Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 23:47:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwn_26837/08_2023/7uwn_26837.pdb" } resolution = 3.01 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= 0.020 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 72 5.16 5 C 6667 2.51 5 N 1898 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 887 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 885 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 101} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2147 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 853 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 84} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1888 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 219} Chain breaks: 3 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3036 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 7, 'PTRANS': 26, 'TRANS': 369} Chain breaks: 8 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 94 Chain: "H" 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 chiralities: 2 Chain: "A" 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 chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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 chiralities: 2 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 chiralities: 2 Time building chain proxies: 5.49, per 1000 atoms: 0.52 Number of scatterers: 10602 At special positions: 0 Unit cell: (116.194, 133.25, 155.636, 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 72 16.00 O 1965 8.00 N 1898 7.00 C 6667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 294 " distance=2.01 Simple disulfide: pdb=" SG CYS D 94 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 137 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 80 " distance=2.03 Simple disulfide: pdb=" SG CYS G 83 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 272 " - pdb=" SG CYS G 288 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 201 " - " ASN A 68 " " NAG C 401 " - " ASN C 54 " " NAG C 402 " - " ASN C 225 " " NAG C 403 " - " ASN C 49 " " NAG C 404 " - " ASN C 206 " " NAG F 401 " - " ASN F 49 " " NAG F 402 " - " ASN F 54 " " NAG G 501 " - " ASN G 213 " " NAG G 502 " - " ASN G 186 " " NAG H 1 " - " ASN C 265 " Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.5 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2572 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 32 sheets defined 8.5% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.682A pdb=" N ILE C 106 " --> pdb=" O ASP C 103 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU C 107 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 192 removed outlier: 3.760A pdb=" N VAL C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.577A pdb=" N PHE C 260 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.767A pdb=" N ILE F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 192 removed outlier: 3.601A pdb=" N VAL F 192 " --> pdb=" O ARG F 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 189 through 192' Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'G' and resid 198 through 203 Processing helix chain 'G' and resid 203 through 208 removed outlier: 3.807A pdb=" N TRP G 207 " --> pdb=" O ILE G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 304 removed outlier: 4.102A pdb=" N HIS G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 389 Processing helix chain 'G' and resid 403 through 405 No H-bonds generated for 'chain 'G' and resid 403 through 405' Processing helix chain 'G' and resid 426 through 431 removed outlier: 3.768A pdb=" N LEU G 431 " --> pdb=" O ARG G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 441 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 3.504A pdb=" N VAL B 45 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE A 133 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN B 50 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU A 135 " --> pdb=" O ASN B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 80 removed outlier: 3.675A pdb=" N LYS A 93 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 91 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 89 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.565A pdb=" N LEU A 122 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.580A pdb=" N GLY A 143 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN A 117 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N SER A 141 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE A 119 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A 139 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 80 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 removed outlier: 3.513A pdb=" N VAL B 140 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.992A pdb=" N ARG C 34 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS C 148 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 94 " --> pdb=" O HIS C 148 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL C 150 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR C 99 " --> pdb=" O ASP C 75 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP C 75 " --> pdb=" O THR C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.063A pdb=" N GLY C 111 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU C 125 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.063A pdb=" N GLY C 111 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.597A pdb=" N THR C 208 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 218 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 246 through 252 removed outlier: 3.990A pdb=" N PHE C 246 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.632A pdb=" N CYS D 99 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 84 through 85 removed outlier: 6.539A pdb=" N ASN D 111 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N CYS D 146 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL D 113 " --> pdb=" O CYS D 144 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS D 144 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN E 50 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS D 137 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N HIS E 52 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N LEU D 139 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 45 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU E 135 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASN D 48 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N LYS E 137 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE E 138 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE E 115 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS E 144 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 113 " --> pdb=" O CYS E 144 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N CYS E 146 " --> pdb=" O ASN E 111 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN E 111 " --> pdb=" O CYS E 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 74 through 78 Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 80 Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.713A pdb=" N SER F 55 " --> pdb=" O CYS F 126 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS F 126 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE F 129 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY F 111 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS F 178 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN F 176 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 84 removed outlier: 4.061A pdb=" N LEU F 76 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU F 97 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F 78 " --> pdb=" O HIS F 95 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS F 95 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU F 80 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 93 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE F 82 " --> pdb=" O PHE F 91 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE F 91 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP F 98 " --> pdb=" O PHE F 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AC6, first strand: chain 'F' and resid 249 through 251 removed outlier: 3.638A pdb=" N HIS F 250 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE F 232 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 24 through 25 removed outlier: 5.564A pdb=" N LEU G 61 " --> pdb=" O HIS G 93 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N HIS G 93 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ALA G 91 " --> pdb=" O PRO G 63 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS G 65 " --> pdb=" O HIS G 89 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N LEU G 82 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU G 164 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 84 " --> pdb=" O CYS G 162 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS G 162 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL G 86 " --> pdb=" O TYR G 160 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY G 156 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL G 92 " --> pdb=" O SER G 154 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER G 154 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 38 through 41 removed outlier: 3.933A pdb=" N SER G 175 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU G 185 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 212 through 215 Processing sheet with id=AD1, first strand: chain 'G' and resid 250 through 255 removed outlier: 3.821A pdb=" N LEU G 254 " --> pdb=" O PHE G 233 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE G 233 " --> pdb=" O LEU G 254 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE G 273 " --> pdb=" O ILE G 287 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 305 through 307 removed outlier: 3.753A pdb=" N ARG G 305 " --> pdb=" O ASP G 317 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP G 317 " --> pdb=" O ARG G 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 338 through 340 Processing sheet with id=AD4, first strand: chain 'G' and resid 338 through 340 removed outlier: 3.597A pdb=" N GLU G 381 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 379 " --> pdb=" O VAL G 371 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 416 through 419 removed outlier: 4.589A pdb=" N LEU G 396 " --> pdb=" O LEU G 412 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLY G 453 " --> pdb=" O ASP G 449 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP G 449 " --> pdb=" O GLY G 453 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU G 455 " --> pdb=" O LEU G 447 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 765 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: 3.16 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3534 1.34 - 1.47: 2503 1.47 - 1.59: 4754 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 10878 Sorted by residual: bond pdb=" C VAL E 113 " pdb=" N PRO E 114 " ideal model delta sigma weight residual 1.333 1.358 -0.026 1.17e-02 7.31e+03 4.79e+00 bond pdb=" C ALA F 254 " pdb=" N PRO F 255 " ideal model delta sigma weight residual 1.333 1.357 -0.025 1.17e-02 7.31e+03 4.47e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CG PRO G 35 " pdb=" CD PRO G 35 " ideal model delta sigma weight residual 1.503 1.564 -0.061 3.40e-02 8.65e+02 3.25e+00 bond pdb=" C VAL F 151 " pdb=" N ASP F 152 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.47e-02 4.63e+03 2.51e+00 ... (remaining 10873 not shown) Histogram of bond angle deviations from ideal: 98.94 - 105.99: 400 105.99 - 113.05: 6163 113.05 - 120.10: 3358 120.10 - 127.15: 4708 127.15 - 134.21: 228 Bond angle restraints: 14857 Sorted by residual: angle pdb=" CB MET D 110 " pdb=" CG MET D 110 " pdb=" SD MET D 110 " ideal model delta sigma weight residual 112.70 123.82 -11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA GLN E 117 " pdb=" CB GLN E 117 " pdb=" CG GLN E 117 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CB GLN E 117 " pdb=" CG GLN E 117 " pdb=" CD GLN E 117 " ideal model delta sigma weight residual 112.60 118.44 -5.84 1.70e+00 3.46e-01 1.18e+01 angle pdb=" CA GLN G 189 " pdb=" CB GLN G 189 " pdb=" CG GLN G 189 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB GLN G 189 " pdb=" CG GLN G 189 " pdb=" CD GLN G 189 " ideal model delta sigma weight residual 112.60 118.23 -5.63 1.70e+00 3.46e-01 1.10e+01 ... (remaining 14852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 5688 18.00 - 36.00: 612 36.00 - 54.00: 166 54.00 - 72.00: 33 72.00 - 90.00: 19 Dihedral angle restraints: 6518 sinusoidal: 2619 harmonic: 3899 Sorted by residual: dihedral pdb=" CB CYS G 272 " pdb=" SG CYS G 272 " pdb=" SG CYS G 288 " pdb=" CB