Starting phenix.real_space_refine on Fri Feb 16 02:38:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq8_33390/02_2024/7xq8_33390.pdb" } resolution = 3.3 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= 0.066 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 1587 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7698 2.51 5 N 2251 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C GLU 527": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 526": "OE1" <-> "OE2" Residue "v TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12452 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 3979 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 196} Link IDs: {'PTRANS': 40, 'TRANS': 554} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 884 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 368 Chain: "L" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1035 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 11, 'TRANS': 198} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 629 Unresolved non-hydrogen angles: 812 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 359 Chain: "v" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 3968 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 40, 'TRANS': 554} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 699 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 6, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 372 Chain: "R" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1035 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 11, 'TRANS': 198} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 629 Unresolved non-hydrogen angles: 812 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 359 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain: "B" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1131 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" 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 Time building chain proxies: 7.35, per 1000 atoms: 0.59 Number of scatterers: 12452 At special positions: 0 Unit cell: (114.162, 140.01, 228.324, 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 42 16.00 O 2461 8.00 N 2251 7.00 C 7698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS v 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 426 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 536 " distance=2.03 Simple disulfide: pdb=" SG CYS v 257 " - pdb=" SG CYS v 320 " distance=1.95 Simple disulfide: pdb=" SG CYS v 367 " - pdb=" SG CYS v 426 " distance=2.03 Simple disulfide: pdb=" SG CYS v 474 " - pdb=" SG CYS v 536 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 122 " distance=2.02 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=1, symmetry=0 Links applied NAG-ASN " NAG A 301 " - " ASN A 63 " " NAG A 302 " - " ASN A 97 " " NAG A 303 " - " ASN A 57 " " NAG A 304 " - " ASN A 88 " " NAG A 305 " - " ASN A 112 " " NAG A 306 " - " ASN A 73 " " NAG B 301 " - " ASN B 101 " " NAG B 302 " - " ASN B 73 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 332 " " NAG C 603 " - " ASN C 402 " " NAG v 601 " - " ASN v 395 " " NAG v 602 " - " ASN v 402 " " NAG v 603 " - " ASN v 332 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.92 Conformation dependent library (CDL) restraints added in 2.6 seconds 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3518 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 13.4% alpha, 40.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.610A pdb=" N TRP C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.508A pdb=" N ASN C 465 " --> pdb=" O ARG C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 597 Processing helix chain 'L' and resid 123 through 129 Processing helix chain 'L' and resid 187 through 191 removed outlier: 3.559A pdb=" N LYS L 190 " --> pdb=" O ASP L 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS L 191 " --> pdb=" O TYR L 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 187 through 191' Processing helix chain 'v' and resid 93 through 97 Processing helix chain 'v' and resid 198 through 204 Processing helix chain 'v' and resid 242 through 246 removed outlier: 4.097A pdb=" N PHE v 246 " --> pdb=" O ARG v 243 " (cutoff:3.500A) Processing helix chain 'v' and resid 309 through 314 Processing helix chain 'v' and resid 353 through 361 Processing helix chain 'v' and resid 414 through 420 Processing helix chain 'v' and resid 569 through 593 removed outlier: 4.221A pdb=" N THR v 589 " --> pdb=" O LEU v 585 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 129 Processing helix chain 'R' and resid 184 through 189 removed outlier: 4.037A pdb=" N GLU R 189 " --> pdb=" O LYS R 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.529A pdb=" N GLY A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.767A pdb=" N GLY A 101 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 171 Proline residue: A 159 - end of helix Processing helix chain 'B' and resid 68 through 72 removed outlier: 4.150A pdb=" N SER B 71 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.560A pdb=" N ASN B 117 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 180 Proline residue: B 176 