Starting phenix.real_space_refine on Fri Feb 16 15:09:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbz_13314/02_2024/7pbz_13314_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 886 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 84 5.16 5 C 9650 2.51 5 N 2408 2.21 5 O 2679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 433": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14822 Number of models: 1 Model: "" Number of chains: 17 Chain: "F" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 893 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Chain: "A" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2695 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 319} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2707 Classifications: {'peptide': 330} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 321} 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" 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: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {'HEX': 1, 'NAG': 1, 'OCT': 2, 'UND': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 1, 'ABU': 1, 'HEX': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'D10': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 46 Unusual residues: {'D10': 2, 'HEX': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.60, per 1000 atoms: 0.58 Number of scatterers: 14822 At special positions: 0 Unit cell: (91.932, 119.968, 125.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 84 16.00 O 2679 8.00 N 2408 7.00 C 9650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS F 409 " - pdb=" SG CYS F 483 " distance=2.04 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 501 " - " ASN A 111 " " NAG D 501 " - " ASN D 111 " " NAG G 1 " - " ASN B 80 " " NAG H 1 " - " ASN B 149 " " NAG I 1 " - " ASN C 80 " " NAG J 1 " - " ASN C 149 " " NAG K 1 " - " ASN E 80 " " NAG L 1 " - " ASN E 149 " Time building additional restraints: 6.19 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS E 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS C 267 " pdb="ZN ZN B 503 " - pdb=" NE2 HIS B 267 " 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 22 sheets defined 35.6% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'F' and resid 475 through 477 No H-bonds generated for 'chain 'F' and resid 475 through 477' Processing helix chain 'F' and resid 496 through 498 No H-bonds generated for 'chain 'F' and resid 496 through 498' Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.589A pdb=" N SER A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 276 removed outlier: 4.096A pdb=" N ASN A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 309 removed outlier: 3.529A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 414 removed outlier: 3.634A pdb=" N ALA A 319 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 242 removed outlier: 3.836A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 269 Processing helix chain 'B' and resid 280 through 307 Processing helix chain 'B' and resid 420 through 445 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 221 through 224 No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 226 through 241 removed outlier: 4.184A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 270 Processing helix chain 'C' and resid 280 through 307 Processing helix chain 'C' and resid 421 through 445 Proline residue: C 432 - end of helix Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.513A pdb=" N THR E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.832A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 307 Processing helix chain 'E' and resid 423 through 448 Proline residue: E 435 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.954A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.511A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 Processing helix chain 'D' and resid 285 through 309 removed outlier: 3.521A pdb=" N LEU D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 416 Proline residue: D 401 - end of helix Processing sheet with id= A, first strand: chain 'F' and resid 2 through 7 Processing sheet with id= B, first strand: chain 'F' and resid 506 through 508 removed outlier: 3.779A pdb=" N ILE F 420 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG F 425 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE F 434 " --> pdb=" O ARG F 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 484 through 486 removed outlier: 3.739A pdb=" N TYR F 501 " --> pdb=" O ALA F 485 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.174A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU A 170 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 41 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 119 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= F, first strand: chain 'A' and resid 196 through 203 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.226A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.893A pdb=" N MET B 49 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.797A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.892A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 164 through 168 removed outlier: 5.896A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 96 through 98 removed outlier: 4.138A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.884A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.324A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 49 through 51 removed outlier: 3.834A pdb=" N MET E 49 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.692A pdb=" N CYS E 150 " --> pdb=" O PHE E 212 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE E 212 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 101 through 106 removed outlier: 7.004A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.287A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= T, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= U, first strand: chain 'D' and resid 196 through 204 Processing sheet with id= V, first strand: chain 'D' and resid 104 through 109 removed outlier: 7.186A pdb=" N ARG D 136 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 107 " --> pdb=" O THR D 134 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 134 " --> pdb=" O SER D 107 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1971 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: 4.37 Time building geometry restraints manager: 6.58 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: 4508 1.34 - 1.46: 3892 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 15185 Sorted by residual: bond pdb=" CG HSM C 601 " pdb=" ND1 HSM C 601 " ideal model delta sigma weight residual 1.383 1.313 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" CD2 HSM C 601 " pdb=" NE2 HSM C 601 " ideal model delta sigma weight residual 1.376 1.314 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N GLN F 1 " pdb=" CA GLN F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 ... (remaining 15180 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.65: 292 105.65 - 112.75: 8020 112.75 - 119.84: 5035 119.84 - 126.94: 7048 126.94 - 134.04: 203 Bond angle restraints: 20598 Sorted by residual: angle pdb=" C ALA A 316 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " ideal model delta sigma weight residual 120.28 131.67 -11.39 1.34e+00 5.57e-01 7.23e+01 angle pdb=" CA CYS E 150 " pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " ideal model delta sigma weight residual 114.40 128.82 -14.42 2.30e+00 1.89e-01 3.93e+01 angle pdb=" C THR C 110 " pdb=" N VAL C 111 " pdb=" CA VAL C 111 " ideal model delta sigma weight residual 122.11 128.27 -6.16 1.12e+00 7.97e-01 3.03e+01 angle pdb=" C VAL C 109 " pdb=" N THR C 110 " pdb=" CA THR C 110 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" C MET A 112 " pdb=" N THR A 113 " pdb=" CA THR A 113 " ideal model delta sigma weight residual 121.54 129.07 -7.53 1.91e+00 2.74e-01 1.55e+01 ... (remaining 20593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 8705 23.34 - 46.67: 406 46.67 - 70.01: 40 70.01 - 93.35: 27 93.35 - 116.68: 26 Dihedral angle restraints: 9204 sinusoidal: 3975 harmonic: 5229 Sorted by residual: dihedral pdb=" CA LEU E 223 " pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA PRO C 276 " pdb=" C PRO C 276 " pdb=" N TYR C 277 " pdb=" CA TYR C 277 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 9201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.837: 2364 0.837 - 1.675: 6 1.675 - 2.512: 0 2.512 - 3.349: 0 3.349 - 4.186: 1 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.91e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-02 2.50e+03 2.67e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-02 2.50e+03 2.48e+03 ... (remaining 2368 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 111 " 0.219 2.00e-02 2.50e+03 2.14e-01 5.72e+02 pdb=" CG ASN A 111 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 111 " -0.083 2.00e-02 2.50e+03 pdb=" ND2 ASN A 111 " -0.319 2.00e-02 2.50e+03 pdb=" C1 NAG A 501 " 0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 149 " 0.178 2.00e-02 2.50e+03 1.90e-01 4.49e+02 pdb=" CG ASN E 149 