CYS G 288 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 50 " pdb=" CB CYS C 50 " ideal model delta sinusoidal sigma weight residual 93.00 167.62 -74.62 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CB CYS G 83 " pdb=" SG CYS G 83 " pdb=" SG CYS G 162 " pdb=" CB CYS G 162 " ideal model delta sinusoidal sigma weight residual -86.00 -150.42 64.42 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 6515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1436 0.061 - 0.122: 261 0.122 - 0.183: 11 0.183 - 0.245: 1 0.245 - 0.306: 1 Chirality restraints: 1710 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 265 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA LEU G 262 " pdb=" N LEU G 262 " pdb=" C LEU G 262 " pdb=" CB LEU G 262 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" C2 NAG F 401 " pdb=" C1 NAG F 401 " pdb=" C3 NAG F 401 " pdb=" N2 NAG F 401 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 1707 not shown) Planarity restraints: 1927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 34 " 0.054 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO G 35 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 35 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 35 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 194 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 195 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 152 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO F 153 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 153 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 153 " -0.022 5.00e-02 4.00e+02 ... (remaining 1924 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 9397 3.22 - 3.78: 15943 3.78 - 4.34: 21052 4.34 - 4.90: 35265 Nonbonded interactions: 81896 Sorted by model distance: nonbonded pdb=" OG SER B 72 " pdb=" O CYS B 144 " model vdw 2.105 2.440 nonbonded pdb=" OG SER A 72 " pdb=" O CYS A 144 " model vdw 2.119 2.440 nonbonded pdb=" O SER F 72 " pdb=" NE2 GLN F 101 " model vdw 2.128 2.520 nonbonded pdb=" OG1 THR F 121 " pdb=" OE1 GLU F 123 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR F 99 " pdb=" O TRP F 142 " model vdw 2.170 2.440 ... (remaining 81891 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 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 45 or (resid 46 and (name N or name CA or nam \ e C or name O or name CB )) or resid 47 through 51 or resid 64 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 136 or (resid 137 and (name N or name CA or name C or name O \ or name CB )) or resid 138 through 150 or (resid 151 through 152 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 42 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 51 or resid 64 through 69 or (resi \ d 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throug \ h 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) or \ resid 109 through 127 or resid 130 through 152)) selection = (chain 'D' and (resid 42 or (resid 43 and (name N or name CA or name C or name O \ or name CB )) or resid 44 through 127 or resid 130 through 136 or (resid 137 an \ d (name N or name CA or name C or name O or name CB )) or resid 138 through 150 \ or (resid 151 through 152 and (name N or name CA or name C or name O or name CB \ )))) } ncs_group { reference = (chain 'C' and (resid 33 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )) or resid 135 or (resid 136 through 137 and (name N o \ r name CA or name C or name O or name CB )) or resid 138 through 139 or (resid 1 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 141 through \ 177 or (resid 178 and (name N or name CA or name C or name O or name CB )) or r \ esid 179 through 183 or (resid 184 and (name N or name CA or name C or name O or \ name CB )) or resid 185 through 190 or (resid 191 and (name N or name CA or nam \ e C or name O or name CB )) or resid 192 through 210 or resid 212 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 23 \ 4 or (resid 247 through 248 and (name N or name CA or name C or name O or name C \ B )) or resid 249 through 257 or (resid 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 268 or resid 281 through 298 or re \ sid 403 through 404)) selection = (chain 'F' and (resid 33 through 169 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 210 or resid 217 through 298 or \ resid 401 through 402)) } 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: 0.680 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: 4.270 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.650 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 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 0.061 10878 Z= 0.270 Angle : 0.641 11.119 14857 Z= 0.331 Chirality : 0.045 0.306 1710 Planarity : 0.005 0.080 1917 Dihedral : 16.587 90.001 3883 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.23), residues: 1275 helix: -1.99 (0.59), residues: 73 sheet: -0.27 (0.25), residues: 461 loop : -0.84 (0.22), residues: 741 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 0.2152 time to fit residues: 55.9053 Evaluate side-chains 179 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.204 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1233 time to fit residues: 5.9867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 HIS G 370 GLN G 380 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 10878 Z= 0.315 Angle : 0.647 9.303 14857 Z= 0.333 Chirality : 0.046 0.235 1710 Planarity : 0.005 0.049 1917 Dihedral : 5.059 25.152 1404 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1275 helix: -2.03 (0.57), residues: 75 sheet: -0.31 (0.24), residues: 503 loop : -0.86 (0.23), residues: 697 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 156 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 37 residues processed: 200 average time/residue: 0.1950 time to fit residues: 57.5948 Evaluate side-chains 193 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.107 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 0.1075 time to fit residues: 8.6351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.0070 chunk 36 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 30.0000 chunk 105 optimal weight: 0.1980 chunk 117 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 GLN G 380 GLN G 443 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10878 Z= 0.177 Angle : 0.565 9.449 14857 Z= 0.286 Chirality : 0.044 0.238 1710 Planarity : 0.004 