Starting phenix.real_space_refine on Sat Mar 23 00:03:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqc_13029/03_2024/7oqc_13029_updated.pdb" } resolution = 4.1 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= 0.006 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: 5 Type Number sf(0) Gaussians P 621 5.49 5 S 82 5.16 5 C 19852 2.51 5 N 5980 2.21 5 O 8515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ARG 377": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ARG 484": "NH1" <-> "NH2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 271": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "b ARG 62": "NH1" <-> "NH2" Residue "b ARG 80": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "g ARG 23": "NH1" <-> "NH2" Residue "i ARG 15": "NH1" <-> "NH2" Residue "i ARG 41": "NH1" <-> "NH2" Residue "i ARG 89": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35050 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1758 Classifications: {'peptide': 267} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 847 Classifications: {'RNA': 63} Modifications used: {'rna3p': 53, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 62} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 53 Chain: "E" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4561 Classifications: {'peptide': 544} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 12, 'TRANS': 531} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "J" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 687 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "1" Number of atoms: 11822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 11822 Classifications: {'RNA': 558} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 35, 'rna3p_pur': 241, 'rna3p_pyr': 258} Link IDs: {'rna2p': 59, 'rna3p': 498} Chain breaks: 1 Chain: "G" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1954 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1570 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 186} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "b" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "e" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 600 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 585 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "g" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 1 Chain: "h" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 771 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 33 Chain: "i" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 805 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1201 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 221 Chain: "D" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 3530 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 19, 'TRANS': 556} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1418 Unresolved non-hydrogen angles: 1833 Unresolved non-hydrogen dihedrals: 1212 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 6, 'TYR:plan': 18, 'ASN:plan1': 32, 'TRP:plan': 12, 'ASP:plan': 21, 'PHE:plan': 26, 'GLU:plan': 23, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 827 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1059 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 14, 'TRANS': 171} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 506 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 7, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 274 Time building chain proxies: 19.24, per 1000 atoms: 0.55 Number of scatterers: 35050 At special positions: 0 Unit cell: (154.28, 228.52, 213.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 621 15.00 O 8515 8.00 N 5980 7.00 C 19852 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: 15.24 Conformation dependent library (CDL) restraints added in 4.7 seconds 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 22 sheets defined 44.3% alpha, 9.2% beta 182 base pairs and 322 stacking pairs defined. Time for finding SS restraints: 15.08 Creating SS restraints... Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 215 through 224 Processing helix chain 'F' and resid 326 through 332 Processing helix chain 'F' and resid 358 through 368 Processing helix chain 'F' and resid 386 through 396 Processing helix chain 'F' and resid 502 through 518 removed outlier: 3.905A pdb=" N ASN F 518 " --> pdb=" O GLU F 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 11 through 22 removed outlier: 3.556A pdb=" N THR E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 Processing helix chain 'E' and resid 50 through 66 removed outlier: 3.912A pdb=" N LEU E 55 " --> pdb=" O GLN E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.931A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 100 Processing helix chain 'E' and resid 106 through 119 removed outlier: 4.561A pdb=" N ASN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 119 " --> pdb=" O PHE E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 137 Processing helix chain 'E' and resid 144 through 157 Processing helix chain 'E' and resid 163 through 173 removed outlier: 3.951A pdb=" N GLU E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.636A pdb=" N SER E 200 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 223 through 254 Processing helix chain 'E' and resid 273 through 289 removed outlier: 3.821A pdb=" N THR E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 289 " --> pdb=" O TYR E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 309 Proline residue: E 305 - end of helix removed outlier: 7.123A pdb=" N HIS E 308 " --> pdb=" O LEU E 304 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR E 309 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 322 Processing helix chain 'E' and resid 327 through 339 removed outlier: 4.135A pdb=" N LYS E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 3.641A pdb=" N SER E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 374 removed outlier: 3.640A pdb=" N LYS E 370 " --> pdb=" O ASN E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 385 through 402 removed outlier: 3.910A pdb=" N PHE E 394 " --> pdb=" O ASP E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.532A pdb=" N ARG E 427 " --> pdb=" O LYS E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 443 Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'E' and resid 461 through 467 Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 476 through 487 Processing helix chain 'E' and resid 494 through 504 Processing helix chain 'E' and resid 518 through 528 removed outlier: 4.331A pdb=" N GLU E 523 " --> pdb=" O PRO E 519 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 539 Processing helix chain 'J' and resid 9 through 12 No H-bonds generated for 'chain 'J' and resid 9 through 12' Processing helix chain 'J' and resid 36 through 40 Processing helix chain 'J' and resid 44 through 51 Processing helix chain 'J' and resid 278 through 301 Processing helix chain 'J' and resid 304 through 311 Processing helix chain 'G' and resid 47 through 56 Processing helix chain 'G' and resid 80 through 92 removed outlier: 3.871A pdb=" N GLU G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N CYS G 85 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 141 removed outlier: 4.008A pdb=" N LYS G 137 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TRP G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 231 through 251 Processing helix chain 'G' and resid 263 through 269 removed outlier: 4.232A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 292 removed outlier: 3.706A pdb=" N GLU G 275 " --> pdb=" O ARG G 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 84 through 93 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'C' and resid 18 through 24 Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 61 through 70 removed outlier: 4.178A pdb=" N GLN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 70 " --> pdb=" O ASN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 99 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.607A pdb=" N SER C 184 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN C 185 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR C 186 " --> pdb=" O TRP C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 181 through 186' Processing helix chain 'b' and resid 55 through 61 removed outlier: 4.075A pdb=" N ASP b 59 " --> pdb=" O LYS b 55 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS b 60 " --> pdb=" O THR b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 130 Processing helix chain 'd' and resid 6 through 13 Processing helix chain 'd' and resid 66 through 68 No H-bonds generated for 'chain 'd' and resid 66 through 68' Processing helix chain 'd' and resid 76 through 79 Processing helix chain 'e' and resid 13 through 23 Processing helix chain 'f' and resid 15 through 20 Processing helix chain 'g' and resid 8 through 10 No H-bonds generated for 'chain 'g' and resid 8 through 10' Processing helix chain 'h' and resid 4 through 8 Processing helix chain 'h' and resid 60 through 68 Processing helix chain 'h' and resid 103 through 106 No H-bonds generated for 'chain 'h' and resid 103 through 106' Processing helix chain 'h' and resid 110 through 118 Processing helix chain 'i' and resid 18 through 27 Processing