Starting phenix.real_space_refine on Sat Mar 16 21:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mup_9251/03_2024/6mup_9251.pdb" } resolution = 3.5 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= 0.001 sd= 0.008 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 P 292 5.49 5 S 24 5.16 5 C 9101 2.51 5 N 2892 2.21 5 O 3494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 23": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 196": "NH1" <-> "NH2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 196": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 814 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 785 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 809 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 687 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 795 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3027 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 174 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 18} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 169 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "M" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1712 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Time building chain proxies: 8.64, per 1000 atoms: 0.55 Number of scatterers: 15803 At special positions: 0 Unit cell: (150.52, 126.14, 116.6, 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) S 24 16.00 P 292 15.00 O 3494 8.00 N 2892 7.00 C 9101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.23 Conformation dependent library (CDL) restraints added in 1.9 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 54.0% alpha, 3.9% beta 63 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.547A pdb=" N ARG A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.812A pdb=" N ALA A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.001A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.798A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.248A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.839A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.896A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.658A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 removed outlier: 3.676A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.517A pdb=" N ARG C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.677A pdb=" N ALA C 86 " --> pdb=" O HIS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.528A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.518A pdb=" N TYR D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 67 removed outlier: 3.799A pdb=" N SER D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.788A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.671A pdb=" N GLN D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 3.595A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.548A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.621A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 114 removed outlier: 4.313A pdb=" N HIS E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 4.387A pdb=" N LEU E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE E 132 " --> pdb=" O LEU E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.535A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 3.851A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.828A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.784A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.512A pdb=" N HIS G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 67 removed outlier: 3.865A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 80 through 88 removed outlier: 4.059A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.696A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.928A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 removed outlier: 3.718A pdb=" N VAL H 66 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP H 68 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 84 Processing helix chain 'H' and resid 91 through 102 removed outlier: 3.610A pdb=" N GLN H 95 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 123 removed outlier: 3.781A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR H 115 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.507A pdb=" N LYS M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 19 No H-bonds generated for 'chain 'M' and resid 17 through 19' Processing helix chain 'M' and resid 20 through 29 removed outlier: 3.504A pdb=" N ILE M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA M 27 " --> pdb=" O THR M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 44 through 60 removed outlier: 3.973A pdb=" N GLN M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE M 53 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU M 55 " --> pdb=" O HIS M 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU M 58 " --> pdb=" O HIS M 54 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG M 60 " --> pdb=" O CYS M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 77 removed outlier: 4.604A pdb=" N LEU M 68 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE M 76 " --> pdb=" O ILE M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 106 removed outlier: 3.853A pdb=" N ASN M 106 " --> pdb=" O LYS M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 183 removed outlier: 4.291A pdb=" N THR M 180 " --> pdb=" O GLY M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 206 Processing helix chain 'M' and resid 206 through 211 removed outlier: 3.761A pdb=" N GLN M 211 " --> pdb=" O LYS M 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 removed outlier: 3.580A pdb=" N ARG N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 19 removed outlier: 6.241A pdb=" N ASN N 19 " --> pdb=" O ILE N 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 16 through 19' Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.614A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 44 through 60 removed outlier: 4.051A pdb=" N GLN N 50 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU N 58 " --> pdb=" O HIS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 76 removed outlier: 4.567A pdb=" N LEU N 68 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 107 Processing helix chain 'N' and resid 171 through 183 removed outlier: 4.097A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN