Starting phenix.real_space_refine on Thu Sep 26 05:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8es8_28571/09_2024/8es8_28571.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7602 2.51 5 N 1982 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11976 Number of models: 1 Model: "" Number of chains: 21 Chain: "Z" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 281 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "D" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 987 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "G" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "A" Number of atoms: 2008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2008 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2292 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 273} Chain: "N" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 837 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 80 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.48, per 1000 atoms: 0.71 Number of scatterers: 11976 At special positions: 0 Unit cell: (95.2, 90.1, 201.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2324 8.00 N 1982 7.00 C 7602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS Z 32 " - pdb=" SG CYS Y 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS B 245 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 101 " - pdb=" SG CYS N 164 " distance=2.04 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 259 " distance=2.04 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 80 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG J 1 " - " NAG J 2 " " NAG Q 1 " - " NAG Q 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1701 " - " ASN A 195 " " NAG A1702 " - " ASN A 184 " " NAG B1701 " - " ASN B 184 " " NAG C 1 " - " ASN D 38 " " NAG G1701 " - " ASN G 92 " " NAG G1702 " - " ASN G 52 " " NAG J 1 " - " ASN A 58 " " NAG Q 1 " - " ASN B 84 " " NAG T 1 " - " ASN D 74 " " NAG U 1 " - " ASN B 107 " " NAG V 1 " - " ASN A 150 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 28 sheets defined 26.7% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'Z' and resid 29 through 56 Processing helix chain 'Y' and resid 28 through 55 removed outlier: 4.372A pdb=" N CYS Y 32 " --> pdb=" O ASP Y 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE Y 41 " --> pdb=" O GLY Y 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 100 through 127 removed outlier: 3.586A pdb=" N GLY D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 126 through 156 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 111 through 136 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 126 through 154 removed outlier: 3.559A pdb=" N VAL E 130 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.676A pdb=" N SER A 87 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.845A pdb=" N SER A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 257 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.525A pdb=" N LYS B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 248 through 289 removed outlier: 3.571A pdb=" N LYS B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 55 removed outlier: 3.514A pdb=" N ILE N 52 " --> pdb=" O ALA N 49 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU N 53 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN N 54 " --> pdb=" O TRP N 51 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 86 removed outlier: 3.515A pdb=" N TRP N 60 " --> pdb=" O GLY N 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY N 83 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 151 removed outlier: 3.687A pdb=" N GLN N 141 " --> pdb=" O ASP N 137 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR N 142 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 162 removed outlier: 3.740A pdb=" N GLN N 155 " --> pdb=" O HIS N 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 175 Processing helix chain 'N' and resid 175 through 180 Processing sheet with id=AA1, first strand: chain 'D' and resid 26 through 28 removed outlier: 5.992A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 42 through 46 removed outlier: 6.368A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.640A pdb=" N VAL D 97 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET E 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'F' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.945A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 122 through 123 removed outlier: 4.454A pdb=" N MET F 123 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE G 108 " --> pdb=" O MET F 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 31 through 34 removed outlier: 3.550A pdb=" N LEU G 43 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 37 through 41 removed outlier: 3.566A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.445A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 49 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LYS A 38 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE A 47 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.445A pdb=" N MET A 11 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N