helix chain 'i' and resid 30 through 39 removed outlier: 4.214A pdb=" N LEU i 33 " --> pdb=" O PRO i 30 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE i 34 " --> pdb=" O MET i 31 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN i 35 " --> pdb=" O SER i 32 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA i 37 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET i 38 " --> pdb=" O ASN i 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL i 39 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 18 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 74 through 85 Processing helix chain 'H' and resid 91 through 123 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 173 through 195 removed outlier: 3.604A pdb=" N GLN H 195 " --> pdb=" O GLY H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 221 Processing helix chain 'H' and resid 224 through 243 Processing helix chain 'D' and resid 45 through 62 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 88 through 99 removed outlier: 4.727A pdb=" N SER D 93 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 117 removed outlier: 3.869A pdb=" N TYR D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix removed outlier: 3.697A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 161 through 173 removed outlier: 3.520A pdb=" N GLU D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 214 through 239 removed outlier: 4.550A pdb=" N GLU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 271 through 284 Processing helix chain 'D' and resid 290 through 302 Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 328 through 339 Processing helix chain 'D' and resid 345 through 359 removed outlier: 3.800A pdb=" N ASN D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 389 through 411 Processing helix chain 'D' and resid 421 through 424 No H-bonds generated for 'chain 'D' and resid 421 through 424' Processing helix chain 'D' and resid 431 through 442 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 468 through 480 Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 502 through 518 removed outlier: 3.797A pdb=" N LEU D 517 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D 518 " --> pdb=" O THR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 527 removed outlier: 3.843A pdb=" N SER D 527 " --> pdb=" O VAL D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 545 removed outlier: 4.202A pdb=" N MET D 545 " --> pdb=" O PRO D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 564 No H-bonds generated for 'chain 'D' and resid 562 through 564' Processing helix chain 'D' and resid 592 through 595 No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.609A pdb=" N LEU B 15 " --> pdb=" O ASP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 66 through 90 Processing helix chain 'B' and resid 120 through 129 removed outlier: 3.941A pdb=" N LYS B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing sheet with id= A, first strand: chain 'F' and resid 163 through 167 removed outlier: 4.647A pdb=" N TYR F 207 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 350 through 354 Processing sheet with id= C, first strand: chain 'F' and resid 444 through 446 Processing sheet with id= D, first strand: chain 'J' and resid 5 through 7 Processing sheet with id= E, first strand: chain 'G' and resid 69 through 76 removed outlier: 3.813A pdb=" N THR G 76 " --> pdb=" O MET G 111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET G 111 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 159 through 163 Processing sheet with id= G, first strand: chain 'A' and resid 107 through 110 Processing sheet with id= H, first strand: chain 'b' and resid 77 through 83 removed outlier: 5.668A pdb=" N CYS b 48 " --> pdb=" O LEU b 82 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG b 21 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL b 97 " --> pdb=" O ARG b 21 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU b 23 " --> pdb=" O THR b 95 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N THR b 95 " --> pdb=" O LEU b 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'b' and resid 43 through 45 Processing sheet with id= J, first strand: chain 'd' and resid 56 through 59 removed outlier: 3.519A pdb=" N SER d 20 " --> pdb=" O VAL d 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'd' and resid 61 through 64 removed outlier: 3.952A pdb=" N GLN d 43 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU d 35 " --> pdb=" O GLN d 43 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG d 45 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU d 33 " --> pdb=" O ARG d 45 