Starting phenix.real_space_refine on Sat Mar 16 17:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shs_40493/03_2024/8shs_40493.pdb" } resolution = 2.66 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9642 2.51 5 N 2591 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3774 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3794 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 7.99, per 1000 atoms: 0.53 Number of scatterers: 15156 At special positions: 0 Unit cell: (98.2345, 103.187, 106.489, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2851 8.00 N 2591 7.00 C 9642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.8 seconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 20 sheets defined 45.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 115 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 137 through 152 removed outlier: 3.537A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 187 through 202 Proline residue: A 198 - end of helix Processing helix chain 'A' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.425A pdb=" N GLY A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 299 through 313 Processing helix chain 'A' and resid 314 through 317 Processing helix chain 'A' and resid 331 through 345 Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 452 through 463 Processing helix chain 'A' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 500 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 97 through 115 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 137 through 152 removed outlier: 3.537A pdb=" N GLY B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 187 through 202 Proline residue: B 198 - end of helix Processing helix chain 'B' and resid 215 through 229 removed outlier: 3.576A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 252 removed outlier: 4.424A pdb=" N GLY B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 299 through 313 Processing helix chain 'B' and resid 314 through 317 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 363 through 380 Processing helix chain 'B' and resid 429 through 439 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU B 499 " --> pdb=" O GLY B 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 500 " --> pdb=" O GLU B 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 137 through 152 removed outlier: 3.536A pdb=" N GLY C 151 " --> pdb=" O ARG C 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 187 through 202 Proline residue: C 198 - end of helix Processing helix chain 'C' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 252 removed outlier: 4.424A pdb=" N GLY C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 278 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 314 through 317 Processing helix chain 'C' and resid 331 through 345 Processing helix chain 'C' and resid 363 through 380 Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'C' and resid 452 through 463 Processing helix chain 'C' and resid 494 through 502 removed outlier: 4.057A pdb=" N LEU C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 97 through 115 Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 137 through 152 removed outlier: 3.535A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TRP D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 187 through 202 Proline residue: D 198 - end of helix Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.577A pdb=" N GLY D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 252 removed outlier: 4.425A pdb=" N GLY D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 278 Processing helix chain 'D' and resid 299 through 313 Processing helix chain 'D' and resid 314 through 317 Processing helix chain 'D' and resid 331 through 345 Processing helix chain 'D' and resid 363 through 380 Processing helix chain 'D' and resid 429 through 439 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 494 through 502 removed outlier: 4.058A pdb=" N LEU D 499 " --> pdb=" O GLY D 495 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN D 500 " --> pdb=" O GLU D 496 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR D 502 " --> pdb=" O GLY D 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS A 66 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 175 removed outlier: 8.193A pdb=" N VAL B 468 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR A 507 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL B 470 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 509 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN B 292 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 328 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE B 294 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR B 325 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE B 427 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 327 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 402 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL A 210 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS A 179 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS A 209 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN A 181 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 261 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 284 " --> pdb=" O SER A 490 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 386 removed outlier: 6.586A pdb=" N VAL A 402 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A 325 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N PHE A 427 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 327 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN A 292 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN A 328 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE A 294 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 442 through 443 removed outlier: 3.712A pdb=" N GLY A 443 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS B 66 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL B 210 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS B 179 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 