HIS A 116 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 13 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'A' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.494A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 88 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B 32 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N PHE B 48 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TRP B 34 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 38 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.494A pdb=" N LEU B 11 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR B 114 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 13 " --> pdb=" O THR B 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 19 through 21 Processing sheet with id=AC1, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.590A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 124 through 128 removed outlier: 5.590A pdb=" N TYR B 188 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 166 removed outlier: 4.737A pdb=" N TRP B 159 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 46 through 47 removed outlier: 6.786A pdb=" N GLY N 26 " --> pdb=" O PHE N 33 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG N 35 " --> pdb=" O ALA N 24 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA N 24 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 37 " --> pdb=" O PHE N 22 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE N 22 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG N 111 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N HIS N 114 " --> pdb=" O LEU N 126 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE N 124 " --> pdb=" O TYR N 116 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TYR N 118 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASP N 122 " --> pdb=" O TYR N 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.871A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.871A pdb=" N PHE N 241 " --> pdb=" O SER N 207 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 222 through 223 Processing sheet with id=AC8, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.925A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 6 through 11 removed outlier: 5.925A pdb=" N PHE M 62 " --> pdb=" O GLY M 29 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER M 55 " --> pdb=" O TYR M 63 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 44 through 45 624 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3829 1.35 - 1.47: 3159 1.47 - 1.60: 5164 1.60 - 1.72: 0 1.72 - 1.84: 98 Bond restraints: 12250 Sorted by residual: bond pdb=" CAI Y01 Y 201 " pdb=" CAK Y01 Y 201 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C1 NAG A1701 " pdb=" O5 NAG A1701 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CAI Y01 Y 201 " pdb=" CAZ Y01 Y 201 " ideal model delta sigma weight residual 1.332 1.381 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG G1702 " pdb=" O5 NAG G1702 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 12245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 16322 2.36 - 4.72: 249 4.72 - 7.08: 21 7.08 - 9.44: 6 9.44 - 11.79: 4 Bond angle restraints: 16602 Sorted by residual: angle pdb=" OAG Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 123.38 111.59 11.79 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAM Y01 Y 201 " pdb=" CAY Y01 Y 201 " pdb=" OAW Y01 Y 201 " ideal model delta sigma weight residual 111.19 122.45 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CA CYS F 119 " pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " ideal model delta sigma weight residual 114.40 122.07 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N ASN A 184 " pdb=" CA ASN A 184 " pdb=" CB ASN A 184 " ideal model delta sigma weight residual 110.29 103.12 7.17 2.15e+00 2.16e-01 1.11e+01 angle pdb=" CAV Y01 Y 201 " pdb=" CAZ Y01 Y 201 " pdb=" CBH Y01 Y 201 " ideal model delta sigma weight residual 116.96 126.57 -9.61 3.00e+00 1.11e-01 1.03e+01 ... (remaining 16597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 7082 21.65 - 43.31: 405 43.31 - 64.96: 66 64.96 - 86.62: 27 86.62 - 108.27: 16 Dihedral angle restraints: 7596 sinusoidal: 3337 harmonic: 4259 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual 93.00 42.29 50.71 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 80 " pdb=" CB CYS M 80 " ideal model delta sinusoidal sigma weight residual 93.00 44.59 48.41 1 1.00e+01 1.00e-02 3.23e+01 dihedral pdb=" CA ASN A 150 " pdb=" C ASN A 150 " pdb=" N VAL A 151 " pdb=" CA VAL A 151 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 7593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1825 0.129 - 0.259: 30 0.259 - 0.388: 5 0.388 - 0.517: 0 0.517 - 0.646: 1 Chirality restraints: 1861 Sorted by residual: chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN A 150 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG A1702 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A1702 " pdb=" O5 NAG A1702 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASN A 195 " pdb=" N ASN A 195 " pdb=" C ASN A 195 " pdb=" CB ASN