmm) REVERT: B 414 MET cc_start: 0.7746 (mpp) cc_final: 0.7437 (ptt) REVERT: B 463 MET cc_start: 0.2853 (mtt) cc_final: 0.2466 (mtm) REVERT: B 496 MET cc_start: 0.7376 (ttp) cc_final: 0.7071 (ttp) REVERT: B 504 ILE cc_start: 0.7618 (pt) cc_final: 0.7391 (pt) REVERT: B 511 LYS cc_start: 0.6979 (mmpt) cc_final: 0.6467 (mttm) REVERT: B 519 ASP cc_start: 0.8297 (t70) cc_final: 0.8024 (t0) REVERT: B 539 VAL cc_start: 0.9248 (t) cc_final: 0.9025 (p) REVERT: B 546 PHE cc_start: 0.8034 (t80) cc_final: 0.7654 (t80) REVERT: B 594 ARG cc_start: 0.7789 (ttp-170) cc_final: 0.7546 (ttp-170) REVERT: B 688 GLU cc_start: 0.8130 (tt0) cc_final: 0.7669 (tp30) REVERT: B 708 MET cc_start: 0.8074 (tpp) cc_final: 0.7829 (tpp) REVERT: B 769 ASP cc_start: 0.6574 (m-30) cc_final: 0.6226 (t0) REVERT: B 1080 ASP cc_start: 0.7627 (t0) cc_final: 0.7032 (t0) REVERT: B 1091 ASP cc_start: 0.6644 (t0) cc_final: 0.6317 (p0) REVERT: B 1141 PHE cc_start: 0.8417 (m-80) cc_final: 0.7778 (m-80) REVERT: B 1191 MET cc_start: 0.8686 (mtt) cc_final: 0.8394 (mmm) REVERT: C 517 PHE cc_start: 0.8008 (p90) cc_final: 0.7341 (p90) REVERT: C 521 LEU cc_start: 0.8751 (mp) cc_final: 0.8531 (mp) REVERT: C 528 CYS cc_start: 0.8966 (m) cc_final: 0.8629 (m) REVERT: C 586 GLN cc_start: 0.8097 (mt0) cc_final: 0.7591 (tm-30) REVERT: C 609 THR cc_start: 0.9260 (m) cc_final: 0.8963 (p) REVERT: C 619 ASN cc_start: 0.7294 (t0) cc_final: 0.7013 (t0) REVERT: C 663 LYS cc_start: 0.7741 (mmpt) cc_final: 0.7137 (pttm) REVERT: C 670 MET cc_start: 0.7814 (mmp) cc_final: 0.7373 (mmp) REVERT: C 783 LYS cc_start: 0.3255 (mtpt) cc_final: 0.2789 (mmtm) REVERT: C 811 LEU cc_start: 0.8549 (mm) cc_final: 0.8263 (mt) REVERT: C 1023 MET cc_start: 0.8839 (mmm) cc_final: 0.8496 (mmm) REVERT: C 1025 ILE cc_start: 0.8269 (mm) cc_final: 0.7982 (pt) REVERT: C 1030 ASP cc_start: 0.8197 (p0) cc_final: 0.7345 (t0) REVERT: C 1116 MET cc_start: 0.8926 (mtm) cc_final: 0.8650 (mtt) REVERT: C 1190 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8968 (mm-30) REVERT: C 1191 MET cc_start: 0.7796 (tpp) cc_final: 0.7239 (tpp) REVERT: C 1195 LEU cc_start: 0.8308 (mm) cc_final: 0.7679 (mm) REVERT: D 404 PRO cc_start: 0.3268 (Cg_endo) cc_final: 0.2939 (Cg_exo) REVERT: D 408 MET cc_start: 0.5776 (mtt) cc_final: 0.3704 (tmm) REVERT: D 432 ILE cc_start: 0.8158 (mm) cc_final: 0.7919 (tp) REVERT: D 463 MET cc_start: 0.3790 (pmm) cc_final: 0.1922 (mtt) REVERT: D 496 MET cc_start: 0.7714 (ttp) cc_final: 0.7351 (ttp) REVERT: D 504 ILE cc_start: 0.7772 (pt) cc_final: 0.7369 (pt) REVERT: D 505 LYS cc_start: 0.6464 (tttm) cc_final: 0.6129 (tptt) REVERT: D 546 PHE cc_start: 0.7731 (t80) cc_final: 0.7290 (t80) REVERT: D 585 MET cc_start: 0.8760 (mmt) cc_final: 0.8304 (mmt) REVERT: D 661 ARG cc_start: 0.8096 (mtt180) cc_final: 0.7646 (mtt-85) REVERT: D 688 GLU cc_start: 0.8079 (tt0) cc_final: 0.7684 (mm-30) REVERT: D 799 LEU cc_start: 0.8717 (tp) cc_final: 0.8512 (tp) REVERT: D 1080 ASP cc_start: 0.8353 (p0) cc_final: 0.8004 (t0) REVERT: D 1141 PHE cc_start: 0.8225 (m-80) cc_final: 0.7421 (m-80) outliers start: 2 outliers final: 0 residues processed: 449 average time/residue: 0.2818 time to fit residues: 202.2943 Evaluate side-chains 330 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 239 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 435 HIS B 714 GLN B 747 ASN B1008 GLN C1204 HIS D 586 GLN D 747 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19882 Z= 0.258 Angle : 0.639 8.254 26864 Z= 