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.801A pdb=" N GLY C 59 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG C 48 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP C 57 " --> pdb=" O ARG C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.146A pdb=" N LYS C 106 " --> pdb=" O PHE C 110D" (cutoff:3.500A) removed outlier: 8.258A pdb=" N PHE C 110D" --> pdb=" O LYS C 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.695A pdb=" N ASP C 155 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR C 188 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 135 removed outlier: 3.695A pdb=" N ASP C 155 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR C 188 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 166 Processing sheet with id=AA7, first strand: chain 'C' and resid 235 through 239 Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 239 Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 277 removed outlier: 3.551A pdb=" N GLN C 268 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 347 through 350 removed outlier: 5.283A pdb=" N LYS C 364 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 413 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR C 366 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ALA C 411 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LEU C 368 " --> pdb=" O GLY C 409 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 409 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR C 370 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 407 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 406 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 395 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.629A pdb=" N VAL C 390 " --> pdb=" O TRP C 382 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP C 382 " --> pdb=" O VAL C 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 453 through 457 removed outlier: 3.534A pdb=" N SER C 519 " --> pdb=" O CYS C 474 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 453 through 457 removed outlier: 5.707A pdb=" N TYR C 515 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.306A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.306A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.751A pdb=" N ASN L 139 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU L 137 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N SER L 179 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASN L 139 " --> pdb=" O LEU L 177 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU L 177 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 132 through 134 Processing sheet with id=AC2, first strand: chain 'L' and resid 155 through 156 Processing sheet with id=AC3, first strand: chain 'v' and resid 13 through 16 Processing sheet with id=AC4, first strand: chain 'v' and resid 20 through 22 removed outlier: 3.708A pdb=" N GLY v 59 " --> pdb=" O TRP v 46 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG v 48 " --> pdb=" O TRP v 57 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP v 57 " --> pdb=" O ARG v 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'v' and resid 20 through 22 removed outlier: 3.566A pdb=" N HIS v 112 " --> pdb=" O ARG v 104 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS v 106 " --> pdb=" O PHE v 110D" (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE v 110D" --> pdb=" O LYS v 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 130 through 135 removed outlier: 3.941A pdb=" N ASP v 155 " --> pdb=" O TYR v 188 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR v 188 " --> pdb=" O ASP v 155 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'v' and resid 130 through 135 removed outlier: 3.941A pdb=" N ASP v 155 " --> pdb=" O TYR v 188 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR v 188 " --> pdb=" O ASP v 155 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'v' and resid 162 through 166 Processing sheet with id=AC9, first strand: chain 'v' and resid 236 through 239 removed outlier: 3.506A pdb=" N ILE v 256 " --> pdb=" O PHE v 239 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE v 256 " --> pdb=" O LEU v 305 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU v 305 " --> pdb=" O ILE v 256 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN v 258 " --> pdb=" O SER v 303 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER v 303 " --> pdb=" O GLN v 258 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR v 260 " --> pdb=" O VAL v 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL v 301 " --> pdb=" O THR v 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'v' and resid 236 through 239 removed outlier: 3.506A pdb=" N ILE v 256 " --> pdb=" O PHE v 239 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE v 256 " --> pdb=" O LEU v 305 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU v 305 " --> pdb=" O ILE v 256 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN v 258 " --> pdb=" O SER v 303 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER v 303 " --> pdb=" O GLN v 258 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR v 260 " --> pdb=" O VAL v 301 