0.046 1917 Dihedral : 4.710 22.959 1404 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.96 (0.23), residues: 1275 helix: -2.08 (0.55), residues: 81 sheet: -0.20 (0.24), residues: 492 loop : -0.70 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 181 average time/residue: 0.2099 time to fit residues: 55.4750 Evaluate side-chains 174 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.132 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.1285 time to fit residues: 5.9988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 50.0000 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 370 GLN G 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10878 Z= 0.218 Angle : 0.575 9.405 14857 Z= 0.290 Chirality : 0.044 0.246 1710 Planarity : 0.004 0.048 1917 Dihedral : 4.754 23.971 1404 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % 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: -0.93 (0.24), residues: 1275 helix: -1.95 (0.54), residues: 86 sheet: -0.15 (0.24), residues: 493 loop : -0.72 (0.23), residues: 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 169 average time/residue: 0.2013 time to fit residues: 50.0377 Evaluate side-chains 166 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.122 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 2 residues processed: 19 average time/residue: 0.1275 time to fit residues: 5.5757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 HIS ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 10878 Z= 0.312 Angle : 0.626 9.437 14857 Z= 0.316 Chirality : 0.046 0.251 1710 Planarity : 0.005 0.048 1917 Dihedral : 5.006 23.602 1404 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.23), residues: 1275 helix: -2.03 (0.53), residues: 86 sheet: -0.25 (0.24), residues: 488 loop : -0.79 (0.23), residues: 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 17 residues processed: 182 average time/residue: 0.2081 time to fit residues: 55.0476 Evaluate side-chains 170 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.013 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.0944 time to fit residues: 4.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 104 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10878 Z= 0.251 Angle : 0.607 11.987 14857 Z= 0.307 Chirality : 0.045 0.249 1710 Planarity : 0.005 0.056 1917 Dihedral : 4.982 24.672 1404 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1275 helix: -2.08 (0.53), residues: 86 sheet: -0.26 (0.24), residues: 490 loop : -0.77 (0.24), residues: 699 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 166 average time/residue: 0.2299 time to fit residues: 54.9137 Evaluate side-chains 164 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.071 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1481 time to fit residues: 4.6231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6126 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10878 Z= 0.259 Angle : 0.599 9.733 14857 Z= 0.304 Chirality : 0.045 0.237 1710 Planarity : 0.005 0.060 1917 Dihedral : 5.000 24.185 1404 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1275 helix: -2.10 (0.53), residues: 86 sheet: -0.30 (0.23), residues: 492 loop : -0.77 (0.24), residues: 697 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 166 average time/residue: 0.2176 time to fit residues: 52.0648 Evaluate side-chains 166 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 1.131 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1043 time to fit residues: 3.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10878 Z= 0.252 Angle : 0.598 9.391 14857 Z= 0.302 Chirality : 0.045 0.245 1710 Planarity : 0.005 0.064 1917 Dihedral : 4.956 23.756 1404 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1275 helix: -2.09 (0.53), residues: 85 sheet: -0.30 (0.23), residues: 493 loop : -0.78 (0.24), residues: 697 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 15 residues processed: 167 average time/residue: 0.2266 time to fit residues: 54.3452 Evaluate side-chains 168 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.157 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.1037 time to fit residues: 4.5582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 HIS F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 10878 Z= 0.278 Angle : 0.632 11.904 14857 Z= 0.318 Chirality : 0.046 0.246 1710 Planarity : 0.005 0.067 1917 Dihedral : 5.057 25.438 1404 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1275 helix: -2.06 (0.56), residues: 79 sheet: -0.34 (0.23), residues: 500 loop : -0.79 (0.24), residues: 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 160 average time/residue: 0.2257 time to fit residues: 51.5408 Evaluate side-chains 159 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.097 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1036 time to fit residues: 2.9211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 HIS ** G 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 10878 Z= 0.332 Angle : 0.664 11.740 14857 Z= 0.336 Chirality : 0.047 0.251 1710 Planarity : 0.005 0.070 1917 Dihedral : 5.222 25.294 1404 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1275 helix: -2.18 (0.56), residues: 79 sheet: -0.40 (0.23), residues: 502 loop : -0.86 (0.24), residues: 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 153 average time/residue: 0.2386 time to fit residues: 52.0486 Evaluate side-chains 154 residues out of total 1235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 1.033 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1144 time to fit residues: 2.2319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 297 HIS ** 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 = 0.4816 r_free = 0.4816 target = 0.216626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.175691 restraints weight = 14305.036| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.93 r_work: 0.4244 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 10878 Z= 0.248 Angle : 0.622 11.485 14857 Z= 0.312 Chirality : 0.045 0.240 1710 Planarity : 0.005 0.067 1917 Dihedral : 5.072 24.191 1404 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.24), residues: 1275 helix: -2.19 (0.55), residues: 79 sheet: -0.31 (0.23), residues: 499 loop : -0.85 (0.24), residues: 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.90 seconds wall clock time: 48 minutes 52.21 seconds (2932.21 seconds total)