A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1858 not shown) Planarity restraints: 2110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 205 " 0.065 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 206 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " -0.033 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" CG ASN G 52 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.020 2.00e-02 2.50e+03 pdb=" C1 NAG G1702 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 150 " 0.025 2.00e-02 2.50e+03 2.43e-02 7.37e+00 pdb=" CG ASN A 150 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 150 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 150 " -0.030 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.026 2.00e-02 2.50e+03 ... (remaining 2107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 253 2.69 - 3.25: 11032 3.25 - 3.80: 17895 3.80 - 4.35: 24045 4.35 - 4.90: 40251 Nonbonded interactions: 93476 Sorted by model distance: nonbonded pdb=" O SER B 8 " pdb=" OG1 THR B 109 " model vdw 2.142 3.040 nonbonded pdb=" NZ LYS N 127 " pdb=" O TRP N 133 " model vdw 2.171 3.120 nonbonded pdb=" OG1 THR G 66 " pdb=" OD1 ASP G 68 " model vdw 2.205 3.040 nonbonded pdb=" O SER N 13 " pdb=" OG SER N 92 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASN G 52 " pdb=" N2 NAG G1702 " model vdw 2.245 3.120 ... (remaining 93471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = (chain 'F' and resid 33 through 155) } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = (chain 'Y' and resid 25 through 55) selection = (chain 'Z' and resid 25 through 55) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12250 Z= 0.267 Angle : 0.712 11.794 16602 Z= 0.362 Chirality : 0.053 0.646 1861 Planarity : 0.005 0.099 2099 Dihedral : 14.956 108.272 4813 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.08 % Allowed : 0.23 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1442 helix: 2.49 (0.27), residues: 342 sheet: 1.24 (0.26), residues: 412 loop : -1.06 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 59 HIS 0.005 0.001 HIS N 70 PHE 0.025 0.002 PHE A 35 TYR 0.013 0.001 TYR D 71 ARG 0.004 0.001 ARG M 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 121 ASN cc_start: 0.6982 (p0) cc_final: 0.6778 (p0) REVERT: F 123 MET cc_start: 0.5901 (ppp) cc_final: 0.5415 (ppp) REVERT: G 129 LEU cc_start: 0.7396 (mm) cc_final: 0.6970 (mt) outliers start: 1 outliers final: 1 residues processed: 256 average time/residue: 1.3365 time to fit residues: 368.0070 Evaluate side-chains 196 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.0870 chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN F 92 GLN G 77 ASN E 62 ASN E 81 HIS A 196 ASN N 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 12250 Z= 0.177 Angle : 0.631 7.563 16602 Z= 0.328 Chirality : 0.046 0.336 1861 Planarity : 0.004 0.063 2099 Dihedral : 10.098 95.169 2048 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.25 % Allowed : 11.96 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1442 helix: 2.64 (0.27), residues: 345 sheet: 1.23 (0.25), residues: 417 loop : -0.95 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 151 HIS 0.004 0.001 HIS N 192 PHE 0.024 0.001 PHE G 118 TYR 0.022 0.001 TYR D 79 ARG 0.004 0.000 ARG N 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 208 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8546 (mttp) cc_final: 0.8131 (mmtm) REVERT: F 121 ASN cc_start: 0.7073 (p0) cc_final: 0.6733 (p0) REVERT: F 144 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5069 (mm) REVERT: G 129 LEU cc_start: 0.7431 (mm) cc_final: 0.7051 (mt) REVERT: E 37 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7385 (mppt) REVERT: E 115 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7632 (ttt180) REVERT: A 109 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7587 (tpp80) outliers start: 29 outliers final: 13 residues processed: 221 average time/residue: 1.2809 time to fit residues: 305.3569 Evaluate side-chains 202 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN B 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 12250 Z= 0.318 Angle : 0.702 9.536 16602 Z= 0.365 Chirality : 0.050 0.339 1861 Planarity : 0.004 0.050 2099 Dihedral : 9.188 98.173 2048 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.72 % Allowed : 14.29 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1442 helix: 2.30 (0.26), residues: 345 sheet: 1.13 (0.25), residues: 430 loop : -1.16 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 PHE 0.027 0.002 PHE A 35 TYR 0.018 0.002 TYR D 71 ARG 0.005 0.001 ARG N 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8516 (mttp) cc_final: 0.8036 (mmtm) REVERT: F 121 ASN cc_start: 0.7220 (p0) cc_final: 0.6862 (p0) REVERT: F 144 LEU cc_start: 0.5346 (OUTLIER) cc_final: 0.4946 (mm) REVERT: E 43 THR cc_start: 0.7964 (p) cc_final: 0.7708 (m) REVERT: A 109 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7798 (tpp80) REVERT: B 254 GLN cc_start: 0.7982 (mm110) cc_final: 0.7673 (tp-100) REVERT: M 19 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7456 (ttpp) outliers start: 35 outliers final: 16 residues processed: 