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL v 301 " --> pdb=" O THR v 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'v' and resid 276 through 278 removed outlier: 3.937A pdb=" N TRP v 271 " --> pdb=" O VAL v 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL v 322 " --> pdb=" O PHE v 329 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'v' and resid 346 through 350 removed outlier: 4.084A pdb=" N THR v 363 " --> pdb=" O ILE v 413 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP v 371 " --> pdb=" O PHE v 405 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N PHE v 405 " --> pdb=" O ASP v 371 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER v 406 " --> pdb=" O SER v 397 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU v 410 " --> pdb=" O HIS v 393 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'v' and resid 389 through 390 removed outlier: 4.323A pdb=" N TRP v 382 " --> pdb=" O VAL v 390 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'v' and resid 453 through 457 removed outlier: 3.690A pdb=" N THR v 473 " --> pdb=" O LEU v 457 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'v' and resid 453 through 457 removed outlier: 3.690A pdb=" N THR v 473 " --> pdb=" O LEU v 457 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'v' and resid 485 through 489 Processing sheet with id=AD8, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AD9, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.022A pdb=" N LEU R 11 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.022A pdb=" N LEU R 11 " --> pdb=" O GLN R 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 116 through 117 removed outlier: 3.588A pdb=" N ASN R 139 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN R 140 " --> pdb=" O TYR R 175 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR R 175 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 116 through 117 removed outlier: 3.588A pdb=" N ASN R 139 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN R 140 " --> pdb=" O TYR R 175 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR R 175 " --> pdb=" O ASN R 140 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 155 through 156 removed outlier: 3.574A pdb=" N CYS R 196 " --> pdb=" O LYS R 209 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS R 209 " --> pdb=" O CYS R 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.728A pdb=" N TYR A 104 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 103 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AE7, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.752A pdb=" N TRP B 47 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 52 through 53 652 hydrogen bonds defined for protein. 1620 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2199 1.31 - 1.43: 3148 1.43 - 1.56: 7237 1.56 - 1.69: 0 1.69 - 1.82: 59 Bond restraints: 12643 Sorted by residual: bond pdb=" C1 NAG A 304 " pdb=" O5 NAG A 304 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" CA PHE v 485 " pdb=" C PHE v 485 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.10e-02 8.26e+03 2.79e+01 bond pdb=" C PHE v 485 " pdb=" O PHE v 485 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.18e-02 7.18e+03 2.17e+01 bond pdb=" C VAL v 486 " pdb=" O VAL v 486 " ideal model delta sigma weight residual 1.238 1.181 0.056 1.28e-02 6.10e+03 1.94e+01 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 12638 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.43: 266 105.43 - 112.59: 6802 112.59 - 119.74: 3752 119.74 - 126.90: 6374 126.90 - 134.06: 140 Bond angle restraints: 17334 Sorted by residual: angle pdb=" N GLY v 531 " pdb=" CA GLY v 531 " pdb=" C GLY v 531 " ideal model delta sigma weight residual 114.61 125.59 -10.98 1.49e+00 4.50e-01 5.43e+01 angle pdb=" C PRO v 233 " pdb=" N PRO v 234 " pdb=" CA PRO v 234 " ideal model delta sigma weight residual 119.84 110.84 9.00 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 114.62 107.91 6.71 1.14e+00 7.69e-01 3.46e+01 angle pdb=" N LYS v 235 " pdb=" CA LYS v 235 " pdb=" C LYS v 235 " ideal model delta sigma weight residual 109.94 117.97 -8.03 1.57e+00 4.06e-01 2.61e+01 angle pdb=" C LEU A 134 " pdb=" N ASP A 135 " pdb=" CA ASP A 135 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 ... (remaining 17329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 7331 24.55 - 49.11: 303 49.11 - 73.66: 34 73.66 - 98.21: 8 98.21 - 122.76: 9 Dihedral angle restraints: 7685 sinusoidal: 2263 harmonic: 5422 Sorted by residual: dihedral pdb=" CB CYS C 337 " pdb=" SG CYS C 337 " pdb=" SG CYS v 337 " pdb=" CB CYS v 337 " ideal model delta sinusoidal sigma weight residual 93.00 178.32 -85.32 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 126 " pdb=" CB CYS B 126 " ideal model delta sinusoidal sigma weight residual 93.00 160.31 -67.31 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CA SER C 263 " pdb=" C SER C 263 " pdb=" N PRO C 264 " pdb=" CA PRO C 264 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 7682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.121: 2133 1.121 - 2.243: 0 2.243 - 3.364: 0 3.364 - 4.486: 0 4.486 - 5.607: 1 