209 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN B 181 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 261 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 284 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY B 443 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS C 66 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 167 through 175 removed outlier: 8.205A pdb=" N VAL D 468 " --> pdb=" O VAL C 505 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 507 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL D 470 " --> pdb=" O THR C 507 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 509 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN D 292 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N GLN D 328 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE D 294 " --> pdb=" O GLN D 328 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR D 325 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE D 427 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 327 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 402 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 235 through 239 removed outlier: 3.919A pdb=" N VAL C 210 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS C 179 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS C 209 " --> pdb=" O CYS C 179 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN C 181 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 261 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 284 " --> pdb=" O SER C 490 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 383 through 386 removed outlier: 6.586A pdb=" N VAL C 402 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 325 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE C 427 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 327 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN C 292 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN C 328 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE C 294 " --> pdb=" O GLN C 328 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY C 443 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 57 removed outlier: 4.029A pdb=" N CYS D 66 " --> pdb=" O THR D 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 235 through 239 removed outlier: 3.920A pdb=" N VAL D 210 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N CYS D 179 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS D 209 " --> pdb=" O CYS D 179 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN D 181 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 261 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 284 " --> pdb=" O SER D 490 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 442 through 443 removed outlier: 3.713A pdb=" N GLY D 443 " --> pdb=" O TYR D 485 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2160 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: 5.09 Time building geometry restraints manager: 6.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5030 1.34 - 1.46: 3216 1.46 - 1.58: 7138 1.58 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15492 Sorted by residual: bond pdb=" N GLY B 240 " pdb=" CA GLY B 240 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.32e-02 5.74e+03 4.57e-01 bond pdb=" N GLY D 240 " pdb=" CA GLY D 240 " ideal model delta sigma weight residual 1.456 1.447 0.009 1.32e-02 5.74e+03 4.56e-01 bond pdb=" N GLY A 240 " pdb=" CA GLY A 240 " ideal model delta sigma weight residual 1.456 1.448 0.008 1.32e-02 5.74e+03 3.94e-01 bond pdb=" N GLY C 240 " pdb=" CA GLY C 240 " ideal model delta sigma weight residual 1.456 1.448 0.008 1.32e-02 5.74e+03 3.93e-01 bond pdb=" C CYS C 179 " pdb=" N GLY C 180 " ideal model delta sigma weight residual 1.332 1.329 0.003 5.00e-03 4.00e+04 3.26e-01 ... (remaining 15487 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.22: 526 107.22 - 113.91: 8639 113.91 - 120.61: 6022 120.61 - 127.30: 5703 127.30 - 134.00: 141 Bond angle restraints: 21031 Sorted by residual: angle pdb=" N PHE D 241 " pdb=" CA PHE D 241 " pdb=" C PHE D 241 " ideal model delta sigma weight residual 107.57 111.22 -3.65 1.94e+00 2.66e-01 3.54e+00 angle pdb=" N PHE B 241 " pdb=" CA PHE B 241 " pdb=" C PHE B 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PHE C 241 " pdb=" CA PHE C 241 " pdb=" C PHE C 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PHE A 241 " pdb=" CA PHE A 241 " pdb=" C PHE A 241 " ideal model delta sigma weight residual 107.57 111.18 -3.61 1.94e+00 2.66e-01 3.47e+00 angle pdb=" N PRO C 215 " pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 112.47 116.19 -3.72 2.06e+00 2.36e-01 3.27e+00 ... (remaining 21026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.88: 8460 10.88 - 21.76: 513 21.76 - 32.63: 140 32.63 - 43.51: 40 43.51 - 54.39: 36 Dihedral angle restraints: 9189 sinusoidal: 3565 harmonic: 5624 Sorted by residual: dihedral pdb=" CA ARG A 103 " pdb=" CB ARG A 103 " pdb=" CG ARG A 103 " pdb=" CD ARG A 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.61 -54.39 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ARG C 103 " pdb=" CB ARG C 103 " pdb=" CG ARG C 103 " pdb=" CD ARG C 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.65 -54.35 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ARG B 103 " pdb=" CB ARG B 103 " pdb=" CG ARG B 103 " pdb=" CD ARG B 103 " ideal model delta sinusoidal sigma weight residual -180.00 -125.68 -54.32 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1454 0.026 - 0.052: 479 0.052 - 0.078: 187 0.078 - 0.104: 136 0.104 - 0.130: 60 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA VAL D 207 " pdb=" N VAL D 207 " pdb=" C VAL D 207 " pdb=" CB VAL D 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 182 " pdb=" N ILE B 182 " pdb=" C ILE B 182 " pdb=" CB ILE B 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 2313 not shown) Planarity restraints: 2763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 214 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO D 215 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 215 