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'e' and resid 90 through 92 Processing sheet with id= M, first strand: chain 'e' and resid 42 through 45 removed outlier: 6.567A pdb=" N VAL e 53 " --> pdb=" O VAL e 44 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY e 78 " --> pdb=" O GLU e 56 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'f' and resid 78 through 83 removed outlier: 6.950A pdb=" N LYS f 30 " --> pdb=" O LEU f 79 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE f 81 " --> pdb=" O GLY f 28 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY f 28 " --> pdb=" O ILE f 81 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU f 83 " --> pdb=" O ARG f 26 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ARG f 26 " --> pdb=" O GLU f 83 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN f 52 " --> pdb=" O VAL f 43 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 71 through 73 removed outlier: 3.997A pdb=" N LYS g 24 " --> pdb=" O ILE g 46 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'g' and resid 60 through 63 removed outlier: 3.763A pdb=" N GLY g 31 " --> pdb=" O VAL g 39 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASP g 41 " --> pdb=" O LEU g 29 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU g 29 " --> pdb=" O ASP g 41 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'h' and resid 80 through 82 removed outlier: 4.325A pdb=" N THR h 23 " --> pdb=" O LEU h 19 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'h' and resid 84 through 87 removed outlier: 3.887A pdb=" N SER h 31 " --> pdb=" O ILE h 39 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR h 41 " --> pdb=" O LEU h 29 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU h 29 " --> pdb=" O THR h 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'i' and resid 85 through 91 Processing sheet with id= T, first strand: chain 'i' and resid 93 through 96 removed outlier: 4.032A pdb=" N VAL i 68 " --> pdb=" O ALA i 60 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA i 60 " --> pdb=" O VAL i 68 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU i 70 " --> pdb=" O VAL i 58 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL i 58 " --> pdb=" O GLU i 70 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 183 through 185 removed outlier: 4.508A pdb=" N TYR B 150 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 174 through 176 1032 hydrogen bonds defined for protein. 2982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 438 hydrogen bonds 764 hydrogen bond angles 0 basepair planarities 182 basepair parallelities 322 stacking parallelities Total time for adding SS restraints: 14.21 Time building geometry restraints manager: 16.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4903 1.32 - 1.45: 12562 1.45 - 1.57: 18028 1.57 - 1.69: 1236 1.69 - 1.82: 134 Bond restraints: 36863 Sorted by residual: bond pdb=" O3' A 1 325 " pdb=" P G 1 326 " ideal model delta sigma weight residual 1.607 1.201 0.406 1.50e-02 4.44e+03 7.33e+02 bond pdb=" N PRO J 274 " pdb=" CD PRO J 274 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.25e+01 bond pdb=" N GLU D 609 " pdb=" CA GLU D 609 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.18e+00 bond pdb=" N LEU D 608 " pdb=" CA LEU D 608 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.26e+00 bond pdb=" N LYS D 610 " pdb=" CA LYS D 610 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.25e-02 6.40e+03 5.89e+00 ... (remaining 36858 not shown) Histogram of bond angle deviations from ideal: 82.18 - 92.54: 2 92.54 - 102.91: 1235 102.91 - 113.28: 23424 113.28 - 123.64: 25055 123.64 - 134.01: 3116 Bond angle restraints: 52832 Sorted by residual: angle pdb=" CA PRO J 274 " pdb=" N PRO J 274 " pdb=" CD PRO J 274 " ideal model delta sigma weight residual 112.00 99.56 12.44 1.40e+00 5.10e-01 7.89e+01 angle pdb=" O3' U 1 442 " pdb=" P U 1 443 " pdb=" OP2 U 1 443 " ideal model delta sigma weight residual 108.00 82.18 25.82 3.00e+00 1.11e-01 7.41e+01 angle pdb=" O3' U 1 442 " pdb=" P U 1 443 " pdb=" OP1 U 1 443 " ideal model delta sigma weight residual 108.00 82.24 25.76 3.00e+00 1.11e-01 7.37e+01 angle pdb=" C GLY d 5 " pdb=" N ILE d 6 " pdb=" CA ILE d 6 " ideal model delta sigma weight residual 120.24 124.02 -3.78 6.30e-01 2.52e+00 3.61e+01 angle pdb=" C ILE g 19 " pdb=" N ASN g 20 " pdb=" CA ASN g 20 " ideal model delta sigma weight residual 121.54 131.49 -9.95 1.91e+00 2.74e-01 2.72e+01 ... (remaining 52827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21556 35.95 - 71.90: 1343 71.90 - 107.85: 134 107.85 - 143.80: 4 143.80 - 179.76: 13 Dihedral angle restraints: 23050 