0.334 Chirality : 0.043 0.205 2998 Planarity : 0.004 0.045 3314 Dihedral : 7.326 87.042 2790 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.33 (0.17), residues: 2460 helix: 1.47 (0.14), residues: 1326 sheet: -1.58 (0.36), residues: 158 loop : -1.23 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 605 HIS 0.007 0.002 HIS B1131 PHE 0.020 0.002 PHE B 658 TYR 0.024 0.002 TYR A 440 ARG 0.004 0.001 ARG A1005 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7108 (mmp) cc_final: 0.6758 (mmm) REVERT: A 427 ASP cc_start: 0.8001 (t0) cc_final: 0.7600 (m-30) REVERT: A 587 GLN cc_start: 0.7043 (mm-40) cc_final: 0.5952 (mm-40) REVERT: A 609 THR cc_start: 0.9218 (m) cc_final: 0.8954 (p) REVERT: A 619 ASN cc_start: 0.7539 (t0) cc_final: 0.7337 (t0) REVERT: A 673 TYR cc_start: 0.6718 (m-80) cc_final: 0.6241 (m-80) REVERT: A 783 LYS cc_start: 0.2685 (tttt) cc_final: 0.2320 (mmtm) REVERT: A 1054 GLU cc_start: 0.6550 (mm-30) cc_final: 0.6298 (tm-30) REVERT: A 1180 TYR cc_start: 0.8527 (m-10) cc_final: 0.8152 (m-80) REVERT: A 1191 MET cc_start: 0.8003 (tpp) cc_final: 0.7345 (tpp) REVERT: A 1195 LEU cc_start: 0.8284 (mm) cc_final: 0.7642 (mm) REVERT: B 404 PRO cc_start: 0.3028 (Cg_endo) cc_final: 0.1255 (Cg_exo) REVERT: B 408 MET cc_start: 0.6146 (mtt) cc_final: 0.3707 (tmm) REVERT: B 414 MET cc_start: 0.7800 (mpp) cc_final: 0.7519 (ptt) REVERT: B 463 MET cc_start: 0.2969 (mtt) cc_final: 0.2490 (mtm) REVERT: B 511 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6566 (mttm) REVERT: B 519 ASP cc_start: 0.8327 (t70) cc_final: 0.8085 (t0) REVERT: B 524 GLU cc_start: 0.8435 (pm20) cc_final: 0.8075 (pm20) REVERT: B 546 PHE cc_start: 0.8001 (t80) cc_final: 0.7557 (t80) REVERT: B 594 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7564 (ttp-170) REVERT: B 688 GLU cc_start: 0.8168 (tt0) cc_final: 0.7693 (tp30) REVERT: B 708 MET cc_start: 0.8032 (tpp) cc_final: 0.7741 (tpp) REVERT: B 769 ASP cc_start: 0.6552 (m-30) cc_final: 0.5982 (t0) REVERT: B 1057 MET cc_start: 0.6998 (mtm) cc_final: 0.6452 (tpt) REVERT: B 1091 ASP cc_start: 0.6811 (t0) cc_final: 0.6463 (p0) REVERT: B 1141 PHE cc_start: 0.8412 (m-80) cc_final: 0.7774 (m-80) REVERT: B 1191 MET cc_start: 0.8750 (mtt) cc_final: 0.8404 (mmm) REVERT: C 415 LEU cc_start: 0.8034 (mt) cc_final: 0.7736 (mt) REVERT: C 517 PHE cc_start: 0.8005 (p90) cc_final: 0.7385 (p90) REVERT: C 528 CYS cc_start: 0.8988 (m) cc_final: 0.8627 (m) REVERT: C 586 GLN cc_start: 0.8032 (mt0) cc_final: 0.7641 (tm-30) REVERT: C 609 THR cc_start: 0.9225 (m) cc_final: 0.8980 (p) REVERT: C 663 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7073 (pttm) REVERT: C 670 MET cc_start: 0.7783 (mmp) cc_final: 0.7189 (mmp) REVERT: C 673 TYR cc_start: 0.6956 (m-80) cc_final: 0.6329 (m-80) REVERT: C 783 LYS cc_start: 0.3201 (mtpt) cc_final: 0.2710 (mmtm) REVERT: C 811 LEU cc_start: 0.8467 (mm) cc_final: 0.8194 (mm) REVERT: C 1009 MET cc_start: 0.8949 (ptp) cc_final: 0.8716 (ptt) REVERT: C 1023 MET cc_start: 0.8789 (mmm) cc_final: 0.8505 (mmm) REVERT: C 1030 ASP cc_start: 0.8121 (p0) cc_final: 0.7250 (t0) REVERT: C 1190 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8980 (mm-30) REVERT: C 1191 MET cc_start: 0.7935 (tpp) cc_final: 0.7424 (tpp) REVERT: C 1195 LEU cc_start: 0.8140 (mm) cc_final: 0.7656 (mm) REVERT: D 404 PRO cc_start: 0.3343 (Cg_endo) cc_final: 0.3033 (Cg_exo) REVERT: D 408 MET cc_start: 0.5903 (mtt) cc_final: 0.4209 (tmm) REVERT: D 463 MET cc_start: 0.4022 (pmm) cc_final: 