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C1 NAG v 603 " pdb=" ND2 ASN v 332 " pdb=" C2 NAG v 603 " pdb=" O5 NAG v 603 " both_signs ideal model delta sigma weight residual False -2.40 3.21 -5.61 2.00e-01 2.50e+01 7.86e+02 chirality pdb=" C1 NAG A 304 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 304 " pdb=" O5 NAG A 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.95e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 395 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2131 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG v 603 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG v 603 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG v 603 " -0.085 2.00e-02 2.50e+03 pdb=" N2 NAG v 603 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG v 603 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN v 332 " 0.049 2.00e-02 2.50e+03 5.88e-02 4.33e+01 pdb=" CG ASN v 332 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN v 332 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN v 332 " -0.104 2.00e-02 2.50e+03 pdb=" C1 NAG v 603 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN v 249 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO v 250 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO v 250 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO v 250 " -0.057 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 21 2.31 - 2.96: 5940 2.96 - 3.61: 16991 3.61 - 4.25: 24126 4.25 - 4.90: 41905 Nonbonded interactions: 88983 Sorted by model distance: nonbonded pdb=" CB PRO v 234 " pdb=" CZ PHE v 329 " model vdw 1.664 3.740 nonbonded pdb=" CB PRO v 233 " pdb=" CD1 PHE v 262 " model vdw 1.796 3.740 nonbonded pdb=" N PRO v 234 " pdb=" CE1 PHE v 262 " model vdw 2.092 3.420 nonbonded pdb=" O PRO v 234 " pdb=" CG PHE v 329 " model vdw 2.093 3.260 nonbonded pdb=" C PRO v 233 " pdb=" CE1 PHE v 262 " model vdw 2.107 3.570 ... (remaining 88978 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 'C' and ((resid 11 through 234 and (name N or name CA or name C or name O \ or name CB )) or resid 235 through 597 or resid 601 through 603)) selection = chain 'v' } ncs_group { reference = chain 'L' selection = chain 'R' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 10.170 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 38.220 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 : 0.005 0.116 12643 Z= 0.335 Angle : 0.757 11.156 17334 Z= 0.437 Chirality : 0.132 5.607 2134 Planarity : 0.008 0.302 2315 Dihedral : 14.235 122.764 4134 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.50 % Favored : 92.91 % Rotamer: Outliers : 1.23 % Allowed : 0.89 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1877 helix: 1.04 (0.37), residues: 203 sheet: -0.27 (0.19), residues: 767 loop : -1.52 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 271 HIS 0.004 0.001 HIS A 36 PHE 0.026 0.002 PHE v 485 TYR 0.010 0.001 TYR C 299 ARG 0.002 0.000 ARG v 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: v 262 PHE cc_start: 0.2034 (OUTLIER) cc_final: 0.1518 (m-10) REVERT: B 155 ASN cc_start: 0.7259 (m110) cc_final: 0.6807 (m-40) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.2451 time to fit residues: 38.5884 Evaluate side-chains 87 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 235 LYS Chi-restraints excluded: chain v residue 262 PHE Chi-restraints excluded: chain v residue 263 SER Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 330 GLN Chi-restraints excluded: chain v residue 486 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 50.0000 chunk 75 optimal weight: 40.0000 chunk 146 optimal weight: 40.0000 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 50.0000 chunk 109 optimal weight: 20.0000 chunk 169 optimal weight: 0.1980 overall best weight: 12.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 249 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 ASN ** v 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 331 GLN v 386 ASN v 393 HIS v 487 GLN A 117 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.038 0.367 12643 Z= 2.571 Angle : 1.961 30.551 17334 Z= 1.010 Chirality : 0.125 2.017 2134 Planarity : 0.013 0.133 2315 Dihedral : 11.601 118.028 2264 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 1.49 % Allowed : 9.91 % Favored : 88.60 % Rotamer: Outliers : 9.27 % Allowed : 17.54 % Favored : 73.18 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 1877 helix: -2.59 (0.27), residues: 220 sheet: -0.73 (0.19), residues: 739 loop : -2.23 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP B 76 HIS 0.034 0.007 HIS A 36 PHE 0.086 0.009 PHE v 479 TYR 0.042 0.008 TYR C 500 ARG 0.018 0.002 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 77 time to evaluate : 1.295 Fit side-chains REVERT: v 262 PHE cc_start: 0.2406 (OUTLIER) cc_final: 0.1324 (m-80) REVERT: v 336 MET cc_start: 0.2881 (OUTLIER) cc_final: 0.2638 (mmt) REVERT: v 564 GLU cc_start: 0.7986 (pt0) cc_final: 0.7764 (pt0) REVERT: B 73 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7920 (p0) REVERT: B 110 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8372 (mp10) outliers start: 83 outliers final: 60 residues processed: 148 average