N 177 " --> pdb=" O PRO N 173 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA N 182 " --> pdb=" O ALA N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 206 Processing helix chain 'N' and resid 206 through 211 removed outlier: 3.763A pdb=" N GLN N 211 " --> pdb=" O LYS N 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.353A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.484A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.336A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.833A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'M' and resid 133 through 134 removed outlier: 5.072A pdb=" N TYR M 151 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA M 161 " --> pdb=" O PHE M 86 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE M 86 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN M 87 " --> pdb=" O VAL M 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 133 through 134 removed outlier: 5.199A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 145 hydrogen bonds 286 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 5.47 Time building geometry restraints manager: 8.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2736 1.32 - 1.45: 5656 1.45 - 1.57: 7685 1.57 - 1.69: 581 1.69 - 1.82: 44 Bond restraints: 16702 Sorted by residual: bond pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 1.331 1.496 -0.166 1.38e-02 5.25e+03 1.44e+02 bond pdb=" C VAL C 107 " pdb=" N LEU C 108 " ideal model delta sigma weight residual 1.331 1.238 0.093 1.48e-02 4.57e+03 3.95e+01 bond pdb=" N PRO K 527 " pdb=" CD PRO K 527 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.17e+01 bond pdb=" C LEU H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.328 1.289 0.039 1.25e-02 6.40e+03 9.62e+00 bond pdb=" CB THR E 113 " pdb=" CG2 THR E 113 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.19e+00 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.79: 1727 105.79 - 114.41: 10010 114.41 - 123.03: 10136 123.03 - 131.65: 1831 131.65 - 140.27: 115 Bond angle restraints: 23819 Sorted by residual: angle pdb=" CA SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 115.90 133.64 -17.74 1.21e+00 6.83e-01 2.15e+02 angle pdb=" O SER M 195 " pdb=" C SER M 195 " pdb=" N ARG M 196 " ideal model delta sigma weight residual 122.59 104.83 17.76 1.35e+00 5.49e-01 1.73e+02 angle pdb=" C SER M 195 " pdb=" N ARG M 196 " pdb=" CA ARG M 196 " ideal model delta sigma weight residual 122.79 140.27 -17.48 1.78e+00 3.16e-01 9.64e+01 angle pdb=" N PRO G 117 " pdb=" CA PRO G 117 " pdb=" CB PRO G 117 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 angle pdb=" C ARG K 521 " pdb=" N ARG K 522 " pdb=" CA ARG K 522 " ideal model delta sigma weight residual 122.93 132.61 -9.68 1.45e+00 4.76e-01 4.46e+01 ... (remaining 23814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7907 35.00 - 70.00: 1387 70.00 - 105.00: 52 105.00 - 140.00: 0 140.00 - 175.01: 2 Dihedral angle restraints: 9348 sinusoidal: 5774 harmonic: 3574 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual 180.00 111.61 68.39 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA LEU E 135 " pdb=" C LEU E 135 " pdb=" N GLU E 136 " pdb=" CA GLU E 136 " ideal model delta harmonic sigma weight residual 180.00 133.88 46.12 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta harmonic sigma weight residual 180.00 133.96 46.04 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 9345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2152 0.074 - 0.149: 489 0.149 - 0.223: 39 0.223 - 0.297: 9 0.297 - 0.372: 1 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA SER K 528 " pdb=" N SER K 528 " pdb=" C SER K 528 " pdb=" CB SER K 528 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CB VAL D 66 " pdb=" CA VAL D 66 " pdb=" CG1 VAL D 66 " pdb=" CG2 VAL D 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2687 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 195 " -0.025 2.00e-02 2.50e+03 5.30e-02 2.81e+01 pdb=" C SER N 195 " 0.092 2.00e-02 2.50e+03 pdb=" O SER N 195 " -0.036 2.00e-02 2.50e+03 pdb=" N ARG N 196 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 526 " -0.429 9.50e-02 1.11e+02 1.92e-01 2.26e+01 pdb=" NE ARG K 526 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 526 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 526 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP L 530 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C TRP L 530 " -0.053 2.00e-02 2.50e+03 pdb=" O TRP L 530 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP L 531 " 0.018 2.00e-02 2.50e+03 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.08: 7 2.08 - 2.79: 3712 2.79 - 3.49: 20724 3.49 - 4.20: 41531 4.20 - 4.90: 62984 Nonbonded interactions: 128958 Sorted by model distance: nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG L 522 " model vdw 1.379 2.520 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.686 2.520 nonbonded pdb=" O TRP K 530 " pdb=" CE3 TRP K 531 " model vdw 1.789 3.340 nonbonded pdb=" CG ASP G 90 " pdb=" NH2 ARG K 522 " model vdw 1.796 3.350 nonbonded pdb=" OE1 GLU C 92 " pdb=" CZ ARG L 522 " model vdw 1.984 3.270 ... (remaining 128953 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 39 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 116) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 519 through 537) selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.670 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 48.330 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 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 : 0.013 0.166 16702 Z= 0.792 Angle : 1.189 17.758 23819 Z= 0.685 Chirality : 0.061 0.372 2690 Planarity : 0.008 0.192 1986 Dihedral : 25.818 175.006 7028 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.28 % Favored : 89.21 % Rotamer: Outliers : 1.08 % Allowed : 6.16 % Favored : 92.76 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.68 % 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: -6.36 (0.16), residues: 1196 helix: -4.62 (0.09), residues: 669 sheet: -2.35 (0.63), residues: 60 loop : -3.59 (0.23), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP N 28 HIS 0.013 0.003 HIS A 115 PHE 0.045 0.004 PHE C 25 TYR 0.036 0.004 TYR H 37 ARG 0.015 0.002 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 331 time to evaluate : 1.264 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: B 43 VAL cc_start: 0.8068 (t) cc_final: 0.7848 (p) REVERT: B 84 MET cc_start: 0.7427 (mmm) cc_final: 0.6826 (mmm) REVERT: B 91 LYS cc_start: 0.8145 (tttm) cc_final: 0.7754 (ttpt) REVERT: C 16 SER cc_start: 0.8214 (m) cc_final: 0.7809 (p) REVERT: C 24 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7899 (mm-40) REVERT: C 36 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7397 (tmtt) REVERT: C 64 GLU cc_start: 0.8015 (tt0) cc_final: 0.7351 (tm-30) REVERT: C 84 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6643 (tp-100) REVERT: C 104 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8082 (mm-40) REVERT: D 42 TYR cc_start: 0.8123 (t80) cc_final: 0.7802 (t80) REVERT: D 76 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7365 (tm-30) REVERT: D 85 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6904 (pttt) REVERT: E 48 LEU cc_start: 0.7826 (tt) cc_final: 0.7610 (tp) REVERT: E 56 LYS cc_start: 0.7009 (tttt) cc_final: 0.6477 (mmmm) REVERT: E 59 HIS cc_start: 0.8410 (m-70) cc_final: 0.8047 (m170) REVERT: E 68 SER cc_start: 0.8277 (t) cc_final: 0.8053 (m) REVERT: E 96 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 107 GLU cc_start: 0.6995 (tm-30) cc_final: 0.6455 (tt0) REVERT: E 124 LYS cc_start: 0.7631 (mptm) cc_final: 0.7404 (mtpt) REVERT: F 44 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7123 (mtpt) REVERT: F 91 LYS cc_start: 0.7784 (tttp) cc_final: 0.7229 (ttmt) REVERT: F 93 GLN cc_start: 0.6669 (tp-100) cc_final: 0.6306 (tp40) REVERT: G 36 LYS cc_start: 0.8855 (mmpt) cc_final: 0.8303 (mmmm) REVERT: G 38 ASN cc_start: 0.8778 (m-40) cc_final: 0.8390 (m-40) REVERT: G 42 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6415 (mtp85) REVERT: G 73 ASN cc_start: 0.6898 (t160) cc_final: 0.6588 (t0) REVERT: G 76 THR cc_start: 0.7617 (p) cc_final: 0.7253 (t) REVERT: G 95 LYS cc_start: 0.7173 (tmtm) cc_final: 0.6800 (mtpt) REVERT: H 38 SER cc_start: 0.8739 (p) cc_final: 0.8294 (t) REVERT: H 46 LYS cc_start: 0.8013 (mmtp) cc_final: 0.7757 (mmtt) REVERT: H 71 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7316 (tm-30) REVERT: H 82 HIS cc_start: 0.7438 (t-90) cc_final: 0.7037 (t-90) REVERT: H 86 ARG cc_start: 0.7213 (mmt90) cc_final: 0.6496 (mtp180) REVERT: H 88 THR cc_start: 0.8392 (p) cc_final: 0.7974 (p) REVERT: H 93 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7203 (mt-10) REVERT: H 99 ARG cc_start: 0.7715 (mtp85) cc_final: 0.7489 (mmm-85) REVERT: H 113 GLU cc_start: 0.7879 (tt0) cc_final: 0.7421 (tm-30) REVERT: L 526 ARG cc_start: 0.6671 (tpp80) cc_final: 0.6337 (mmm160) REVERT: L 527 PRO cc_start: 0.7722 (Cg_endo) cc_final: 0.7379 (Cg_exo) REVERT: M 1 MET cc_start: 0.2631 (ptt) cc_final: 0.2397 (ptp) REVERT: M 59 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7506 (mmtm) REVERT: M 69 LEU cc_start: 0.8622 (tp) cc_final: 0.8389 (tp) REVERT: N 1 MET cc_start: 0.0331 (ptt) cc_final: -0.0534 (mtm) REVERT: N 74 MET cc_start: 0.7954 (tpp) cc_final: 0.7611 (tpt) REVERT: N 150 THR cc_start: 0.8516 (m) cc_final: 0.8028 (p) REVERT: N 165 SER cc_start: 0.6882 (m) cc_final: 0.6677 (m) outliers start: 11 outliers final: 2 residues processed: 339 average time/residue: 0.3798 time to fit residues: 171.3748 Evaluate side-chains 239 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain K residue 533 VAL Chi-restraints excluded: chain K residue 536 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 50.0000 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 133 optimal weight: 0.0000 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS C 73 ASN C 94 ASN C 104 GLN D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 73 ASN G 94 ASN H 63 ASN H 67 ASN M 19 ASN M 40 ASN M 129 ASN M 145 ASN N 19 ASN N 129 ASN N 187 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16702 Z= 0.195 Angle : 0.670 8.058 23819 Z= 0.387 Chirality : 0.039 0.284 2690 Planarity : 0.005 0.056 1986 Dihedral : 29.802 173.330 4656 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.54 % Allowed : 11.45 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -4.83 (0.19), residues: 1196 helix: -3.19 (0.14), residues: 680 sheet: -2.36 (0.62), residues: 64 loop : -3.09 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 531 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE M 8 TYR 0.024 0.002 TYR B 51 ARG 0.006 0.001 ARG K 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 273 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7933 (m-80) cc_final: 0.7686 (m-80) REVERT: B 64 ASN cc_start: 0.8201 (m-40) cc_final: 0.7938 (m-40) REVERT: B 84 MET cc_start: 0.6449 (mmm) cc_final: 0.6190 (mmt) REVERT: B 91 LYS cc_start: 0.8035 (tttm) cc_final: 0.7660 (ttpt) REVERT: B 93 GLN cc_start: 0.7796 (tp40) cc_final: 0.6879 (tp40) REVERT: C 36 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7445 (tmtt) REVERT: C 71 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7410 (mtm180) REVERT: C 95 LYS cc_start: 0.8156 (tptp) cc_final: 0.7744 (ttmt) REVERT: C 104 GLN cc_start: 0.8752 (mm110) cc_final: 0.8535 (mm110) REVERT: D 42 TYR cc_start: 0.7906 (t80) cc_final: 0.7687 (t80) REVERT: D 62 MET cc_start: 0.7260 (mmm) cc_final: 0.7036 (tpp) REVERT: D 68 ASP cc_start: 0.7724 (t70) cc_final: 0.7029 (t0) REVERT: E 56 LYS cc_start: 0.7054 (tttt) cc_final: 0.6656 (mmmm) REVERT: E 80 ARG cc_start: 0.6779 (OUTLIER) cc_final: 0.5869 (ttm110) REVERT: E 95 GLN cc_start: 0.7281 (tt0) cc_final: 0.6922 (tt0) REVERT: E 96 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8628 (mm-30) REVERT: E 107 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6585 (tt0) REVERT: F 52 GLU cc_start: 0.8356 (tp30) cc_final: 0.7847 (tp30) REVERT: F 91 LYS cc_start: 0.7478 (tttp) cc_final: 0.6830 (ttmt) REVERT: F 93 GLN cc_start: 0.6833 (tp-100) cc_final: 0.6404 (tp40) REVERT: G 24 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8186 (mm-40) REVERT: G 35 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7569 (ttm110) REVERT: G 36 LYS cc_start: 0.8505 (mmpt) cc_final: 0.8162 (mmmm) REVERT: G 76 THR cc_start: 0.7684 (p) cc_final: 0.7436 (t) REVERT: G 91 GLU cc_start: 0.7371 (tt0) cc_final: 0.7043 (tt0) REVERT: G 92 GLU cc_start: 0.7419 (mp0) cc_final: 0.6936 (mp0) REVERT: G 95 LYS cc_start: 0.7301 (tmtm) cc_final: 0.6931 (mtpt) REVERT: H 46 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7797 (mmtt) REVERT: H 82 HIS cc_start: 0.7232 (t-90) cc_final: 0.6973 (t-90) REVERT: H 86 ARG cc_start: 0.7062 (mmt90) cc_final: 0.6341 (mtp-110) REVERT: H 88 THR cc_start: 0.8333 (p) cc_final: 0.7856 (p) REVERT: H 113 GLU cc_start: 0.7208 (tt0) cc_final: 0.6700 (mt-10) REVERT: M 1 MET cc_start: 0.2787 (ptt) cc_final: 0.1834 (ptp) REVERT: M 24 ILE cc_start: 0.7947 (mm) cc_final: 0.7713 (tp) REVERT: M 59 LYS cc_start: 0.7389 (mtpp) cc_final: 0.7035 (mmtm) REVERT: M 137 TRP cc_start: 0.6859 (m100) cc_final: 0.6365 (m100) REVERT: N 1 MET cc_start: 0.0188 (ptt) cc_final: -0.0611 (mtm) REVERT: N 78 GLN cc_start: 0.6096 (OUTLIER) cc_final: 0.5641 (pm20) REVERT: N 150 THR cc_start: 0.8617 (m) cc_final: 0.8161 (p) REVERT: N 165 SER cc_start: 0.6868 (m) cc_final: 0.6095 (t) outliers start: 26 outliers final: 11 residues processed: 285 average time/residue: 0.3623 time to fit residues: 139.6057 Evaluate side-chains 235 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 191 MET Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 36 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS N 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16702 Z= 0.241 Angle : 0.623 7.756 23819 Z= 0.360 Chirality : 0.037 0.223 2690 Planarity : 0.004 0.057 1986 Dihedral : 29.685 173.473 4651 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.03 % Favored : 91.89 % Rotamer: Outliers : 3.52 % Allowed : 14.87 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.21), residues: 1196 helix: -2.26 (0.17), residues: 689 sheet: -2.02 (0.62), residues: 64 loop : -2.99 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 28 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE M 8 TYR 0.012 0.002 TYR D 83 ARG 0.005 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 PHE cc_start: 0.7721 (m-80) cc_final: 0.7377 (m-80) REVERT: A 133 ARG cc_start: 0.6558 (ttm-80) cc_final: 0.5014 (ttm-80) REVERT: A 136 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6846 (tm-30) REVERT: B 64 ASN cc_start: 0.8101 (m-40) cc_final: 0.7794 (m-40) REVERT: B 91 LYS cc_start: 0.7982 (tttm) cc_final: 0.7609 (ttpt) REVERT: B 93 GLN cc_start: 0.7716 (tp40) cc_final: 0.7175 (tp40) REVERT: C 24 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7789 (mm-40) REVERT: C 36 LYS cc_start: 0.7759 (mmmt) cc_final: 0.7331 (tmtt) REVERT: C 41 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7358 (tp30) REVERT: C 95 LYS cc_start: 0.8131 (tptp) cc_final: 0.7632 (ttmt) REVERT: C 104 GLN cc_start: 0.8714 (mm110) cc_final: 0.8398 (mm-40) REVERT: D 68 ASP cc_start: 0.7791 (t70) cc_final: 0.7022 (t0) REVERT: D 71 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7110 (tm-30) REVERT: E 56 LYS cc_start: 0.7197 (tttt) cc_final: 0.6829 (mmmm) REVERT: E 95 GLN cc_start: 0.7481 (tt0) cc_final: 0.7234 (tt0) REVERT: E 107 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6864 (tt0) REVERT: E 136 GLU cc_start: 0.6882 (pm20) cc_final: 0.6625 (pm20) REVERT: F 44 LYS cc_start: 0.7206 (mtpt) cc_final: 0.6527 (mtpt) REVERT: F 52 GLU cc_start: 0.8457 (tp30) cc_final: 0.7748 (tp30) REVERT: F 91 LYS cc_start: 0.7508 (tttp) cc_final: 0.6936 (ttmt) REVERT: F 93 GLN cc_start: 0.7413 (tp-100) cc_final: 0.7133 (tp40) REVERT: G 24 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8163 (mm-40) REVERT: G 36 LYS cc_start: 0.8616 (mmpt) cc_final: 0.8190 (mmmm) REVERT: G 38 ASN cc_start: 0.8670 (m-40) cc_final: 0.8145 (t0) REVERT: G 76 THR cc_start: 0.7423 (p) cc_final: 0.7129 (t) REVERT: G 91 GLU cc_start: 0.7357 (tt0) cc_final: 0.7114 (tt0) REVERT: G 95 LYS cc_start: 0.7409 (tmtm) cc_final: 0.7047 (mtpt) REVERT: H 35 GLU cc_start: 0.7555 (pt0) cc_final: 0.7271 (pt0) REVERT: H 68 ASP cc_start: 0.6842 (t70) cc_final: 0.6130 (t0) REVERT: H 82 HIS cc_start: 0.7545 (t-90) cc_final: 0.7340 (t-90) REVERT: H 86 ARG cc_start: 0.7057 (mmt90) cc_final: 0.6371 (mtp180) REVERT: H 88 THR cc_start: 0.8410 (p) cc_final: 0.7969 (p) REVERT: H 113 GLU cc_start: 0.7366 (tt0) cc_final: 0.7086 (mt-10) REVERT: M 1 MET cc_start: 0.2535 (ptt) cc_final: 0.1549 (ptp) REVERT: M 51 HIS cc_start: 0.6903 (t-90) cc_final: 0.6338 (t-170) REVERT: M 59 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7013 (mmtm) REVERT: M 137 TRP cc_start: 0.6866 (m100) cc_final: 0.6255 (m100) REVERT: M 148 LYS cc_start: 0.8588 (mttm) cc_final: 0.7844 (ptpt) REVERT: N 1 MET cc_start: 0.0324 (ptt) cc_final: -0.0444 (mtm) REVERT: N 78 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5762 (pm20) REVERT: N 137 TRP cc_start: 0.8395 (m100) cc_final: 0.8030 (m100) REVERT: N 150 THR cc_start: 0.8420 (m) cc_final: 0.7821 (p) outliers start: 36 outliers final: 22 residues processed: 271 average time/residue: 0.3889 time to fit residues: 145.6251 Evaluate side-chains 245 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 133 ILE Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 122 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 84 ASN G 73 ASN H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16702 Z= 0.291 Angle : 0.634 6.938 23819 Z= 0.363 Chirality : 0.038 0.192 2690 Planarity : 0.004 0.055 1986 Dihedral : 29.618 171.042 4651 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 4.40 % Allowed : 16.14 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.22), residues: 1196 helix: -1.78 (0.18), residues: 688 sheet: -1.75 (0.65), residues: 64 loop : -2.91 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 28 HIS 0.006 0.001 HIS G 31 PHE 0.014 0.001 PHE C 25 TYR 0.016 0.002 TYR D 83 ARG 0.006 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 225 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6637 (ttm-80) cc_final: 0.4840 (ttm-80) REVERT: A 136 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6944 (tm-30) REVERT: B 91 LYS cc_start: 0.7994 (tttm) cc_final: 0.7615 (ttpt) REVERT: C 24 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8077 (mm-40) REVERT: C 36 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7386 (tmtt) REVERT: C 38 ASN cc_start: 0.8408 (t0) cc_final: 0.6825 (t0) REVERT: C 41 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7624 (tp30) REVERT: C 64 GLU cc_start: 0.7838 (tt0) cc_final: 0.7160 (tm-30) REVERT: C 95 LYS cc_start: 0.8044 (tptp) cc_final: 0.7375 (ttmt) REVERT: C 104 GLN cc_start: 0.8617 (mm110) cc_final: 0.8264 (mm-40) REVERT: D 62 MET cc_start: 0.7575 (mmm) cc_final: 0.7252 (mmt) REVERT: D 