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 215 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 214 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 215 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 214 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 215 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.019 5.00e-02 4.00e+02 ... (remaining 2760 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4724 2.83 - 3.35: 14118 3.35 - 3.86: 25862 3.86 - 4.38: 31214 4.38 - 4.90: 53452 Nonbonded interactions: 129370 Sorted by model distance: nonbonded pdb=" OG1 THR C 202 " pdb=" ND2 ASN C 204 " model vdw 2.309 2.520 nonbonded pdb=" OG1 THR B 202 " pdb=" ND2 ASN B 204 " model vdw 2.309 2.520 nonbonded pdb=" OG1 THR A 202 " pdb=" ND2 ASN A 204 " model vdw 2.310 2.520 nonbonded pdb=" OG1 THR D 202 " pdb=" ND2 ASN D 204 " model vdw 2.310 2.520 nonbonded pdb=" NH1 ARG B 101 " pdb=" O ALA B 201 " model vdw 2.320 2.520 ... (remaining 129365 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' selection = (chain 'B' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) selection = (chain 'C' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) selection = (chain 'D' and (resid 24 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 379 or (resid 380 and (name N or n \ ame CA or name C or name O or name CB )) or resid 381 through 414 or (resid 415 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 41 \ 7 through 430 or (resid 431 and (name N or name CA or name C or name O or name C \ B )) or resid 432 through 517)) } 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.670 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 41.060 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 : 0.002 0.018 15492 Z= 0.110 Angle : 0.417 3.723 21031 Z= 0.236 Chirality : 0.040 0.130 2316 Planarity : 0.004 0.034 2763 Dihedral : 8.936 54.391 5605 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.50 % Allowed : 2.33 % Favored : 97.16 % 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: 1.56 (0.20), residues: 1968 helix: 1.87 (0.18), residues: 824 sheet: 0.66 (0.28), residues: 388 loop : 0.44 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 469 HIS 0.003 0.001 HIS B 173 PHE 0.012 0.001 PHE C 367 TYR 0.005 0.001 TYR C 149 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 228 average time/residue: 1.5932 time to fit residues: 393.4738 Evaluate side-chains 113 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 46 HIS A 100 HIS A 173 HIS A 192 GLN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN A 317 GLN A 407 GLN A 423 GLN A 516 ASN B 30 GLN B 43 ASN B 46 HIS B 100 HIS B 173 HIS B 192 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN B 317 GLN B 407 GLN B 423 GLN C 43 ASN C 46 HIS C 100 HIS C 173 HIS C 192 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 GLN C 317 GLN C 407 GLN C 423 GLN D 30 GLN D 43 ASN D 46 HIS D 100 HIS D 173 HIS D 192 GLN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN D 317 GLN D 407 GLN D 423 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 15492 Z= 0.296 Angle : 0.469 5.152 21031 Z= 0.248 Chirality : 0.043 0.161 2316 Planarity : 0.004 0.034 2763 Dihedral : 3.828 34.913 2124 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 9.70 % Favored : 88.66 % 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: 1.45 (0.20), residues: 1968 helix: 1.76 (0.19), residues: 836 sheet: 0.49 (0.26), residues: 412 loop : 0.44 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 45 HIS 0.003 0.001 HIS B 308 PHE 0.017 0.001 PHE B 367 TYR 0.009 0.001 TYR B 485 ARG 0.003 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 0 residues processed: 131 average time/residue: 1.4090 time to fit residues: 202.2493 Evaluate side-chains 105 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 361 GLN A 423 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 GLN B 361 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN C 361 GLN C 423 GLN ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 361 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15492 Z= 0.224 Angle : 0.423 4.532 21031 Z= 0.225 Chirality : 0.041 0.133 2316 Planarity : 0.003 0.032 2763 Dihedral : 3.894 35.667 2124 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.07 % Allowed : 10.96 % Favored : 87.96 % 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: 1.45 (0.20), residues: 1968 helix: 1.77 (0.18), residues: 836 sheet: 0.44 (0.26), residues: 412 loop : 0.48 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 45 HIS 0.002 0.001 HIS D 308 PHE 0.019 0.001 PHE B 241 TYR 0.008 0.001 TYR B 149 ARG 0.002 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 123 average time/residue: 1.3430 time to fit residues: 182.8671 Evaluate side-chains 110 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 15492 Z= 0.488 Angle : 0.547 7.331 21031 Z= 0.288 Chirality : 0.046 0.169 2316 Planarity : 0.004 0.039 2763 Dihedral : 4.453 43.398 2124 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.01 % Allowed : 11.72 % Favored : 87.27 % 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: 1.19 (0.20), residues: 1968 helix: 1.54 (0.18), residues: 836 sheet: 0.27 (0.25), residues: 400 loop : 0.38 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 302 HIS 0.005 0.001 HIS C 308 PHE 0.019 0.002 PHE C 367 TYR 0.013 0.001 TYR D 149 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 1.707 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 124 average time/residue: 1.4817 time to fit residues: 202.4483 Evaluate side-chains 105 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 78 optimal weight: 0.2980 chunk 161 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15492 Z= 0.238 Angle : 0.439 4.747 21031 Z= 0.233 Chirality : 0.042 0.137 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.258 41.383 2124 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.45 % Allowed : 11.66 % Favored : 86.89 % 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: 1.31 (0.20), residues: 1968 helix: 1.71 (0.19), residues: 836 sheet: 0.22 (0.25), residues: 400 loop : 0.43 