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN E 149 " -0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN E 149 " -0.293 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.234 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 80 " 0.141 2.00e-02 2.50e+03 1.38e-01 2.37e+02 pdb=" CG ASN C 80 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 80 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN C 80 " -0.207 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.165 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 344 2.69 - 3.24: 14150 3.24 - 3.79: 23338 3.79 - 4.35: 32307 4.35 - 4.90: 54396 Nonbonded interactions: 124535 Sorted by model distance: nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP B 162 " model vdw 2.136 2.440 nonbonded pdb=" O THR A 99 " pdb=" OG1 THR E 110 " model vdw 2.149 2.440 nonbonded pdb=" O THR E 233 " pdb=" OG SER E 236 " model vdw 2.168 2.440 nonbonded pdb=" OG SER E 104 " pdb=" O THR E 131 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR A 113 " pdb=" O THR B 96 " model vdw 2.182 2.440 ... (remaining 124530 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 12 through 416) selection = (chain 'D' and resid 12 through 416) } ncs_group { reference = (chain 'B' and resid 8 through 447) selection = (chain 'C' and resid 8 through 447) selection = (chain 'E' and resid 8 through 450) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 13.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 29.520 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.550 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.090 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.070 15185 Z= 0.277 Angle : 0.771 14.424 20598 Z= 0.384 Chirality : 0.121 4.186 2371 Planarity : 0.006 0.143 2522 Dihedral : 15.133 116.681 5826 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.33 (0.20), residues: 1753 helix: 1.56 (0.22), residues: 587 sheet: -0.26 (0.23), residues: 454 loop : -0.49 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 67 HIS 0.006 0.001 HIS E 267 PHE 0.013 0.001 PHE D 298 TYR 0.029 0.001 TYR B 299 ARG 0.032 0.001 ARG E 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: F 454 ARG cc_start: 0.8201 (mtm110) cc_final: 0.7910 (mtp180) REVERT: F 465 THR cc_start: 0.8003 (p) cc_final: 0.7645 (p) REVERT: F 468 LEU cc_start: 0.7691 (tt) cc_final: 0.7317 (tt) REVERT: F 477 ASP cc_start: 0.7562 (m-30) cc_final: 0.6940 (m-30) REVERT: A 248 ASN cc_start: 0.8314 (t0) cc_final: 0.7160 (p0) REVERT: B 153 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 224 GLN cc_start: 0.8533 (mm110) cc_final: 0.8255 (mm110) REVERT: C 95 ASP cc_start: 0.7790 (t70) cc_final: 0.7423 (t0) REVERT: C 137 MET cc_start: 0.8296 (mmp) cc_final: 0.7988 (tpp) REVERT: C 283 MET cc_start: 0.8222 (mmt) cc_final: 0.8020 (mmt) REVERT: C 426 TRP cc_start: 0.7877 (t60) cc_final: 0.7429 (t60) REVERT: E 224 GLN cc_start: 0.8432 (tp40) cc_final: 0.7087 (tm-30) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.6919 time to fit residues: 434.5039 Evaluate side-chains 163 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9980 chunk 133 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 464 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 GLN A 116 ASN B 64 GLN C 148 GLN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 HIS D 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15185 Z= 0.278 Angle : 0.625 10.294 20598 Z= 0.312 Chirality : 0.046 0.301 2371 Planarity : 0.004 0.069 2522 Dihedral : 10.723 100.219 2500 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 9.04 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.62 (0.20), residues: 1753 helix: 1.87 (0.22), residues: 590 sheet: 0.01 (0.23), residues: 455 loop : -0.50 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 70 HIS 0.005 0.001 HIS B 267 PHE 0.018 0.002 PHE B 301 TYR 0.023 0.001 TYR B 299 ARG 0.006 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 1.732 Fit side-chains REVERT: F 433 GLU cc_start: 0.8647 (pt0) cc_final: 0.8393 (pt0) REVERT: F 463 LYS cc_start: 0.8543 (tptp) cc_final: 0.8338 (tptp) REVERT: F 465 THR cc_start: 0.8069 (p) cc_final: 0.7393 (p) REVERT: F 467 TYR cc_start: 0.7125 (m-10) cc_final: 0.6846 (m-80) REVERT: F 477 ASP cc_start: 0.8032 (m-30) cc_final: 0.7455 (m-30) REVERT: F 504 GLN cc_start: 0.7369 (pm20) cc_final: 0.7118 (pm20) REVERT: A 213 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.7674 (mmp) REVERT: B 9 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8030 (tpp) REVERT: B 224 GLN cc_start: 0.8617 (mm110) cc_final: 0.8330 (mm110) REVERT: C 95 ASP cc_start: 0.7885 (t70) cc_final: 0.7371 (t0) REVERT: C 138 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: C 426 TRP cc_start: 0.7880 (t60) cc_final: 0.7450 (t60) REVERT: E 224 GLN cc_start: 0.8376 (tp40) cc_final: 0.7514 (tm-30) REVERT: D 63 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7813 (t70) REVERT: D 274 ARG cc_start: 0.8245 (mpt-90) cc_final: 0.7936 (mpt-90) outliers start: 22 outliers final: 8 residues processed: 178 average time/residue: 1.4572 time to fit residues: 282.8116 Evaluate side-chains 168 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN ** F 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN C 113 ASN C 303 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.063 15185 Z= 0.596 Angle : 0.712 12.111 20598 Z= 0.362 Chirality : 0.049 0.397 2371 Planarity : 0.005 0.063 2522 Dihedral : 9.926 91.682 2500 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.67 % Allowed : 10.31 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.46 (0.20), residues: 1753 helix: 1.73 (0.22), residues: 590 sheet: -0.08 (0.23), residues: 466 loop : -0.59 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 412 HIS 0.007 0.001 HIS D 102 PHE 0.019 0.002 PHE B 293 TYR 0.025 0.002 TYR B 299 ARG 0.005 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 164 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 465 THR cc_start: 0.7994 (p) cc_final: 0.7629 (p) REVERT: F 477 ASP cc_start: 0.7989 (m-30) cc_final: 0.7761 (m-30) REVERT: B 9 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8053 (tpp) REVERT: B 153 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 224 GLN cc_start: 0.8724 (mm110) cc_final: 0.8479 (mm110) REVERT: C 95 ASP cc_start: 0.7944 (t70) cc_final: 0.7312 (t0) REVERT: C 138 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: C 426 TRP cc_start: 0.7858 (t60) cc_final: 0.7450 (t60) REVERT: E 224 GLN cc_start: 0.8501 (tp40) cc_final: 0.7981 (tm-30) REVERT: D 63 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7882 (t70) REVERT: D 274 ARG cc_start: 0.8229 (mpt-90) cc_final: 0.7882 (mpt-90) outliers start: 42 outliers final: 16 residues processed: 186 average time/residue: 1.4461 time to fit residues: 293.6942 Evaluate side-chains 170 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN F 504 GLN B 439 ASN ** C 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15185 Z= 0.185 Angle : 0.569 10.318 20598 Z= 0.289 Chirality : 0.043 0.289 2371 Planarity : 0.004 0.049 2522 Dihedral : 8.939 84.260 2500 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.29 % Allowed : 12.67 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.67 (0.20), residues: 1753 helix: 1.97 (0.22), residues: 594 sheet: 0.02 (0.23), residues: 456 loop : -0.52 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 67 HIS 0.004 0.001 HIS E 267 PHE 0.015 0.001 PHE B 293 TYR 0.027 0.001 TYR B 299 ARG 0.005 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 463 LYS cc_start: 0.8624 (tptp) cc_final: 0.8281 (tptp) REVERT: F 465 THR cc_start: 0.8117 (p) cc_final: 0.7541 (p) REVERT: F 477 ASP cc_start: 0.7917 (m-30) cc_final: 0.7701 (m-30) REVERT: A 213 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.7675 (mmp) REVERT: B 9 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7998 (tpp) REVERT: B 224 GLN cc_start: 0.8564 (mm110) cc_final: 0.8249 (mm110) REVERT: C 95 ASP cc_start: 0.7831 (t70) cc_final: 0.7250 (t70) REVERT: C 138 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: C 426 TRP cc_start: 0.7788 (t60) cc_final: 0.7401 (t60) REVERT: E 224 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: D 63 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (t70) outliers start: 36 outliers final: 12 residues processed: 185 average time/residue: 1.5224 time to fit residues: 306.8997 Evaluate side-chains 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 504 GLN Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN F 504 GLN B 224 GLN C 303 ASN E 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15185 Z= 0.216 Angle : 0.563 10.505 20598 Z= 0.285 Chirality : 0.044 0.299 2371 Planarity : 0.003 0.042 2522 Dihedral : 8.482 76.085 2500 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.74 % Allowed : 13.43 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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 (0.20), residues: 1753 helix: 2.05 (0.22), residues: 591 sheet: 0.08 (0.23), residues: 458 loop : -0.48 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.015 0.001 PHE B 293 TYR 0.025 0.001 TYR B 299 ARG 0.005 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 