68 ASP cc_start: 0.7706 (t70) cc_final: 0.6980 (t0) REVERT: D 71 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7213 (tm-30) REVERT: E 56 LYS cc_start: 0.7246 (tttt) cc_final: 0.6884 (mmmm) REVERT: E 96 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8125 (mt-10) REVERT: E 107 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6930 (tt0) REVERT: E 136 GLU cc_start: 0.6666 (pm20) cc_final: 0.6363 (pm20) REVERT: F 52 GLU cc_start: 0.8505 (tp30) cc_final: 0.7808 (tp30) REVERT: F 91 LYS cc_start: 0.7568 (tttp) cc_final: 0.7146 (ttmt) REVERT: F 93 GLN cc_start: 0.7446 (tp-100) cc_final: 0.6912 (tp40) REVERT: G 36 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8174 (mmmm) REVERT: G 38 ASN cc_start: 0.8771 (t0) cc_final: 0.8051 (t0) REVERT: G 73 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6729 (t0) REVERT: G 76 THR cc_start: 0.7493 (p) cc_final: 0.7267 (t) REVERT: G 91 GLU cc_start: 0.7167 (tt0) cc_final: 0.6909 (tt0) REVERT: G 92 GLU cc_start: 0.7481 (mp0) cc_final: 0.7035 (mp0) REVERT: G 95 LYS cc_start: 0.7333 (tmtm) cc_final: 0.6951 (mtpt) REVERT: H 68 ASP cc_start: 0.6779 (t70) cc_final: 0.6033 (t0) REVERT: H 86 ARG cc_start: 0.7001 (mmt90) cc_final: 0.6252 (mtp180) REVERT: H 88 THR cc_start: 0.8391 (p) cc_final: 0.7833 (p) REVERT: H 113 GLU cc_start: 0.7543 (tt0) cc_final: 0.7262 (mt-10) REVERT: K 534 LYS cc_start: 0.4789 (OUTLIER) cc_final: 0.3884 (mmmt) REVERT: M 1 MET cc_start: 0.2288 (ptt) cc_final: 0.1289 (ptp) REVERT: M 59 LYS cc_start: 0.7344 (mtpp) cc_final: 0.6948 (mmmt) REVERT: M 137 TRP cc_start: 0.6761 (m100) cc_final: 0.6423 (m100) REVERT: M 148 LYS cc_start: 0.8515 (mttm) cc_final: 0.8211 (mttm) REVERT: N 1 MET cc_start: 0.0240 (ptt) cc_final: -0.0277 (mtm) REVERT: N 18 MET cc_start: 0.7774 (mmm) cc_final: 0.7460 (tpt) REVERT: N 78 GLN cc_start: 0.6178 (OUTLIER) cc_final: 0.5714 (pm20) REVERT: N 137 TRP cc_start: 0.8454 (m100) cc_final: 0.7995 (m100) REVERT: N 150 THR cc_start: 0.8589 (m) cc_final: 0.7898 (p) outliers start: 45 outliers final: 30 residues processed: 251 average time/residue: 0.3394 time to fit residues: 116.5728 Evaluate side-chains 242 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 209 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 534 LYS Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS M 145 ASN N 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16702 Z= 0.215 Angle : 0.586 9.247 23819 Z= 0.340 Chirality : 0.036 0.168 2690 Planarity : 0.004 0.056 1986 Dihedral : 29.458 171.887 4651 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 4.11 % Allowed : 17.61 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1196 helix: -1.38 (0.19), residues: 675 sheet: -1.80 (0.62), residues: 70 loop : -2.67 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 28 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE B 100 TYR 0.014 0.001 TYR N 73 ARG 0.006 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6670 (ttm-80) cc_final: 0.4475 (ttm-80) REVERT: A 136 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6964 (tm-30) REVERT: B 91 LYS cc_start: 0.7999 (tttm) cc_final: 0.7623 (ttpt) REVERT: B 93 GLN cc_start: 0.7625 (tp40) cc_final: 0.7416 (tp40) REVERT: C 24 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7995 (mm-40) REVERT: C 36 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7346 (tmtt) REVERT: C 38 ASN cc_start: 0.8382 (t0) cc_final: 0.6831 (t0) REVERT: C 41 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7393 (tp30) REVERT: C 95 LYS cc_start: 0.7957 (tptp) cc_final: 0.7332 (ttmt) REVERT: C 104 GLN cc_start: 0.8647 (mm110) cc_final: 0.8282 (mm-40) REVERT: D 37 TYR cc_start: 0.7906 (m-80) cc_final: 0.7691 (m-80) REVERT: D 68 ASP cc_start: 0.7741 (t70) cc_final: 0.7032 (t0) REVERT: D 71 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7267 (tm-30) REVERT: D 86 ARG cc_start: 0.6345 (tpp-160) cc_final: 0.6083 (tpp-160) REVERT: E 56 LYS cc_start: 0.7328 (tttt) cc_final: 0.7035 (mmmm) REVERT: E 96 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8053 (mt-10) REVERT: E 107 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6918 (tt0) REVERT: E 131 ARG cc_start: 0.6410 (tpt90) cc_final: 0.5966 (ttt180) REVERT: E 136 GLU cc_start: 0.6553 (pm20) cc_final: 0.6202 (pm20) REVERT: F 25 ASN cc_start: 0.6753 (t0) cc_final: 0.6516 (t0) REVERT: F 52 GLU cc_start: 0.8497 (tp30) cc_final: 0.7793 (tp30) REVERT: F 91 LYS cc_start: 0.7584 (tttp) cc_final: 0.7162 (ttmt) REVERT: F 93 GLN cc_start: 0.7381 (tp-100) cc_final: 0.7048 (mm110) REVERT: G 36 LYS cc_start: 0.8643 (mmpt) cc_final: 0.8131 (mmmm) REVERT: G 38 ASN cc_start: 0.8761 (t0) cc_final: 0.8183 (t0) REVERT: G 73 ASN cc_start: 0.7682 (t0) cc_final: 0.7257 (t0) REVERT: G 76 THR cc_start: 0.7455 (p) cc_final: 0.7208 (t) REVERT: G 91 GLU cc_start: 0.7138 (tt0) cc_final: 0.6844 (tt0) REVERT: G 95 LYS cc_start: 0.7371 (tmtm) cc_final: 0.6982 (mtpt) REVERT: H 59 MET cc_start: 0.6901 (tpt) cc_final: 0.6637 (tpp) REVERT: H 68 ASP cc_start: 0.6809 (t70) cc_final: 0.6049 (t0) REVERT: H 86 ARG cc_start: 0.6985 (mmt90) cc_final: 0.6214 (mtp180) REVERT: H 88 THR cc_start: 0.8413 (p) cc_final: 0.7881 (p) REVERT: H 113 GLU cc_start: 0.7427 (tt0) cc_final: 0.7066 (mt-10) REVERT: K 534 LYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4011 (mmmt) REVERT: M 1 MET cc_start: 0.2273 (ptt) cc_final: 0.1392 (ptp) REVERT: M 59 LYS cc_start: 0.7332 (mtpp) cc_final: 0.6931 (mmmt) REVERT: M 88 MET cc_start: 0.1448 (mtm) cc_final: 0.1245 (mtm) REVERT: M 137 TRP cc_start: 0.6748 (m100) cc_final: 0.6440 (m100) REVERT: M 146 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6422 (tp40) REVERT: M 148 LYS cc_start: 0.8508 (mttm) cc_final: 0.8150 (mttm) REVERT: N 1 MET cc_start: 0.0161 (ptt) cc_final: -0.0323 (mtm) REVERT: N 18 MET cc_start: 0.7798 (mmm) cc_final: 0.7469 (tpt) REVERT: N 78 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5654 (pm20) REVERT: N 137 TRP cc_start: 0.8347 (m100) cc_final: 0.8006 (m100) REVERT: N 150 THR cc_start: 0.8431 (m) cc_final: 0.7761 (p) outliers start: 42 outliers final: 30 residues processed: 249 average time/residue: 0.3322 time to fit residues: 113.6592 Evaluate side-chains 250 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 534 LYS Chi-restraints excluded: chain K residue 536 GLU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 142 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 