time/residue: 0.1989 time to fit residues: 45.9050 Evaluate side-chains 135 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 71 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain v residue 262 PHE Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 336 MET Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 356 SER Chi-restraints excluded: chain v residue 370 THR Chi-restraints excluded: chain v residue 379 THR Chi-restraints excluded: chain v residue 429 THR Chi-restraints excluded: chain v residue 453 ASP Chi-restraints excluded: chain v residue 459 PRO Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 530 THR Chi-restraints excluded: chain v residue 535 THR Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 541 GLU Chi-restraints excluded: chain v residue 553 ASP Chi-restraints excluded: chain v residue 579 VAL Chi-restraints excluded: chain v residue 584 SER Chi-restraints excluded: chain v residue 585 LEU Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain B residue 55 ARG Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 50.0000 chunk 52 optimal weight: 0.8980 chunk 141 optimal weight: 50.0000 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 168 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 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 249 ASN ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12643 Z= 0.305 Angle : 0.740 13.503 17334 Z= 0.382 Chirality : 0.057 1.244 2134 Planarity : 0.006 0.099 2315 Dihedral : 9.426 118.010 2256 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.35 % Favored : 91.96 % Rotamer: Outliers : 2.68 % Allowed : 21.45 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.56 (0.19), residues: 1877 helix: -0.07 (0.35), residues: 205 sheet: -0.38 (0.19), residues: 743 loop : -1.82 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.008 0.001 HIS v 400 PHE 0.026 0.002 PHE C 354 TYR 0.011 0.001 TYR v 375 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.527 Fit side-chains REVERT: v 564 GLU cc_start: 0.7678 (pt0) cc_final: 0.7451 (pt0) outliers start: 24 outliers final: 17 residues processed: 100 average time/residue: 0.2269 time to fit residues: 35.4395 Evaluate side-chains 92 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain v residue 317 MET Chi-restraints excluded: chain v residue 319 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 88 optimal weight: 50.0000 chunk 18 optimal weight: 50.0000 chunk 81 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 0.3980 chunk 180 optimal weight: 0.5980 chunk 89 optimal weight: 50.0000 chunk 161 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12643 Z= 0.226 Angle : 0.632 9.508 17334 Z= 0.327 Chirality : 0.049 0.659 2134 Planarity : 0.005 0.095 2315 Dihedral : 8.330 116.389 2254 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.30 % Favored : 92.17 % Rotamer: Outliers : 3.91 % Allowed : 20.22 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.19), residues: 1877 helix: 0.88 (0.36), residues: 210 sheet: -0.00 (0.19), residues: 739 loop : -1.52 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 47 HIS 0.006 0.001 HIS A 36 PHE 0.018 0.001 PHE C 479 TYR 0.012 0.001 TYR v 375 ARG 0.005 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 1.373 Fit side-chains revert: symmetry clash REVERT: v 553 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7214 (p0) outliers start: 35 outliers final: 25 residues processed: 104 average time/residue: 0.1960 time to fit residues: 32.3812 Evaluate side-chains 101 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 75 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 553 ASP Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 2 optimal weight: 80.0000 chunk 134 optimal weight: 0.3980 chunk 74 optimal weight: 50.0000 chunk 154 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 220.0000 chunk 92 optimal weight: 50.0000 chunk 162 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 overall best weight: 8.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.254 12643 Z= 1.822 Angle : 1.503 27.143 17334 Z= 0.773 Chirality : 0.090 0.689 2134 Planarity : 0.011 0.108 2315 Dihedral : 10.384 119.903 2250 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.39 % Favored : 88.71 % Rotamer: Outliers : 9.05 % Allowed : 22.57 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.19), residues: 1877 helix: -1.75 (0.30), residues: 212 sheet: -0.44 (0.19), residues: 770 loop : -2.06 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.007 TRP B 76 HIS 0.024 0.005 HIS A 36 PHE 0.074 0.006 PHE v 479 TYR 0.035 0.006 TYR v 515 ARG 0.013 0.002 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 77 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 489 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7503 (mtm) REVERT: v 564 GLU cc_start: 0.8054 (pt0) cc_final: 0.7836 (pt0) REVERT: B 73 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7872 (p0) REVERT: B 110 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8185 (mp10) outliers start: 81 outliers final: 62 residues processed: 143 average time/residue: 0.2025 time to fit residues: 44.9753 Evaluate side-chains 139 