0.2129 (mtt) REVERT: D 471 LYS cc_start: 0.6059 (mttp) cc_final: 0.5716 (ttmt) REVERT: D 496 MET cc_start: 0.7703 (ttp) cc_final: 0.7286 (ttp) REVERT: D 504 ILE cc_start: 0.7773 (pt) cc_final: 0.7506 (pt) REVERT: D 519 ASP cc_start: 0.8235 (t70) cc_final: 0.8022 (t0) REVERT: D 546 PHE cc_start: 0.7702 (t80) cc_final: 0.7322 (t80) REVERT: D 585 MET cc_start: 0.8875 (mmt) cc_final: 0.8481 (mmt) REVERT: D 661 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7882 (mtp85) REVERT: D 688 GLU cc_start: 0.8118 (tt0) cc_final: 0.7720 (mm-30) REVERT: D 769 ASP cc_start: 0.6767 (m-30) cc_final: 0.6214 (t0) REVERT: D 799 LEU cc_start: 0.8663 (tp) cc_final: 0.8432 (tp) REVERT: D 1153 ILE cc_start: 0.8596 (mm) cc_final: 0.7986 (mp) REVERT: D 1191 MET cc_start: 0.9033 (mmp) cc_final: 0.8829 (mmm) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.2873 time to fit residues: 193.8355 Evaluate side-chains 322 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 7.9990 chunk 27 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 175 optimal weight: 0.2980 chunk 135 optimal weight: 0.0570 chunk 201 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1053 ASN A1204 HIS B 791 ASN B1008 GLN C 569 ASN C1159 ASN C1204 HIS D 714 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19882 Z= 0.162 Angle : 0.579 7.911 26864 Z= 0.298 Chirality : 0.041 0.188 2998 Planarity : 0.003 0.040 3314 Dihedral : 6.782 80.633 2790 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.46 (0.17), residues: 2460 helix: 1.64 (0.14), residues: 1328 sheet: -1.79 (0.39), residues: 134 loop : -1.25 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 605 HIS 0.013 0.002 HIS C1204 PHE 0.024 0.001 PHE C 579 TYR 0.021 0.002 TYR B 523 ARG 0.003 0.000 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.6761 (mmp) cc_final: 0.6504 (mmm) REVERT: A 427 ASP cc_start: 0.7969 (t0) cc_final: 0.7577 (m-30) REVERT: A 538 VAL cc_start: 0.8779 (t) cc_final: 0.8530 (m) REVERT: A 609 THR cc_start: 0.9201 (m) cc_final: 0.8977 (p) REVERT: A 619 ASN cc_start: 0.7188 (t0) cc_final: 0.6811 (t0) REVERT: A 673 TYR cc_start: 0.6691 (m-80) cc_final: 0.6199 (m-80) REVERT: A 708 MET cc_start: 0.5277 (tpt) cc_final: 0.5009 (tpt) REVERT: A 783 LYS cc_start: 0.2700 (tttt) cc_final: 0.2453 (mmtm) REVERT: A 811 LEU cc_start: 0.8462 (mm) cc_final: 0.8261 (mm) REVERT: A 1080 ASP cc_start: 0.7629 (m-30) cc_final: 0.7285 (t0) REVERT: A 1174 SER cc_start: 0.6355 (p) cc_final: 0.6099 (t) REVERT: A 1191 MET cc_start: 0.7932 (tpp) cc_final: 0.7246 (tpp) REVERT: A 1195 LEU cc_start: 0.8324 (mm) cc_final: 0.7643 (mm) REVERT: B 404 PRO cc_start: 0.3337 (Cg_endo) cc_final: 0.1668 (Cg_exo) REVERT: B 408 MET cc_start: 0.6235 (mtt) cc_final: 0.3858 (tmm) REVERT: B 463 MET cc_start: 0.2670 (mtt) cc_final: 0.2224 (mtm) REVERT: B 511 LYS cc_start: 0.7019 (mmpt) cc_final: 0.6613 (mttt) REVERT: B 546 PHE cc_start: 0.7819 (t80) cc_final: 0.7503 (t80) REVERT: B 573 ILE cc_start: 0.7787 (pt) cc_final: 0.7558 (pt) REVERT: B 594 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7549 (ttp-170) REVERT: B 688 GLU cc_start: 0.8158 (tt0) cc_final: 0.7512 (tp30) REVERT: B 708 MET cc_start: 0.7992 (tpp) cc_final: 0.7687 (tpp) REVERT: B 769 ASP cc_start: 0.6504 (m-30) cc_final: 0.6086 (t0) REVERT: B 1091 ASP cc_start: 0.6784 (t0) cc_final: 0.6483 (p0) REVERT: B 1141 PHE cc_start: 0.8395 (m-80) cc_final: 0.7761 (m-80) REVERT: B 1191 MET cc_start: 0.8694 (mtt) cc_final: 0.8392 (mmm) REVERT: C 517 PHE