0.0970 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16702 Z= 0.207 Angle : 0.569 7.526 23819 Z= 0.330 Chirality : 0.035 0.165 2690 Planarity : 0.004 0.057 1986 Dihedral : 29.308 173.650 4651 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.70 % Allowed : 18.59 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.23), residues: 1196 helix: -1.04 (0.19), residues: 688 sheet: -1.62 (0.63), residues: 70 loop : -2.57 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 28 HIS 0.002 0.000 HIS M 51 PHE 0.010 0.001 PHE A 78 TYR 0.010 0.001 TYR B 88 ARG 0.005 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (p0) REVERT: B 91 LYS cc_start: 0.8025 (tttm) cc_final: 0.7662 (ttpt) REVERT: B 92 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7724 (ttp80) REVERT: C 24 GLN cc_start: 0.8436 (mm-40) cc_final: 0.7978 (mm-40) REVERT: C 36 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7330 (tmtt) REVERT: C 38 ASN cc_start: 0.8361 (t0) cc_final: 0.6729 (t0) REVERT: C 41 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7338 (tp30) REVERT: C 95 LYS cc_start: 0.7957 (tptp) cc_final: 0.7307 (ttmt) REVERT: C 104 GLN cc_start: 0.8594 (mm110) cc_final: 0.8242 (mm-40) REVERT: D 68 ASP cc_start: 0.7765 (t70) cc_final: 0.7071 (t0) REVERT: D 71 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7241 (tm-30) REVERT: D 86 ARG cc_start: 0.6459 (tpp-160) cc_final: 0.6195 (tpp-160) REVERT: E 56 LYS cc_start: 0.7368 (tttt) cc_final: 0.7122 (mmmm) REVERT: E 96 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8034 (mt-10) REVERT: E 107 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6875 (tt0) REVERT: E 131 ARG cc_start: 0.6509 (tpt90) cc_final: 0.6034 (ttt180) REVERT: F 52 GLU cc_start: 0.8494 (tp30) cc_final: 0.7679 (tp30) REVERT: F 91 LYS cc_start: 0.7621 (tttp) cc_final: 0.7196 (ttmt) REVERT: F 93 GLN cc_start: 0.7340 (tp-100) cc_final: 0.7070 (mm110) REVERT: G 36 LYS cc_start: 0.8614 (mmpt) cc_final: 0.8096 (mmmm) REVERT: G 38 ASN cc_start: 0.8793 (t0) cc_final: 0.8175 (t0) REVERT: G 91 GLU cc_start: 0.7045 (tt0) cc_final: 0.6709 (tt0) REVERT: G 95 LYS cc_start: 0.7378 (tmtm) cc_final: 0.6961 (mtpt) REVERT: G 104 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7707 (mm110) REVERT: H 68 ASP cc_start: 0.6860 (t70) cc_final: 0.6122 (t0) REVERT: H 86 ARG cc_start: 0.7016 (mmt90) cc_final: 0.6081 (mtp180) REVERT: H 88 THR cc_start: 0.8414 (p) cc_final: 0.7880 (p) REVERT: H 113 GLU cc_start: 0.7376 (tt0) cc_final: 0.7028 (mt-10) REVERT: K 534 LYS cc_start: 0.5025 (pttt) cc_final: 0.4079 (mmmt) REVERT: M 1 MET cc_start: 0.2282 (ptt) cc_final: 0.1443 (ptp) REVERT: M 50 GLN cc_start: 0.8479 (pp30) cc_final: 0.8190 (pp30) REVERT: M 59 LYS cc_start: 0.7281 (mtpp) cc_final: 0.6904 (mmmt) REVERT: M 88 MET cc_start: 0.1399 (mtm) cc_final: 0.1198 (mtm) REVERT: M 137 TRP cc_start: 0.6684 (m100) cc_final: 0.6411 (m100) REVERT: M 146 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6451 (tp40) REVERT: M 148 LYS cc_start: 0.8484 (mttm) cc_final: 0.8140 (mttm) REVERT: N 1 MET cc_start: 0.0237 (ptt) cc_final: -0.0246 (mtm) REVERT: N 18 MET cc_start: 0.7859 (mmm) cc_final: 0.7595 (tpt) REVERT: N 78 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: N 118 ASN cc_start: 0.2187 (OUTLIER) cc_final: 0.1523 (m-40) outliers start: 48 outliers final: 27 residues processed: 267 average time/residue: 0.3429 time to fit residues: 126.3209 Evaluate side-chains 243 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 118 ASN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 87 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS M 75 GLN ** M 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 16702 Z= 0.507 Angle : 0.754 10.451 23819 Z= 0.419 Chirality : 0.044 0.195 2690 Planarity : 0.005 0.069 1986 Dihedral : 29.784 176.735 4648 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.45 % Favored : 89.38 % Rotamer: Outliers : 5.09 % Allowed : 18.79 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.23), residues: 1196 helix: -1.39 (0.19), residues: 683 sheet: -1.52 (0.64), residues: 70 loop : -2.74 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 132 HIS 0.006 0.001 HIS A 59 PHE 0.021 0.002 PHE C 25 TYR 0.038 0.002 TYR H 83 ARG 0.014 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ARG cc_start: 0.6886 (ttm-80) cc_final: 0.4845 (ttm-80) REVERT: B 84 MET cc_start: 0.6770 (mmm) cc_final: 0.6111 (mmt) REVERT: B 91 LYS cc_start: 0.8030 (tttm) cc_final: 0.7787 (ttpt) REVERT: B 92 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7920 (ttp80) REVERT: C 36 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7397 (tmtt) REVERT: C 38 ASN cc_start: 0.8267 (t0) cc_final: 0.6757 (t0) REVERT: C 41 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7489 (tp30) REVERT: C 64 GLU cc_start: 0.7860 (tt0) cc_final: 0.7097 (tm-30) REVERT: C 95 LYS cc_start: 0.7960 (tptp) cc_final: 0.7311 (ttmt) REVERT: C 104 GLN cc_start: 0.8461 (mm110) cc_final: 0.8125 (mm-40) REVERT: D 68 ASP cc_start: 0.7645 (t70) cc_final: 0.6960 (t0) REVERT: D 71 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7227 (tm-30) REVERT: D 86 ARG cc_start: 0.6865 (tpp-160) cc_final: 0.6524 (tpp-160) REVERT: E 56 LYS cc_start: 0.7430 (tttt) cc_final: 0.7014 (mmmm) REVERT: E 92 LEU cc_start: 0.7437 (tp) cc_final: 0.7194 (tt) REVERT: E 107 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6940 (tt0) REVERT: E 131 ARG cc_start: 0.6452 (tpt90) cc_final: 0.6015 (ttt180) REVERT: E 136 GLU cc_start: 0.6027 (pm20) cc_final: 0.5525 (pm20) REVERT: F 44 LYS cc_start: 0.7305 (mtpt) cc_final: 0.6581 (mtpt) REVERT: F 52 GLU cc_start: 0.8525 (tp30) cc_final: 0.7893 (tp30) REVERT: F 91 LYS cc_start: 0.7733 (tttp) cc_final: 0.7351 (ttmt) REVERT: F 93 GLN cc_start: 0.7473 (tp-100) cc_final: 0.7213 (mm110) REVERT: G 36 LYS cc_start: 0.8743 (mmpt) cc_final: 0.8248 (mmmm) REVERT: G 38 ASN cc_start: 0.8726 (t0) cc_final: 0.8114 (t0) REVERT: G 73 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6825 (t0) REVERT: G 91 GLU cc_start: 0.7148 (tt0) cc_final: 0.6883 (tt0) REVERT: G 95 LYS cc_start: 0.7411 (tmtm) cc_final: 0.6997 (mtpt) REVERT: G 104 GLN cc_start: 0.8500 (mm-40) cc_final: 0.7901 (mm-40) REVERT: H 86 ARG cc_start: 0.7135 (mmt90) cc_final: 0.6228 (mtp180) REVERT: H 88 THR cc_start: 0.8398 (p) cc_final: 0.7813 (p) REVERT: H 113 GLU cc_start: 0.7575 (tt0) cc_final: 