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 74 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 410 GLU Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 541 GLU Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 360 THR Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 390 VAL Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 422 GLU Chi-restraints excluded: chain v residue 453 ASP Chi-restraints excluded: chain v residue 459 PRO Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 473 THR Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 502 THR Chi-restraints excluded: chain v residue 535 THR Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 541 GLU Chi-restraints excluded: chain v residue 553 ASP Chi-restraints excluded: chain v residue 556 THR Chi-restraints excluded: chain v residue 570 LEU Chi-restraints excluded: chain v residue 573 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 40.0000 chunk 162 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 150 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 59 optimal weight: 0.0020 chunk 94 optimal weight: 50.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12643 Z= 0.241 Angle : 0.702 10.105 17334 Z= 0.360 Chirality : 0.050 0.547 2134 Planarity : 0.005 0.078 2315 Dihedral : 8.571 117.041 2250 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.03 % Favored : 92.38 % Rotamer: Outliers : 4.58 % Allowed : 27.60 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.19), residues: 1877 helix: 0.10 (0.35), residues: 217 sheet: -0.11 (0.19), residues: 738 loop : -1.62 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 47 HIS 0.006 0.001 HIS v 400 PHE 0.021 0.002 PHE C 479 TYR 0.012 0.001 TYR v 375 ARG 0.007 0.001 ARG v 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 81 time to evaluate : 1.370 Fit side-chains REVERT: v 564 GLU cc_start: 0.7641 (pt0) cc_final: 0.7383 (pt0) outliers start: 41 outliers final: 32 residues processed: 112 average time/residue: 0.1934 time to fit residues: 34.4220 Evaluate side-chains 104 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 72 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 451 ARG Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 553 ASP Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 0.9990 chunk 20 optimal weight: 50.0000 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 102 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 101 optimal weight: 50.0000 chunk 180 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 12643 Z= 0.553 Angle : 0.806 14.600 17334 Z= 0.412 Chirality : 0.054 0.519 2134 Planarity : 0.006 0.078 2315 Dihedral : 8.582 117.862 2250 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.94 % Favored : 91.42 % Rotamer: Outliers : 6.26 % Allowed : 25.81 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.19), residues: 1877 helix: -0.02 (0.34), residues: 218 sheet: -0.10 (0.20), residues: 740 loop : -1.55 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 271 HIS 0.009 0.002 HIS A 36 PHE 0.027 0.003 PHE C 479 TYR 0.016 0.002 TYR v 375 ARG 0.007 0.001 ARG v 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 79 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: C 489 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7167 (mtm) REVERT: v 564 GLU cc_start: 0.7855 (pt0) cc_final: 0.7612 (pt0) outliers start: 56 outliers final: 43 residues processed: 120 average time/residue: 0.1977 time to fit residues: 37.8942 Evaluate side-chains 118 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 74 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain v residue 247 PHE Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 467 ARG Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 107 optimal weight: 20.0000 chunk 54 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 89 optimal weight: 120.0000 chunk 16 optimal weight: 40.0000 chunk 141 optimal weight: 70.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 12643 Z= 0.483 Angle : 0.772 13.363 17334 Z= 0.394 Chirality : 0.053 0.499 2134 Planarity : 0.006 0.080 2315 Dihedral : 8.333 117.593 2250 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.83 % Favored : 91.53 % Rotamer: Outliers : 6.15 % Allowed : 26.15 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.19), residues: 1877 helix: 0.10 (0.35), residues: 218 sheet: -0.01 (0.20), residues: 736 loop : -1.55 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 271 HIS 0.009 0.002 HIS A 36 PHE 0.025 0.002 PHE C 479 TYR 0.015 0.002 TYR v 375 ARG 0.004 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 79 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: v 564 GLU cc_start: 0.7782 (pt0) cc_final: 0.7513 (pt0) REVERT: B 73 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7533 (p0) outliers start: 55 outliers final: 47 residues processed: 121 average time/residue: 0.2171 time to fit residues: 40.5847 Evaluate side-chains 125 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 77 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain v residue 247 PHE Chi-restraints excluded: chain v residue 278 VAL Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 353 