222 average time/residue: 1.2081 time to fit residues: 290.6692 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 129 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN A 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12250 Z= 0.160 Angle : 0.607 8.262 16602 Z= 0.314 Chirality : 0.046 0.395 1861 Planarity : 0.004 0.039 2099 Dihedral : 8.214 92.939 2048 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.87 % Allowed : 15.30 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1442 helix: 2.63 (0.27), residues: 342 sheet: 1.19 (0.25), residues: 432 loop : -1.05 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 151 HIS 0.004 0.001 HIS N 70 PHE 0.022 0.001 PHE G 118 TYR 0.017 0.001 TYR F 111 ARG 0.010 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8539 (mttp) cc_final: 0.8085 (mmtm) REVERT: F 99 TYR cc_start: 0.5857 (p90) cc_final: 0.5649 (p90) REVERT: F 106 GLU cc_start: 0.6776 (tp30) cc_final: 0.6120 (tp30) REVERT: F 121 ASN cc_start: 0.7257 (p0) cc_final: 0.6946 (p0) REVERT: F 144 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4902 (mm) REVERT: G 129 LEU cc_start: 0.7407 (mm) cc_final: 0.7032 (mt) REVERT: E 90 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8310 (tp) REVERT: E 115 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7657 (ttt180) REVERT: E 120 GLU cc_start: 0.5589 (pp20) cc_final: 0.5171 (pm20) REVERT: B 253 GLN cc_start: 0.7768 (tt0) cc_final: 0.7558 (tt0) outliers start: 37 outliers final: 14 residues processed: 225 average time/residue: 1.2405 time to fit residues: 302.1176 Evaluate side-chains 207 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12250 Z= 0.235 Angle : 0.646 9.169 16602 Z= 0.334 Chirality : 0.048 0.389 1861 Planarity : 0.004 0.036 2099 Dihedral : 8.033 102.395 2048 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.18 % Allowed : 16.07 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1442 helix: 2.51 (0.27), residues: 343 sheet: 1.28 (0.25), residues: 421 loop : -1.07 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.024 0.002 PHE A 35 TYR 0.022 0.001 TYR F 111 ARG 0.008 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 121 ASN cc_start: 0.7253 (p0) cc_final: 0.6971 (p0) REVERT: F 144 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4916 (mm) REVERT: E 115 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7646 (ttt180) outliers start: 41 outliers final: 22 residues processed: 217 average time/residue: 1.1823 time to fit residues: 278.6432 Evaluate side-chains 212 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12250 Z= 0.333 Angle : 0.723 10.444 16602 Z= 0.375 Chirality : 0.051 0.424 1861 Planarity : 0.005 0.039 2099 Dihedral : 8.007 90.723 2048 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.04 % Allowed : 16.69 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.21), residues: 1442 helix: 2.20 (0.26), residues: 343 sheet: 1.12 (0.24), residues: 432 loop : -1.24 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 151 HIS 0.006 0.001 HIS N 70 PHE 0.025 0.002 PHE A 35 TYR 0.026 0.002 TYR B 252 ARG 0.013 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 193 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 85 LYS cc_start: 0.8403 (mttp) cc_final: 0.7944 (mmtm) REVERT: F 121 ASN cc_start: 0.7114 (p0) cc_final: 0.6898 (p0) REVERT: F 144 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4950 (mm) REVERT: G 38 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: E 90 LEU cc_start: 0.8877 (mt) cc_final: 0.8408 (tp) REVERT: E 115 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7711 (ttt180) REVERT: B 48 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8173 (p90) REVERT: B 254 GLN cc_start: 0.7922 (mm110) cc_final: 0.7598 (tp-100) outliers start: 52 outliers final: 17 residues processed: 220 average time/residue: 1.2492 time to fit residues: 297.1655 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 70 LYS Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12250 Z= 0.222 Angle : 0.660 9.331 16602 Z= 0.341 Chirality : 0.048 0.433 1861 Planarity : 0.004 0.038 2099 Dihedral : 7.403 58.281 2046 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.03 % Allowed : 18.40 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1442 helix: 2.38 (0.27), residues: 343 sheet: 1.14 (0.25), residues: 425 loop : -1.16 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.018 0.002 PHE A 35 TYR 0.020 0.001 TYR B 252 ARG 0.011 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: D 84 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.7018 (m) REVERT: F 144 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4970 (mm) REVERT: G 129 LEU cc_start: 0.7551 (mm) cc_final: 0.7191 (mt) REVERT: E 115 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7691 (ttt180) REVERT: A 186 SER cc_start: 0.7581 (OUTLIER) cc_final: 0.7244 (m) REVERT: B 48 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8137 (p90) REVERT: B 253 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7677 (tt0) REVERT: B 254 GLN cc_start: 0.7916 (mm110) cc_final: 0.7611 (tp-100) outliers start: 39 outliers final: 17 residues processed: 213 average time/residue: 