cc_start: 0.7880 (p90) cc_final: 0.7188 (p90) REVERT: C 521 LEU cc_start: 0.8708 (mp) cc_final: 0.8481 (mp) REVERT: C 528 CYS cc_start: 0.8996 (m) cc_final: 0.8723 (m) REVERT: C 531 PHE cc_start: 0.8395 (m-10) cc_final: 0.8190 (m-10) REVERT: C 586 GLN cc_start: 0.8091 (mt0) cc_final: 0.7500 (tm-30) REVERT: C 609 THR cc_start: 0.9249 (m) cc_final: 0.8956 (p) REVERT: C 663 LYS cc_start: 0.7717 (mmpt) cc_final: 0.7179 (pttm) REVERT: C 670 MET cc_start: 0.7821 (mmp) cc_final: 0.7364 (mmp) REVERT: C 783 LYS cc_start: 0.3304 (mtpt) cc_final: 0.2854 (mmtm) REVERT: C 811 LEU cc_start: 0.8464 (mm) cc_final: 0.8193 (mt) REVERT: C 1023 MET cc_start: 0.8874 (mmm) cc_final: 0.8651 (mmm) REVERT: C 1025 ILE cc_start: 0.8316 (mm) cc_final: 0.8001 (pt) REVERT: C 1030 ASP cc_start: 0.7977 (p0) cc_final: 0.7210 (t0) REVERT: C 1069 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6368 (tp30) REVERT: C 1141 PHE cc_start: 0.8075 (m-10) cc_final: 0.7802 (m-10) REVERT: C 1190 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8977 (mm-30) REVERT: C 1191 MET cc_start: 0.7801 (tpp) cc_final: 0.7152 (tpp) REVERT: C 1195 LEU cc_start: 0.8239 (mm) cc_final: 0.7558 (mm) REVERT: D 408 MET cc_start: 0.5805 (mtt) cc_final: 0.3630 (tmm) REVERT: D 463 MET cc_start: 0.3794 (pmm) cc_final: 0.2071 (mtm) REVERT: D 471 LYS cc_start: 0.5987 (mttp) cc_final: 0.5656 (ttmt) REVERT: D 496 MET cc_start: 0.7672 (ttp) cc_final: 0.7265 (ttp) REVERT: D 504 ILE cc_start: 0.7755 (pt) cc_final: 0.7292 (pt) REVERT: D 519 ASP cc_start: 0.8271 (t70) cc_final: 0.8034 (t0) REVERT: D 546 PHE cc_start: 0.7738 (t80) cc_final: 0.7322 (t80) REVERT: D 661 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7849 (mtp85) REVERT: D 688 GLU cc_start: 0.8089 (tt0) cc_final: 0.7459 (tp30) REVERT: D 720 THR cc_start: 0.6384 (p) cc_final: 0.6161 (p) REVERT: D 799 LEU cc_start: 0.8673 (tp) cc_final: 0.8442 (tp) REVERT: D 1068 LEU cc_start: 0.7676 (pp) cc_final: 0.7058 (pp) REVERT: D 1069 GLU cc_start: 0.6899 (tp30) cc_final: 0.6363 (mp0) REVERT: D 1141 PHE cc_start: 0.8226 (m-80) cc_final: 0.7794 (m-80) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2772 time to fit residues: 200.7443 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 6.9990 chunk 95 optimal weight: 0.0070 chunk 142 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B1131 HIS C1159 ASN C1204 HIS D1081 HIS D1131 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.5399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19882 Z= 0.183 Angle : 0.587 8.664 26864 Z= 0.303 Chirality : 0.040 0.166 2998 Planarity : 0.004 0.039 3314 Dihedral : 6.439 72.769 2790 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.17), residues: 2460 helix: 1.70 (0.14), residues: 1326 sheet: -1.86 (0.39), residues: 138 loop : -1.16 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 605 HIS 0.009 0.001 HIS B1131 PHE 0.019 0.001 PHE C 579 TYR 0.017 0.001 TYR C 440 ARG 0.005 0.000 ARG D 675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.6809 (mmt) cc_final: 0.6556 (mmm) REVERT: A 427 ASP cc_start: 0.7953 (t0) cc_final: 0.7544 (m-30) REVERT: A 538 VAL cc_start: 0.8809 (t) cc_final: 0.8570 (m) REVERT: A 609 THR cc_start: 0.9258 (m) cc_final: 0.8983 (p) REVERT: A 619 ASN cc_start: 0.7288 (t0) cc_final: 0.6945 (t0) REVERT: A 673 TYR cc_start: 0.6757 (m-80) cc_final: 0.6265 (m-80) REVERT: A 783 LYS cc_start: 0.2703 (tttt) cc_final: 0.2363 (mmtm) REVERT: A 811 LEU cc_start: 0.8517 (mm) cc_final: 0.8287 (mm) REVERT: A 1080 ASP cc_start: 0.7597 (m-30) cc_final: 0.7198 (t0) REVERT: A 1104 SER cc_start: 0.8418 (m) cc_final: 0.8148 (t) REVERT: A 1191 MET cc_start: 0.7904 (tpp) cc_final: 0.7232 (tpp) REVERT: A 1195 LEU cc_start: 0.8288 (mm) cc_final: 0.7618 (mm) REVERT: B 404 PRO cc_start: 0.3397 (Cg_endo) cc_final: 0.1728 (Cg_exo) REVERT: B 408 MET cc_start: 0.6164 (mtt) cc_final: 0.3842 (tmm) REVERT: B 463 MET cc_start: 0.2593 (mtt) cc_final: 0.2351 (mtm) REVERT: B 511 LYS cc_start: 0.7009 (mmpt) cc_final: 0.6556 (mttm) REVERT: B 546 PHE cc_start: 0.7851 (t80) cc_final: 0.7415 (t80) REVERT: B 594 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.7568 (ttp-170) REVERT: B 688 GLU cc_start: 0.8163 (tt0) cc_final: 0.7515 (tp30) REVERT: B 704 LEU cc_start: 0.7836 (pp) cc_final: 0.7515 (mt) REVERT: B 708 MET cc_start: 0.7959 (tpp) cc_final: 0.7703 (tpp) REVERT: B 713 GLU cc_start: 0.7607 (tp30) cc_final: 0.6548 (mm-30) REVERT: B 720 THR cc_start: 0.7120 (p) cc_final: 0.5543 (p) REVERT: B 769 ASP cc_start: 0.6561 (m-30) cc_final: 0.5994 (t0) REVERT: B 1091 ASP cc_start: 0.6743 (t0) cc_final: 0.6442 (p0) REVERT: B 1141 PHE cc_start: 0.8425 (m-80) cc_final: 0.7804 (m-80) REVERT: B 1191 MET cc_start: 0.8773 (mtt) cc_final: 0.8415 (mmm) REVERT: C 409 LYS cc_start: 0.5312 (tptt) cc_final: 0.4969 (tttm) REVERT: C 415 LEU cc_start: 0.7863 (mt) cc_final: 0.7607 (mt) REVERT: C 460 TRP cc_start: 0.6218 (m100) cc_final: 0.4711 (m100) REVERT: C 517 PHE cc_start: 0.7904 (p90) cc_final: 0.7225 (p90) REVERT: C 521 LEU cc_start: 0.8594 (mp) cc_final: 0.8353 (mp) REVERT: C 528 CYS cc_start: 0.8991 (m) cc_final: 0.8700 (m) REVERT: C 586 GLN cc_start: 0.8149 (mt0) cc_final: 0.7546 (tm-30) REVERT: C 609 THR cc_start: 0.9283 (m) cc_final: 0.8966 (p) REVERT: C 663 LYS cc_start: 0.7717 (mmpt) cc_final: 0.7175 (pttm) REVERT: C 670 MET cc_start: 0.7789 (mmp) cc_final: 0.7241 (mmp) REVERT: C 783 LYS cc_start: 0.3386 (mtpt) cc_final: 0.2915 (mmtm) REVERT: C 807 MET cc_start: 0.8670 (mtt) cc_final: 0.8235 (tmm) REVERT: C 811 LEU cc_start: 0.8551 (mm) cc_final: 0.7876 (mm) REVERT: C 1023 MET cc_start: 0.8837 (mmm) cc_final: 0.8597 (mmm) REVERT: C 1030 ASP cc_start: 0.8218 (p0) cc_final: 0.7529 (p0) REVERT: C 1057 MET cc_start: 0.8256 (mmm) cc_final: 0.8024 (mmm) REVERT: C 1069 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6306 (tp30) REVERT: C 1181 PHE cc_start: 0.8083 (m-80) cc_final: 0.7774 (m-80) REVERT: C 1190 GLU cc_start: 0.9227 (mm-30) cc_final: 0.9021 (mm-30) REVERT: C 1191 MET cc_start: 0.7780 (tpp) cc_final: 0.7302 (tpp) REVERT: C 1200 PHE cc_start: 0.8650 (t80) cc_final: 0.8250 (t80) REVERT: D 408 MET cc_start: 0.5830 (mtt) cc_final: 0.4224 (tmm) REVERT: D 463 MET cc_start: 0.3831 (pmm) cc_final: 0.2249 (mtt) REVERT: D 471 LYS cc_start: 0.6032 (mttp) cc_final: 0.5689 (ttmt) REVERT: D 496 MET cc_start: 0.7623 (ttp) cc_final: 0.7164 (ttp) REVERT: D 504 ILE cc_start: 0.7744 (pt) cc_final: 0.7253 (pt) REVERT: D 546 PHE cc_start: 0.7767 (t80) cc_final: 0.7326 (t80) REVERT: D 661 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7519 (mtt-85) REVERT: D 688 GLU cc_start: 0.8099 (tt0) cc_final: 0.7465 (tp30) REVERT: D 797 TYR cc_start: 0.8551 (m-80) cc_final: 0.8351 (m-80) REVERT: D 799 LEU cc_start: 0.8665 (tp) cc_final: 0.8432 (tp) REVERT: D 1068 LEU cc_start: 0.7567 (pp) cc_final: 0.7015 (pp) REVERT: D 1069 GLU cc_start: 0.6931 (tp30) cc_final: 0.6426 (mp0) REVERT: D 1080 ASP cc_start: 0.7837 (m-30) cc_final: 0.7589 (m-30) REVERT: D 1141 PHE cc_start: 0.8228 (m-80) cc_final: 0.7800 (m-80) REVERT: A 1301 GLU cc_start: 0.6567 (mp0) cc_final: 0.5859 (mm-30) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.2778 time to fit residues: 195.1790 Evaluate side-chains 332 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 146 optimal weight: 0.0020 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN A1204 HIS ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B1008 GLN B1171 ASN ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19882 Z= 0.177 Angle : 0.597 10.209 26864 Z= 0.304 Chirality : 0.041 0.204 2998 Planarity : 0.003 0.039 3314 Dihedral : 6.132 58.891 2790 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.48 (0.17), residues: 2460 helix: 1.68 (0.14), residues: 1316 sheet: -1.94 (0.39), residues: 138 loop : -1.22 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 605 HIS 0.007 0.001 HIS A1204 PHE 0.018 0.001 PHE C 579 TYR 0.019 0.001 TYR D 702 ARG 0.004 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 THR cc_start: 0.7716 (p) cc_final: 0.7288 (t) REVERT: A 408 MET cc_start: 0.6818 (mmt) cc_final: 0.6453 (mmm) REVERT: A 427 ASP cc_start: 0.7961 (t0) cc_final: 0.7567 (m-30) REVERT: A 538 VAL cc_start: 0.8795 (t) cc_final: 0.8563 (m) REVERT: A 609 THR cc_start: 0.9266 (m) cc_final: 0.9012 (p) REVERT: A 673 TYR cc_start: 0.6750 (m-80) cc_final: 0.6245 (m-80) REVERT: A 783 LYS cc_start: 0.2676 (tttt) cc_final: 0.2342 (mmtm) REVERT: A 811 LEU cc_start: 0.8545 (mm) cc_final: 0.8304 (mm) REVERT: A 1080 ASP cc_start: 0.7567 (m-30) cc_final: 0.7219 (t0) REVERT: A 1104 SER cc_start: 0.8452 (m) cc_final: 0.8207 (t) REVERT: A 1191 MET cc_start: 0.7907 (tpp) cc_final: 0.7233 (tpp) REVERT: A 1195 LEU cc_start: 0.8224 (mm) cc_final: 0.7600 (mm) REVERT: B 404 PRO cc_start: 0.3448 (Cg_endo) cc_final: 0.1796 (Cg_exo) REVERT: B 408 MET cc_start: 0.6066 (mtt) cc_final: 0.3769 (tmm) REVERT: B 463 MET cc_start: 0.2625 (mtt) cc_final: 0.2391 (mtt) REVERT: B 503 MET cc_start: 0.7681 (tmm) cc_final: 0.7049 (tmm) REVERT: B 511 LYS cc_start: 0.6906 (mmpt) cc_final: 0.6460 (mttm) REVERT: B 546 PHE cc_start: 0.7858 (t80) cc_final: 0.7410 (t80) REVERT: B 594 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7561 (ttp-170) REVERT: B 688 GLU cc_start: 0.8159 (tt0) cc_final: 0.7504 (tp30) REVERT: B 704 LEU cc_start: 0.7845 (pp) cc_final: 0.7605 (mt) REVERT: B 708 MET cc_start: 0.7953 (tpp) cc_final: 0.7698 (tpp) REVERT: B 713 GLU cc_start: 0.7592 (tp30) cc_final: 0.6502 (mm-30) REVERT: B 720 THR cc_start: 0.7168 (p) cc_final: 0.5745 (p) REVERT: B 769 ASP cc_start: 0.6538 (m-30) cc_final: 0.6052 (t0) REVERT: B 1068 LEU cc_start: 0.7600 (pp) cc_final: 0.7159 (pp) REVERT: B 1069 GLU cc_start: 0.6836 (tp30) cc_final: 0.6335 (mp0) REVERT: B 1091 ASP cc_start: 0.6787 (t0) cc_final: 0.6454 (p0) REVERT: B 1141 PHE cc_start: 0.8455 (m-80) cc_final: 0.7825 (m-80) REVERT: B 1187 ILE cc_start: 0.8676 (mt) cc_final: 0.8295 (mp) REVERT: B 1191 MET cc_start: 0.8768 (mtt) cc_final: 0.8416 (mmm) REVERT: C 409 LYS cc_start: 0.5238 (tptt) cc_final: 0.4859 (tttm) REVERT: C 415 LEU cc_start: 0.8101 (mt) cc_final: 0.7639 (mt) REVERT: C 460 TRP cc_start: 0.6250 (m100) cc_final: 0.4740 (m100) REVERT: C 517 PHE cc_start: 0.7881 (p90) cc_final: 0.7251 (p90) REVERT: C 528 CYS cc_start: 0.9012 (m) cc_final: 0.8681 (m) REVERT: C 586 GLN cc_start: 0.8151 (mt0) cc_final: 0.7423 (tm-30) REVERT: C 609 THR cc_start: 0.9252 (m) cc_final: 0.8976 (p) REVERT: C 