SER Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 451 ARG Chi-restraints excluded: chain v residue 467 ARG Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 589 THR Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 178 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 157 optimal weight: 50.0000 chunk 167 optimal weight: 0.7980 chunk 101 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 151 optimal weight: 50.0000 chunk 158 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12643 Z= 0.228 Angle : 0.656 11.533 17334 Z= 0.333 Chirality : 0.049 0.468 2134 Planarity : 0.005 0.082 2315 Dihedral : 7.744 116.335 2249 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.35 % Favored : 92.17 % Rotamer: Outliers : 4.02 % Allowed : 27.60 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1877 helix: 0.75 (0.36), residues: 218 sheet: 0.11 (0.19), residues: 758 loop : -1.35 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 271 HIS 0.004 0.001 HIS A 36 PHE 0.016 0.001 PHE C 354 TYR 0.014 0.001 TYR v 375 ARG 0.005 0.001 ARG v 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 78 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: C 489 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7055 (mtm) REVERT: v 564 GLU cc_start: 0.7706 (pt0) cc_final: 0.7445 (pt0) REVERT: B 110 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7972 (mp10) outliers start: 36 outliers final: 31 residues processed: 102 average time/residue: 0.2002 time to fit residues: 32.4798 Evaluate side-chains 109 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 76 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain v residue 247 PHE Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 451 ARG Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 0.8980 chunk 108 optimal weight: 30.0000 chunk 84 optimal weight: 40.0000 chunk 123 optimal weight: 0.9990 chunk 186 optimal weight: 0.0980 chunk 171 optimal weight: 1.9990 chunk 148 optimal weight: 50.0000 chunk 15 optimal weight: 40.0000 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12643 Z= 0.227 Angle : 0.644 12.210 17334 Z= 0.324 Chirality : 0.048 0.433 2134 Planarity : 0.005 0.082 2315 Dihedral : 7.213 116.042 2249 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.35 % Favored : 92.17 % Rotamer: Outliers : 4.25 % Allowed : 27.71 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.20), residues: 1877 helix: 1.05 (0.36), residues: 221 sheet: 0.27 (0.19), residues: 757 loop : -1.28 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 271 HIS 0.004 0.001 HIS A 36 PHE 0.019 0.001 PHE C 479 TYR 0.013 0.001 TYR v 375 ARG 0.003 0.000 ARG v 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3754 Ramachandran restraints generated. 1877 Oldfield, 0 Emsley, 1877 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 79 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: v 315 GLN cc_start: 0.5889 (mp10) cc_final: 0.5600 (mp10) REVERT: v 594 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.6568 (t80) REVERT: B 110 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7885 (mp10) outliers start: 38 outliers final: 31 residues processed: 107 average time/residue: 0.2018 time to fit residues: 34.4523 Evaluate side-chains 110 residues out of total 1653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 77 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 375 TYR Chi-restraints excluded: chain C residue 426 CYS Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 498 GLU Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain v residue 247 PHE Chi-restraints excluded: chain v residue 285 ASP Chi-restraints excluded: chain v residue 383 THR Chi-restraints excluded: chain v residue 414 CYS Chi-restraints excluded: chain v residue 451 ARG Chi-restraints excluded: chain v residue 472 ILE Chi-restraints excluded: chain v residue 486 VAL Chi-restraints excluded: chain v residue 537 VAL Chi-restraints excluded: chain v residue 594 PHE Chi-restraints excluded: chain v residue 596 VAL Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 148 optimal weight: 30.0000 chunk 62 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 130 optimal weight: 0.0270 overall best weight: 3.5444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.216480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173648 restraints weight = 19307.254| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 3.57 r_work: 0.3486 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.135 12643 Z= 0.779 Angle : 0.897 17.805 17334 Z= 0.459 Chirality : 0.058 0.416 2134 Planarity : 0.007 0.082 2315 Dihedral : 7.985 119.368 2249 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.52 % Favored : 90.84 % Rotamer: Outliers : 5.47 % Allowed : 26.48 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.20), residues: 1877 helix: -0.08 (0.34), residues: 219 sheet: 0.15 (0.20), residues: 743 loop : -1.49 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 76 HIS 0.011 0.002 HIS A 36 PHE 0.035 0.003 PHE v 479 TYR 0.018 0.003 TYR v 500 ARG 0.005 0.001 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2339.75 seconds wall clock time: 43 minutes 12.97 seconds (2592.97 seconds total)