1.2172 time to fit residues: 280.7138 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 94 GLN E 92 GLN E 109 ASN E 121 ASN N 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12250 Z= 0.257 Angle : 0.687 9.489 16602 Z= 0.357 Chirality : 0.048 0.425 1861 Planarity : 0.004 0.039 2099 Dihedral : 7.344 59.224 2046 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.18 % Allowed : 19.02 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1442 helix: 2.31 (0.26), residues: 343 sheet: 1.08 (0.25), residues: 428 loop : -1.17 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.021 0.002 PHE G 118 TYR 0.026 0.002 TYR D 79 ARG 0.012 0.001 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6811 (mm) cc_final: 0.6520 (mp) REVERT: F 85 LYS cc_start: 0.8421 (mttp) cc_final: 0.7875 (mmtm) REVERT: F 144 LEU cc_start: 0.5314 (OUTLIER) cc_final: 0.4993 (mm) REVERT: G 54 THR cc_start: 0.6054 (OUTLIER) cc_final: 0.5061 (p) REVERT: E 115 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7732 (ttt180) REVERT: B 48 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8159 (p90) REVERT: B 254 GLN cc_start: 0.7947 (mm110) cc_final: 0.7633 (tp-100) outliers start: 41 outliers final: 19 residues processed: 211 average time/residue: 1.3171 time to fit residues: 299.8187 Evaluate side-chains 205 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 87 CYS Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 ASN B 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12250 Z= 0.244 Angle : 0.683 9.252 16602 Z= 0.354 Chirality : 0.048 0.423 1861 Planarity : 0.004 0.037 2099 Dihedral : 7.260 59.997 2046 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.80 % Allowed : 19.49 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1442 helix: 2.32 (0.26), residues: 343 sheet: 1.14 (0.25), residues: 424 loop : -1.16 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 151 HIS 0.005 0.001 HIS N 70 PHE 0.020 0.002 PHE A 35 TYR 0.027 0.001 TYR D 79 ARG 0.006 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6739 (mm) cc_final: 0.6491 (mp) REVERT: F 85 LYS cc_start: 0.8423 (mttp) cc_final: 0.7882 (mmtm) REVERT: F 91 GLU cc_start: 0.7577 (mp0) cc_final: 0.7369 (mp0) REVERT: F 144 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4988 (mm) REVERT: E 115 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7730 (ttt180) REVERT: B 48 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8151 (p90) outliers start: 36 outliers final: 20 residues processed: 208 average time/residue: 1.2827 time to fit residues: 288.1068 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 141 optimal weight: 0.1980 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12250 Z= 0.190 Angle : 0.661 10.611 16602 Z= 0.340 Chirality : 0.046 0.414 1861 Planarity : 0.003 0.035 2099 Dihedral : 7.045 58.316 2046 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.02 % Allowed : 20.50 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1442 helix: 2.46 (0.27), residues: 342 sheet: 1.10 (0.25), residues: 433 loop : -1.05 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 151 HIS 0.004 0.001 HIS N 70 PHE 0.021 0.001 PHE G 118 TYR 0.028 0.001 TYR D 79 ARG 0.005 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 58 LEU cc_start: 0.6674 (mm) cc_final: 0.6469 (mp) REVERT: F 85 LYS cc_start: 0.8449 (mttp) cc_final: 0.7940 (mmtm) REVERT: F 144 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4873 (mm) REVERT: G 129 LEU cc_start: 0.7554 (mm) cc_final: 0.7197 (mt) REVERT: E 115 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7691 (ttt180) REVERT: B 48 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8101 (p90) REVERT: B 263 TYR cc_start: 0.7885 (m-80) cc_final: 0.7502 (m-80) outliers start: 26 outliers final: 17 residues processed: 207 average time/residue: 1.2272 time to fit residues: 274.3699 Evaluate side-chains 202 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 115 ARG Chi-restraints excluded: chain A residue 72 ARG Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 VAL Chi-restraints excluded: chain N residue 261 VAL Chi-restraints excluded: chain M residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 23 GLN ** E 121 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 = 0.3946 r_free = 0.3946 target = 0.141385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094699 restraints weight = 18214.945| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.37 r_work: 0.3027 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12250 Z= 0.369 Angle : 0.763 11.022 16602 Z= 0.397 Chirality : 0.051 0.416 1861 Planarity : 0.005 0.039 2099 Dihedral : 7.535 58.991 2046 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.25 % Allowed : 20.89 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1442 helix: 1.99 (0.26), residues: 343 sheet: 1.08 (0.25), residues: 420 loop : -1.22 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 151 HIS 0.007 0.001 HIS N 70 PHE 0.023 0.002 PHE A 35 TYR 0.016 0.002 TYR D 71 ARG 0.008 0.001 ARG N 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5513.76 seconds wall clock time: 100 minutes 18.38 seconds (6018.38 seconds total)