0.7295 (mt-10) REVERT: K 525 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7273 (ptp90) REVERT: K 534 LYS cc_start: 0.5570 (OUTLIER) cc_final: 0.4681 (mmmt) REVERT: M 1 MET cc_start: 0.2280 (ptt) cc_final: 0.1348 (ptp) REVERT: M 40 ASN cc_start: 0.7654 (t0) cc_final: 0.7230 (t0) REVERT: M 148 LYS cc_start: 0.8396 (mttm) cc_final: 0.8005 (mttm) REVERT: N 1 MET cc_start: 0.0433 (ptt) cc_final: 0.0036 (mtm) REVERT: N 78 GLN cc_start: 0.6104 (OUTLIER) cc_final: 0.5651 (pm20) REVERT: N 137 TRP cc_start: 0.8432 (m100) cc_final: 0.7875 (m100) outliers start: 52 outliers final: 41 residues processed: 245 average time/residue: 0.3397 time to fit residues: 113.2123 Evaluate side-chains 248 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 525 ARG Chi-restraints excluded: chain K residue 534 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 30.0000 chunk 96 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 128 optimal weight: 0.0670 chunk 135 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16702 Z= 0.177 Angle : 0.590 8.538 23819 Z= 0.340 Chirality : 0.035 0.175 2690 Planarity : 0.004 0.062 1986 Dihedral : 29.231 174.101 4648 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.35 % Allowed : 22.11 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.24), residues: 1196 helix: -0.84 (0.20), residues: 686 sheet: -1.24 (0.66), residues: 70 loop : -2.47 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 47 HIS 0.003 0.001 HIS N 77 PHE 0.009 0.001 PHE B 100 TYR 0.022 0.001 TYR B 88 ARG 0.010 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 THR cc_start: 0.7481 (t) cc_final: 0.7242 (p) REVERT: A 82 VAL cc_start: 0.7810 (t) cc_final: 0.7507 (p) REVERT: B 43 VAL cc_start: 0.7062 (p) cc_final: 0.6842 (p) REVERT: B 67 ARG cc_start: 0.6328 (ttp80) cc_final: 0.5885 (ttm-80) REVERT: B 84 MET cc_start: 0.6707 (mmm) cc_final: 0.6408 (mmt) REVERT: B 91 LYS cc_start: 0.7962 (tttm) cc_final: 0.7739 (ttpt) REVERT: B 92 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7783 (ttp80) REVERT: B 96 THR cc_start: 0.7232 (m) cc_final: 0.6958 (p) REVERT: C 24 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8031 (mm-40) REVERT: C 36 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7392 (tmtt) REVERT: C 38 ASN cc_start: 0.8275 (t0) cc_final: 0.6617 (t0) REVERT: C 41 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7434 (tp30) REVERT: C 95 LYS cc_start: 0.7913 (tptp) cc_final: 0.7219 (ttmt) REVERT: C 104 GLN cc_start: 0.8536 (mm110) cc_final: 0.8300 (mm-40) REVERT: D 68 ASP cc_start: 0.7728 (t70) cc_final: 0.7002 (t0) REVERT: D 71 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7254 (tm-30) REVERT: E 56 LYS cc_start: 0.7531 (tttt) cc_final: 0.7178 (mmmm) REVERT: E 96 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8569 (mm-30) REVERT: E 131 ARG cc_start: 0.6514 (tpt90) cc_final: 0.6061 (ttt180) REVERT: E 136 GLU cc_start: 0.6195 (pm20) cc_final: 0.5873 (pm20) REVERT: F 44 LYS cc_start: 0.7432 (mtpt) cc_final: 0.6640 (mtpt) REVERT: F 52 GLU cc_start: 0.8325 (tp30) cc_final: 0.7564 (tp30) REVERT: F 91 LYS cc_start: 0.7590 (tttp) cc_final: 0.7169 (ttmt) REVERT: F 93 GLN cc_start: 0.7259 (tp-100) cc_final: 0.6988 (mm110) REVERT: G 36 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8126 (mmmm) REVERT: G 38 ASN cc_start: 0.8523 (t0) cc_final: 0.7760 (t0) REVERT: G 91 GLU cc_start: 0.7005 (tt0) cc_final: 0.6704 (tt0) REVERT: G 95 LYS cc_start: 0.7388 (tmtm) cc_final: 0.7020 (mtpt) REVERT: G 104 GLN cc_start: 0.8397 (mm-40) cc_final: 0.7764 (mm110) REVERT: H 68 ASP cc_start: 0.6835 (t70) cc_final: 0.6093 (t0) REVERT: H 86 ARG cc_start: 0.7055 (mmt90) cc_final: 0.6020 (mtp180) REVERT: H 88 THR cc_start: 0.8347 (p) cc_final: 0.7826 (p) REVERT: H 113 GLU cc_start: 0.7400 (tt0) cc_final: 0.7049 (mt-10) REVERT: K 534 LYS cc_start: 0.5147 (pttt) cc_final: 0.4151 (mmmt) REVERT: M 1 MET cc_start: 0.2224 (ptt) cc_final: 0.1342 (ptp) REVERT: M 50 GLN cc_start: 0.8596 (pp30) cc_final: 0.8262 (pp30) REVERT: M 137 TRP cc_start: 0.6694 (m100) cc_final: 0.6401 (m100) REVERT: M 146 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6183 (tp-100) REVERT: M 148 LYS cc_start: 0.8521 (mttm) cc_final: 0.8150 (mttm) REVERT: N 1 MET cc_start: 0.0146 (ptt) cc_final: -0.0316 (mtm) REVERT: N 78 GLN cc_start: 0.5947 (OUTLIER) cc_final: 0.5567 (pm20) REVERT: N 137 TRP cc_start: 0.8228 (m100) cc_final: 0.7785 (m100) outliers start: 24 outliers final: 18 residues processed: 247 average time/residue: 0.3474 time to fit residues: 118.1334 Evaluate side-chains 241 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 40 optimal weight: 0.0470 chunk 119 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 6.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN ** M 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 16702 Z= 0.614 Angle : 0.817 8.471 23819 Z= 0.449 Chirality : 0.047 0.215 2690 Planarity : 0.005 0.077 1986 Dihedral : 29.879 179.629 4648 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.95 % Favored : 88.88 % Rotamer: Outliers : 3.82 % Allowed : 21.23 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -2.93 (0.22), residues: 1196 helix: -1.38 (0.18), residues: 687 sheet: -1.31 (0.64), residues: 70 loop : -2.84 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 132 HIS 0.008 0.002 HIS A 115 PHE 0.021 0.002 PHE C 25 TYR 0.040 0.003 TYR H 83 ARG 0.013 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: A 82 VAL cc_start: 0.7896 (t) cc_final: 0.7643 (p) REVERT: A 133 ARG cc_start: 0.6345 (ttm-80) cc_final: 0.5447 (ttt-90) REVERT: B 67 ARG cc_start: 0.6484 (ttp80) cc_final: 0.6055 (ttm-80) REVERT: B 84 MET cc_start: 0.6811 (mmm) cc_final: 0.6088 (mmt) REVERT: B 91 LYS cc_start: 0.8104 (tttm) cc_final: 0.7902 (ttpt) REVERT: B 92 ARG cc_start: 0.8375 (ttp80) cc_final: 0.7826 (ttp80) REVERT: B 96 THR cc_start: 0.7367 (m) cc_final: 0.7053 (p) REVERT: C 36 LYS cc_start: 0.7824 (mmmt) cc_final: 0.7380 (tttm) REVERT: C 38 ASN cc_start: 0.8230 (t0) cc_final: 0.6799 (t0) REVERT: C 41 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7598 (tp30) REVERT: C 64 GLU cc_start: 0.7864 (tt0) cc_final: 0.7106 (tm-30) REVERT: C 73 ASN cc_start: 0.7749 (t0) cc_final: 0.7321 (t0) REVERT: C 95 LYS cc_start: 0.7946 (tptp) cc_final: 0.7312 (ttmt) REVERT: C 104 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8082 (mm-40) REVERT: D 