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.002 0.001 HIS D 252 PHE 0.013 0.001 PHE D 367 TYR 0.009 0.001 TYR C 149 ARG 0.002 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.591 Fit side-chains REVERT: C 410 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.7219 (mtt) outliers start: 23 outliers final: 14 residues processed: 122 average time/residue: 1.2744 time to fit residues: 172.3321 Evaluate side-chains 109 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 480 SER Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 0.1980 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15492 Z= 0.216 Angle : 0.429 4.666 21031 Z= 0.227 Chirality : 0.042 0.158 2316 Planarity : 0.003 0.033 2763 Dihedral : 4.104 38.642 2124 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.45 % Allowed : 11.78 % Favored : 86.77 % 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: 1.42 (0.20), residues: 1968 helix: 1.81 (0.19), residues: 836 sheet: 0.27 (0.25), residues: 400 loop : 0.48 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 45 HIS 0.002 0.001 HIS C 308 PHE 0.011 0.001 PHE A 367 TYR 0.010 0.001 TYR C 442 ARG 0.002 0.000 ARG C 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.670 Fit side-chains REVERT: C 410 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7239 (mtt) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 1.1773 time to fit residues: 158.9102 Evaluate side-chains 109 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 0.0770 chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15492 Z= 0.176 Angle : 0.415 5.412 21031 Z= 0.218 Chirality : 0.041 0.141 2316 Planarity : 0.003 0.033 2763 Dihedral : 3.998 36.399 2124 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.01 % Allowed : 12.16 % Favored : 86.83 % 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: 1.51 (0.20), residues: 1968 helix: 1.90 (0.19), residues: 836 sheet: 0.30 (0.25), residues: 412 loop : 0.52 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP D 45 HIS 0.002 0.001 HIS B 308 PHE 0.010 0.001 PHE C 367 TYR 0.007 0.001 TYR C 442 ARG 0.002 0.000 ARG D 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.789 Fit side-chains REVERT: C 410 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7228 (mtt) outliers start: 16 outliers final: 14 residues processed: 116 average time/residue: 1.2242 time to fit residues: 158.7317 Evaluate side-chains 110 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 503 THR Chi-restraints excluded: chain D residue 504 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 15492 Z= 0.412 Angle : 0.505 5.263 21031 Z= 0.266 Chirality : 0.044 0.165 2316 Planarity : 0.004 0.035 2763 Dihedral : 4.381 41.215 2124 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.07 % Allowed : 12.67 % Favored : 86.26 % 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: 1.34 (0.20), residues: 1968 helix: 1.74 (0.18), residues: 836 sheet: 0.22 (0.25), residues: 400 loop : 0.45 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.004 0.001 HIS C 308 PHE 0.016 0.001 PHE D 367 TYR 0.013 0.001 TYR A 149 ARG 0.003 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.849 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 1.2058 time to fit residues: 148.5562 Evaluate side-chains 99 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15492 Z= 0.171 Angle : 0.422 4.592 21031 Z= 0.223 Chirality : 0.041 0.144 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.114 37.950 2124 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.69 % Allowed : 13.48 % Favored : 85.82 % 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: 1.57 (0.20), residues: 1968 helix: 1.94 (0.19), residues: 836 sheet: 0.32 (0.25), residues: 400 loop : 0.55 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 45 HIS 0.002 0.001 HIS C 308 PHE 0.009 0.001 PHE A 427 TYR 0.009 0.001 TYR B 442 ARG 0.002 0.000 ARG D 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.556 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 1.1056 time to fit residues: 129.6554 Evaluate side-chains 98 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15492 Z= 0.196 Angle : 0.420 4.357 21031 Z= 0.222 Chirality : 0.041 0.162 2316 Planarity : 0.003 0.034 2763 Dihedral : 4.035 36.129 2124 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.82 % Allowed : 13.61 % Favored : 85.57 % 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: 1.63 (0.20), residues: 1968 helix: 1.98 (0.19), residues: 836 sheet: 0.37 (0.25), residues: 400 loop : 0.60 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 45 HIS 0.002 0.001 HIS A 308 PHE 0.010 0.001 PHE C 367 TYR 0.010 0.001 TYR A 442 ARG 0.002 0.000 ARG D 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.754 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 100 average time/residue: 1.2137 time to fit residues: 138.9965 Evaluate side-chains 101 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 480 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 480 SER Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 480 SER Chi-restraints excluded: chain D residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** 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 = 0.3393 r_free = 0.3393 target = 0.101039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.077286 restraints weight = 26634.168| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.87 r_work: 0.2881 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15492 Z= 0.267 Angle : 0.441 4.809 21031 Z= 0.233 Chirality : 0.042 0.148 2316 Planarity : 0.003 0.033 2763 Dihedral : 4.130 37.170 2124 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.82 % Allowed : 13.48 % Favored : 85.70 % 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: 1.57 (0.20), residues: 1968 helix: 1.94 (0.19), residues: 836 sheet: 0.36 (0.25), residues: 400 loop : 0.54 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 45 HIS 0.003 0.001 HIS D 308 PHE 0.012 0.001 PHE D 367 TYR 0.009 0.001 TYR B 149 ARG 0.002 0.000 ARG D 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3968.04 seconds wall clock time: 71 minutes 38.85 seconds (4298.85 seconds total)