463 LYS cc_start: 0.8656 (tptp) cc_final: 0.8360 (tptp) REVERT: F 465 THR cc_start: 0.8118 (p) cc_final: 0.7537 (p) REVERT: A 213 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.7642 (mmp) REVERT: B 9 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8024 (tpp) REVERT: B 14 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: B 224 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8245 (mm110) REVERT: C 95 ASP cc_start: 0.7885 (t70) cc_final: 0.7440 (t70) REVERT: C 138 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8509 (mtt) REVERT: C 426 TRP cc_start: 0.7805 (t60) cc_final: 0.7421 (t60) REVERT: E 224 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: D 63 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7786 (t70) outliers start: 43 outliers final: 19 residues processed: 189 average time/residue: 1.4275 time to fit residues: 294.8925 Evaluate side-chains 185 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 80 ASN Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 164 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN E 224 GLN D 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15185 Z= 0.175 Angle : 0.554 10.301 20598 Z= 0.279 Chirality : 0.043 0.303 2371 Planarity : 0.003 0.043 2522 Dihedral : 8.034 64.729 2500 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.10 % Allowed : 14.96 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.83 (0.21), residues: 1753 helix: 2.07 (0.22), residues: 594 sheet: 0.15 (0.24), residues: 462 loop : -0.44 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.014 0.001 PHE B 293 TYR 0.025 0.001 TYR B 299 ARG 0.005 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 463 LYS cc_start: 0.8647 (tptp) cc_final: 0.8447 (tptp) REVERT: F 465 THR cc_start: 0.8167 (p) cc_final: 0.7541 (p) REVERT: F 504 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8139 (pm20) REVERT: A 213 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.7639 (mmp) REVERT: B 224 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8266 (mm110) REVERT: C 426 TRP cc_start: 0.7810 (t60) cc_final: 0.7439 (t60) REVERT: E 224 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: D 63 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7806 (t70) outliers start: 33 outliers final: 17 residues processed: 183 average time/residue: 1.4417 time to fit residues: 288.1213 Evaluate side-chains 179 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 169 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15185 Z= 0.220 Angle : 0.562 10.462 20598 Z= 0.283 Chirality : 0.044 0.305 2371 Planarity : 0.003 0.046 2522 Dihedral : 7.753 59.979 2500 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.23 % Allowed : 15.15 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.84 (0.20), residues: 1753 helix: 2.08 (0.22), residues: 594 sheet: 0.18 (0.24), residues: 462 loop : -0.45 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.013 0.001 PHE B 293 TYR 0.025 0.001 TYR B 299 ARG 0.006 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 465 THR cc_start: 0.8162 (p) cc_final: 0.7548 (p) REVERT: F 504 GLN cc_start: 0.8652 (mm-40) cc_final: 0.8182 (pm20) REVERT: B 224 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8286 (mm110) REVERT: C 301 PHE cc_start: 0.7948 (t80) cc_final: 0.7523 (t80) REVERT: C 426 TRP cc_start: 0.7808 (t60) cc_final: 0.7582 (t60) REVERT: E 224 GLN cc_start: 0.8307 (tp40) cc_final: 0.7774 (tm-30) REVERT: D 63 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7808 (t70) outliers start: 35 outliers final: 20 residues processed: 179 average time/residue: 1.5102 time to fit residues: 294.6860 Evaluate side-chains 177 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN C 303 ASN E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15185 Z= 0.197 Angle : 0.557 11.185 20598 Z= 0.281 Chirality : 0.043 0.301 2371 Planarity : 0.003 0.048 2522 Dihedral : 7.389 59.302 2500 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.23 % Allowed : 15.34 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.87 (0.20), residues: 1753 helix: 2.12 (0.22), residues: 591 sheet: 0.18 (0.23), residues: 471 loop : -0.43 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.014 0.001 PHE C 293 TYR 0.025 0.001 TYR B 299 ARG 0.007 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: F 406 ARG cc_start: 0.8161 (tpt-90) cc_final: 0.7743 (tpp80) REVERT: F 465 THR cc_start: 0.8155 (p) cc_final: 0.7711 (p) REVERT: F 504 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8207 (pm20) REVERT: B 9 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8038 (tpp) REVERT: B 49 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6682 (tmm) REVERT: B 224 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8282 (mm110) REVERT: C 301 PHE cc_start: 0.7954 (t80) cc_final: 0.7550 (t80) REVERT: D 63 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7786 (t70) outliers start: 35 outliers final: 19 residues processed: 180 average time/residue: 1.4940 time to fit residues: 293.1681 Evaluate side-chains 181 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15185 Z= 0.179 Angle : 0.551 10.255 20598 Z= 0.279 Chirality : 0.043 0.300 2371 Planarity : 0.003 0.048 2522 Dihedral : 7.113 58.706 2500 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.10 % Allowed : 15.60 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.91 (0.21), residues: 1753 helix: 2.17 (0.22), residues: 590 sheet: 0.20 (0.23), residues: 471 loop : -0.42 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS E 267 PHE 0.016 0.001 PHE B 301 TYR 0.025 0.001 TYR B 299 ARG 0.011 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 6 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: F 465 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7951 (p) REVERT: F 504 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8212 (mm-40) REVERT: B 49 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6750 (tmm) REVERT: B 224 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8271 (mm110) REVERT: C 301 PHE cc_start: 0.7939 (t80) cc_final: 0.7548 (t80) REVERT: E 224 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7810 (tm-30) REVERT: D 63 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7780 (t70) outliers start: 33 outliers final: 20 residues processed: 180 average time/residue: 1.4302 time to fit residues: 281.1933 Evaluate side-chains 178 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.005 0.047 15185 Z= 0.350 Angle : 0.613 11.110 20598 Z= 0.313 Chirality : 0.045 0.331 2371 Planarity : 0.004 0.051 2522 Dihedral : 7.272 58.544 2500 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.72 % Allowed : 16.10 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.81 (0.20), residues: 1753 helix: 2.10 (0.22), residues: 593 sheet: 0.21 (0.23), residues: 463 loop : -0.55 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 237 HIS 0.004 0.001 HIS E 267 PHE 0.015 0.001 PHE A 304 TYR 0.027 0.002 TYR B 299 ARG 0.005 0.000 ARG C 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3506 Ramachandran restraints generated. 1753 Oldfield, 0 Emsley, 1753 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 3 GLN cc_start: 0.8883 (mp10) cc_final: 0.8657 (mm-40) REVERT: F 465 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7931 (p) REVERT: F 504 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8281 (mm-40) REVERT: A 274 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7428 (mmm-85) REVERT: B 49 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6803 (tmm) REVERT: B 224 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8389 (mm110) REVERT: C 301 PHE cc_start: 0.7975 (t80) cc_final: 0.7569 (t80) REVERT: E 224 GLN cc_start: 0.8377 (tp-100) cc_final: 0.7835 (tp-100) REVERT: D 63 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7825 (t70) REVERT: D 229 GLN cc_start: 0.8509 (tp40) cc_final: 0.8137 (tp40) outliers start: 27 outliers final: 19 residues processed: 163 average time/residue: 1.5348 time to fit residues: 273.7064 Evaluate side-chains 172 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 430 LYS Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 409 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 461 ASN C 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.060783 restraints weight = 32571.922| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.84 r_work: 0.2734 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15185 Z= 0.202 Angle : 0.576 11.995 20598 Z= 0.293 Chirality : 0.043 0.295 2371 Planarity : 0.003 0.048 2522 Dihedral : 7.033 59.673 2500 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.65 % Allowed : 16.10 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.04 % 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: 0.88 (0.21), residues: 1753 helix: 2.13 (0.22), residues: 593 sheet: 0.19 (0.23), residues: 467 loop : -0.46 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.003 0.001 HIS E 267 PHE 0.021 0.001 PHE B 301 TYR 0.026 0.001 TYR B 299 ARG 0.005 0.000 ARG C 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5530.59 seconds wall clock time: 100 minutes 32.87 seconds (6032.87 seconds total)