68 ASP cc_start: 0.7651 (t70) cc_final: 0.6975 (t0) REVERT: D 71 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 86 ARG cc_start: 0.6645 (tpp80) cc_final: 0.6339 (tpp80) REVERT: E 56 LYS cc_start: 0.7782 (tttt) cc_final: 0.7440 (mmmm) REVERT: E 73 GLU cc_start: 0.7384 (tt0) cc_final: 0.6920 (tt0) REVERT: E 92 LEU cc_start: 0.7480 (tp) cc_final: 0.7250 (tt) REVERT: E 131 ARG cc_start: 0.6552 (tpt90) cc_final: 0.5955 (ttt180) REVERT: E 136 GLU cc_start: 0.5893 (pm20) cc_final: 0.5315 (pm20) REVERT: F 25 ASN cc_start: 0.6414 (t0) cc_final: 0.6116 (t0) REVERT: F 44 LYS cc_start: 0.7373 (mtpt) cc_final: 0.6661 (mtpt) REVERT: F 52 GLU cc_start: 0.8484 (tp30) cc_final: 0.7896 (tp30) REVERT: F 91 LYS cc_start: 0.7741 (tttp) cc_final: 0.7352 (ttmt) REVERT: G 36 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8256 (mmmm) REVERT: G 38 ASN cc_start: 0.8661 (t0) cc_final: 0.8038 (t0) REVERT: G 91 GLU cc_start: 0.7139 (tt0) cc_final: 0.6904 (tt0) REVERT: G 95 LYS cc_start: 0.7379 (tmtm) cc_final: 0.6982 (mtpt) REVERT: G 104 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7892 (mm-40) REVERT: H 86 ARG cc_start: 0.7173 (mmt90) cc_final: 0.6253 (mtp180) REVERT: H 88 THR cc_start: 0.8397 (p) cc_final: 0.7866 (p) REVERT: H 113 GLU cc_start: 0.7651 (tt0) cc_final: 0.7381 (mt-10) REVERT: K 534 LYS cc_start: 0.5704 (pttt) cc_final: 0.5069 (mmmt) REVERT: M 1 MET cc_start: 0.2330 (ptt) cc_final: 0.1488 (ptp) REVERT: N 1 MET cc_start: 0.0459 (ptt) cc_final: 0.0033 (mtm) REVERT: N 77 HIS cc_start: 0.6870 (m-70) cc_final: 0.6613 (m170) REVERT: N 78 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5607 (pm20) outliers start: 39 outliers final: 33 residues processed: 242 average time/residue: 0.3406 time to fit residues: 112.8226 Evaluate side-chains 242 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 40 ASN Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain M residue 162 PHE Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 158 THR Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 116 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 30.0000 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16702 Z= 0.182 Angle : 0.614 7.707 23819 Z= 0.352 Chirality : 0.036 0.152 2690 Planarity : 0.004 0.066 1986 Dihedral : 29.321 175.217 4648 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.86 % Allowed : 22.90 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: -2.25 (0.24), residues: 1196 helix: -0.80 (0.20), residues: 686 sheet: -1.07 (0.64), residues: 70 loop : -2.59 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.003 0.001 HIS N 77 PHE 0.013 0.001 PHE B 100 TYR 0.027 0.001 TYR H 83 ARG 0.009 0.001 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: A 82 VAL cc_start: 0.7932 (t) cc_final: 0.7623 (p) REVERT: B 84 MET cc_start: 0.6623 (mmm) cc_final: 0.6310 (mmt) REVERT: B 91 LYS cc_start: 0.7855 (tttm) cc_final: 0.7642 (ttpt) REVERT: B 92 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7686 (ttp80) REVERT: B 96 THR cc_start: 0.7241 (m) cc_final: 0.6977 (p) REVERT: C 24 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8100 (mm-40) REVERT: C 36 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7407 (tmtt) REVERT: C 38 ASN cc_start: 0.8272 (t0) cc_final: 0.6628 (t0) REVERT: C 95 LYS cc_start: 0.8014 (tptp) cc_final: 0.7357 (ttmt) REVERT: C 104 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8216 (mm-40) REVERT: D 68 ASP cc_start: 0.7713 (t70) cc_final: 0.6954 (t0) REVERT: D 71 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7340 (tm-30) REVERT: D 85 LYS cc_start: 0.7486 (mttt) cc_final: 0.7252 (mmtp) REVERT: D 86 ARG cc_start: 0.6358 (tpp80) cc_final: 0.6081 (tpp80) REVERT: E 56 LYS cc_start: 0.7639 (tttt) cc_final: 0.7344 (mmmm) REVERT: E 96 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8521 (mm-30) REVERT: E 131 ARG cc_start: 0.6455 (tpt90) cc_final: 0.5839 (tpt-90) REVERT: E 136 GLU cc_start: 0.6246 (pm20) cc_final: 0.5948 (pm20) REVERT: F 44 LYS cc_start: 0.7413 (mtpt) cc_final: 0.6625 (mtpt) REVERT: F 52 GLU cc_start: 0.8306 (tp30) cc_final: 0.7718 (tp30) REVERT: F 91 LYS cc_start: 0.7577 (tttp) cc_final: 0.7140 (ttmt) REVERT: F 93 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7347 (mm110) REVERT: G 36 LYS cc_start: 0.8565 (mmpt) cc_final: 0.8120 (mmmm) REVERT: G 38 ASN cc_start: 0.8570 (t0) cc_final: 0.7727 (t0) REVERT: G 91 GLU cc_start: 0.7055 (tt0) cc_final: 0.6755 (tt0) REVERT: G 95 LYS cc_start: 0.7345 (tmtm) cc_final: 0.6950 (mtpt) REVERT: G 104 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8010 (mm110) REVERT: H 68 ASP cc_start: 0.6773 (t70) cc_final: 0.6023 (t0) REVERT: H 86 ARG cc_start: 0.7091 (mmt90) cc_final: 0.6035 (mtp180) REVERT: H 88 THR cc_start: 0.8358 (p) cc_final: 0.7874 (p) REVERT: H 113 GLU cc_start: 0.7435 (tt0) cc_final: 0.7057 (mt-10) REVERT: K 534 LYS cc_start: 0.5495 (pttt) cc_final: 0.4617 (mmmt) REVERT: M 1 MET cc_start: 0.2070 (ptt) cc_final: 0.1146 (ptp) REVERT: N 1 MET cc_start: 0.0121 (ptt) cc_final: -0.0172 (mtm) REVERT: N 78 GLN cc_start: 0.5873 (OUTLIER) cc_final: 0.5460 (pm20) outliers start: 19 outliers final: 15 residues processed: 235 average time/residue: 0.3364 time to fit residues: 109.1657 Evaluate side-chains 230 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 78 GLN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 48 optimal weight: 0.4980 chunk 119 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115234 restraints weight = 24650.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118471 restraints weight = 12366.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120168 restraints weight = 8712.614| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16702 Z= 0.221 Angle : 0.598 8.432 23819 Z= 0.342 Chirality : 0.036 0.161 2690 Planarity : 0.004 0.065 1986 Dihedral : 29.353 176.999 4648 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.15 % Allowed : 23.39 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.99 (0.24), residues: 1196 helix: -0.57 (0.20), residues: 680 sheet: -1.09 (0.64), residues: 70 loop : -2.47 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP M 137 HIS 0.003 0.001 HIS N 77 PHE 0.013 0.001 PHE B 100 TYR 0.038 0.002 TYR B 88 ARG 0.009 0.000 ARG G 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3090.14 seconds wall clock time: 56 minutes 17.14 seconds (3377.14 seconds total)