663 LYS cc_start: 0.7652 (mmpt) cc_final: 0.7090 (pttm) REVERT: C 670 MET cc_start: 0.7817 (mmp) cc_final: 0.7362 (mmp) REVERT: C 783 LYS cc_start: 0.3377 (mtpt) cc_final: 0.2899 (mmtm) REVERT: C 811 LEU cc_start: 0.8522 (mm) cc_final: 0.8255 (mm) REVERT: C 1023 MET cc_start: 0.8808 (mmm) cc_final: 0.8573 (mmm) REVERT: C 1030 ASP cc_start: 0.8169 (p0) cc_final: 0.7467 (p0) REVERT: C 1069 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6233 (tp30) REVERT: C 1191 MET cc_start: 0.7779 (tpp) cc_final: 0.7337 (tpp) REVERT: D 408 MET cc_start: 0.5826 (mtt) cc_final: 0.4257 (tmm) REVERT: D 463 MET cc_start: 0.3828 (pmm) cc_final: 0.2266 (mtt) REVERT: D 471 LYS cc_start: 0.5993 (mttp) cc_final: 0.5639 (ttmt) REVERT: D 496 MET cc_start: 0.7564 (ttp) cc_final: 0.7086 (ttp) REVERT: D 504 ILE cc_start: 0.7720 (pt) cc_final: 0.7173 (pt) REVERT: D 546 PHE cc_start: 0.7752 (t80) cc_final: 0.7333 (t80) REVERT: D 661 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7608 (mtt-85) REVERT: D 688 GLU cc_start: 0.8095 (tt0) cc_final: 0.7470 (tp30) REVERT: D 799 LEU cc_start: 0.8664 (tp) cc_final: 0.8423 (tp) REVERT: D 1068 LEU cc_start: 0.7518 (pp) cc_final: 0.6979 (pp) REVERT: D 1069 GLU cc_start: 0.6892 (tp30) cc_final: 0.6392 (mp0) REVERT: D 1141 PHE cc_start: 0.8241 (m-80) cc_final: 0.7810 (m-80) REVERT: D 1194 VAL cc_start: 0.8607 (t) cc_final: 0.8403 (t) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.2849 time to fit residues: 200.5935 Evaluate side-chains 331 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A1148 ASN A1204 HIS ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN B1008 GLN B1132 ASN C1148 ASN C1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19882 Z= 0.364 Angle : 0.752 10.743 26864 Z= 0.396 Chirality : 0.046 0.209 2998 Planarity : 0.005 0.039 3314 Dihedral : 6.558 59.844 2790 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.18 (0.17), residues: 2460 helix: 1.03 (0.14), residues: 1326 sheet: -2.02 (0.38), residues: 154 loop : -1.38 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP D 605 HIS 0.008 0.002 HIS A1198 PHE 0.036 0.003 PHE C1141 TYR 0.032 0.003 TYR D 797 ARG 0.019 0.001 ARG C 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7317 (mmt) cc_final: 0.6954 (mmm) REVERT: A 463 MET cc_start: 0.2396 (ttp) cc_final: 0.1614 (ptm) REVERT: A 517 PHE cc_start: 0.7752 (p90) cc_final: 0.7531 (p90) REVERT: A 609 THR cc_start: 0.9240 (m) cc_final: 0.8959 (p) REVERT: A 619 ASN cc_start: 0.7567 (t0) cc_final: 0.7055 (t0) REVERT: A 673 TYR cc_start: 0.6867 (m-80) cc_final: 0.6377 (m-80) REVERT: A 783 LYS cc_start: 0.2687 (tttt) cc_final: 0.2290 (mmtm) REVERT: A 811 LEU cc_start: 0.8484 (mm) cc_final: 0.8278 (mm) REVERT: A 1034 TYR cc_start: 0.6178 (m-10) cc_final: 0.5977 (m-10) REVERT: A 1057 MET cc_start: 0.8302 (mmm) cc_final: 0.8022 (mmm) REVERT: A 1068 LEU cc_start: 0.8723 (mp) cc_final: 0.8370 (tp) REVERT: A 1191 MET cc_start: 0.8008 (tpp) cc_final: 0.7339 (tpp) REVERT: A 1195 LEU cc_start: 0.8116 (mm) cc_final: 0.7475 (mm) REVERT: B 408 MET cc_start: 0.6017 (mtt) cc_final: 0.3975 (tmm) REVERT: B 414 MET cc_start: 0.7941 (mtt) cc_final: 0.7662 (ptt) REVERT: B 503 MET cc_start: 0.7678 (tmm) cc_final: 0.7424 (tmm) REVERT: B 511 LYS cc_start: 0.7099 (mmpt) cc_final: 0.6641 (mttm) REVERT: B 546 PHE cc_start: 0.7938 (t80) cc_final: 0.7500 (t80) REVERT: B 573 ILE cc_start: 0.7711 (pt) cc_final: 0.7235 (pt) REVERT: B 594 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7554 (ttp-170) REVERT: B 688 GLU cc_start: 0.8201 (tt0) cc_final: 0.7602 (tp30) REVERT: B 708 MET cc_start: 0.8021 (tpp) cc_final: 0.7688 (tpp) REVERT: B 769 ASP cc_start: 0.6494 (m-30) cc_final: 0.6009 (t0) REVERT: B 803 LEU cc_start: 0.9026 (mt) cc_final: 0.8805 (mt) REVERT: B 1141 PHE cc_start: 0.8384 (m-80) cc_final: 0.7780 (m-80) REVERT: B 1191 MET cc_start: 0.8783 (mtt) cc_final: 0.8443 (mmm) REVERT: C 420 ARG cc_start: 0.7243 (mpp80) cc_final: 0.6924 (mtm110) REVERT: C 528 CYS cc_start: 0.9023 (m) cc_final: 0.8674 (m) REVERT: C 586 GLN cc_start: 0.8170 (mt0) cc_final: 0.7601 (tm-30) REVERT: C 609 THR cc_start: 0.9246 (m) cc_final: 0.8942 (p) REVERT: C 643 THR cc_start: 0.5952 (p) cc_final: 0.5544 (t) REVERT: C 663 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7039 (pttm) REVERT: C 670 MET cc_start: 0.7789 (mmp) cc_final: 0.7248 (mmp) REVERT: C 673 TYR cc_start: 0.6968 (m-80) cc_final: 0.6505 (m-80) REVERT: C 783 LYS cc_start: 0.3358 (mtpt) cc_final: 0.2875 (mmtm) REVERT: C 811 LEU cc_start: 0.8533 (mm) cc_final: 0.8291 (mm) REVERT: C 1023 MET cc_start: 0.8844 (mmm) cc_final: 0.8558 (mmm) REVERT: C 1030 ASP cc_start: 0.8206 (p0) cc_final: 0.7480 (p0) REVERT: C 1104 SER cc_start: 0.8735 (t) cc_final: 0.8478 (p) REVERT: C 1181 PHE cc_start: 0.8100 (m-80) cc_final: 0.7781 (m-10) REVERT: D 408 MET cc_start: 0.6118 (mtt) cc_final: 0.4279 (tmm) REVERT: D 463 MET cc_start: 0.4510 (pmm) cc_final: 0.2556 (mtp) REVERT: D 471 LYS cc_start: 0.6079 (mttp) cc_final: 0.5721 (ttmt) REVERT: D 496 MET cc_start: 0.7414 (ttp) cc_final: 0.6995 (ttp) REVERT: D 546 PHE cc_start: 0.7880 (t80) cc_final: 0.7357 (t80) REVERT: D 585 MET cc_start: 0.8774 (mmt) cc_final: 0.8536 (mmt) REVERT: D 661 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7639 (mtt-85) REVERT: D 688 GLU cc_start: 0.8080 (tt0) cc_final: 0.7550 (tp30) REVERT: D 769 ASP cc_start: 0.6605 (m-30) cc_final: 0.6161 (t0) REVERT: D 1098 ARG cc_start: 0.8658 (mmt180) cc_final: 0.8231 (mmt180) REVERT: D 1141 PHE cc_start: 0.8170 (m-80) cc_final: 0.7786 (m-80) REVERT: D 1191 MET cc_start: 0.9031 (mmp) cc_final: 0.8790 (mmm) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2750 time to fit residues: 176.7421 Evaluate side-chains 305 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 0.0770 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 197 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 173 optimal weight: 0.2980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1204 HIS ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 GLN C 569 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.068196 restraints weight = 88649.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.070220 restraints weight = 59823.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.071663 restraints weight = 44731.955| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19882 Z= 0.179 Angle : 0.619 9.131 26864 Z= 0.317 Chirality : 0.041 0.186 2998 Planarity : 0.004 0.040 3314 Dihedral : 6.041 59.660 2790 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.23 (0.17), residues: 2460 helix: 1.47 (0.14), residues: 1292 sheet: -2.07 (0.37), residues: 156 loop : -1.23 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 605 HIS 0.007 0.001 HIS D 412 PHE 0.036 0.002 PHE D 541 TYR 0.034 0.002 TYR D 702 ARG 0.004 0.000 ARG A1005 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.64 seconds wall clock time: 90 minutes 58.05 seconds (5458.05 seconds total)