sinusoidal: 13989 harmonic: 9061 Sorted by residual: dihedral pdb=" O4' C 1 144 " pdb=" C1' C 1 144 " pdb=" N1 C 1 144 " pdb=" C2 C 1 144 " ideal model delta sinusoidal sigma weight residual 200.00 42.89 157.11 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' C 1 148 " pdb=" C1' C 1 148 " pdb=" N1 C 1 148 " pdb=" C2 C 1 148 " ideal model delta sinusoidal sigma weight residual 200.00 47.17 152.83 1 1.50e+01 4.44e-03 8.06e+01 dihedral pdb=" O4' C 1 151 " pdb=" C1' C 1 151 " pdb=" N1 C 1 151 " pdb=" C2 C 1 151 " ideal model delta sinusoidal sigma weight residual -128.00 51.42 -179.42 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 6465 0.383 - 0.767: 0 0.767 - 1.150: 0 1.150 - 1.533: 0 1.533 - 1.917: 1 Chirality restraints: 6466 Sorted by residual: chirality pdb=" P U 1 443 " pdb=" OP1 U 1 443 " pdb=" OP2 U 1 443 " pdb=" O5' U 1 443 " both_signs ideal model delta sigma weight residual True 2.41 0.49 1.92 2.00e-01 2.50e+01 9.18e+01 chirality pdb=" CB ILE b 86 " pdb=" CA ILE b 86 " pdb=" CG1 ILE b 86 " pdb=" CG2 ILE b 86 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C3' G 1 152 " pdb=" C4' G 1 152 " pdb=" O3' G 1 152 " pdb=" C2' G 1 152 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.51e+00 ... (remaining 6463 not shown) Planarity restraints: 4606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' N I 141 " -0.461 2.00e-02 2.50e+03 4.51e-01 4.07e+03 pdb=" C2' N I 141 " -0.384 2.00e-02 2.50e+03 pdb=" C3' N I 141 " -0.493 2.00e-02 2.50e+03 pdb=" C4' N I 141 " 0.387 2.00e-02 2.50e+03 pdb=" C5' N I 141 " 0.180 2.00e-02 2.50e+03 pdb=" O2' N I 141 " 0.899 2.00e-02 2.50e+03 pdb=" O3' N I 141 " -0.180 2.00e-02 2.50e+03 pdb=" O4' N I 141 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N I 111 " -0.452 2.00e-02 2.50e+03 4.47e-01 3.99e+03 pdb=" C2' N I 111 " -0.390 2.00e-02 2.50e+03 pdb=" C3' N I 111 " -0.504 2.00e-02 2.50e+03 pdb=" C4' N I 111 " 0.387 2.00e-02 2.50e+03 pdb=" C5' N I 111 " 0.169 2.00e-02 2.50e+03 pdb=" O2' N I 111 " 0.881 2.00e-02 2.50e+03 pdb=" O3' N I 111 " -0.163 2.00e-02 2.50e+03 pdb=" O4' N I 111 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N I 118 " 0.482 2.00e-02 2.50e+03 4.46e-01 3.98e+03 pdb=" C2' N I 118 " 0.405 2.00e-02 2.50e+03 pdb=" C3' N I 118 " 0.492 2.00e-02 2.50e+03 pdb=" C4' N I 118 " -0.402 2.00e-02 2.50e+03 pdb=" C5' N I 118 " -0.132 2.00e-02 2.50e+03 pdb=" O2' N I 118 " -0.863 2.00e-02 2.50e+03 pdb=" O3' N I 118 " 0.135 2.00e-02 2.50e+03 pdb=" O4' N I 118 " -0.116 2.00e-02 2.50e+03 ... (remaining 4603 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6583 2.78 - 3.31: 30286 3.31 - 3.84: 63577 3.84 - 4.37: 70228 4.37 - 4.90: 107642 Nonbonded interactions: 278316 Sorted by model distance: nonbonded pdb=" O2 U 1 217 " pdb=" O6 G 1 220 " model vdw 2.245 2.432 nonbonded pdb=" O4 U 1 384 " pdb=" O6 G 1 434 " model vdw 2.249 2.432 nonbonded pdb=" O2' A 1 73 " pdb=" OP1 G 1 75 " model vdw 2.283 2.440 nonbonded pdb=" O2' U 1 299 " pdb=" OD2 ASP C 44 " model vdw 2.287 2.440 nonbonded pdb=" O6 G 1 389 " pdb=" O4 U 1 430 " model vdw 2.303 2.432 ... (remaining 278311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.980 Check model and map are aligned: 0.500 Set scattering table: 0.290 Process input model: 102.450 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.406 36863 Z= 0.258 Angle : 0.796 25.822 52832 Z= 0.408 Chirality : 0.049 1.917 6466 Planarity : 0.045 0.451 4606 Dihedral : 19.443 179.756 17136 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 0.58 % Allowed : 4.09 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.11), residues: 3010 helix: -2.53 (0.08), residues: 1466 sheet: -1.64 (0.27), residues: 295 loop : -2.67 (0.14), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 186 HIS 0.010 0.001 HIS E 296 PHE 0.029 0.002 PHE E 94 TYR 0.043 0.002 TYR E 316 ARG 0.010 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 932 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 ILE cc_start: 0.8284 (mp) cc_final: 0.8054 (mp) REVERT: F 446 TYR cc_start: 0.7782 (m-80) cc_final: 0.7475 (m-10) REVERT: F 495 ILE cc_start: 0.8272 (pt) cc_final: 0.7789 (mm) REVERT: F 510 LEU cc_start: 0.8253 (mt) cc_final: 0.8009 (mt) REVERT: E 5 THR cc_start: 0.7547 (m) cc_final: 0.6882 (m) REVERT: E 74 TYR cc_start: 0.8455 (m-80) cc_final: 0.7164 (m-80) REVERT: E 253 SER cc_start: 0.7632 (m) cc_final: 0.7071 (t) REVERT: E 286 THR cc_start: 0.8732 (m) cc_final: 0.8119 (p) REVERT: E 351 LEU cc_start: 0.8971 (tp) cc_final: 0.8307 (tt) REVERT: E 447 PHE cc_start: 0.6548 (m-80) cc_final: 0.6220 (m-80) REVERT: E 533 MET cc_start: 0.7177 (tpt) cc_final: 0.6735 (ptm) REVERT: G 122 ILE cc_start: 0.7917 (tt) cc_final: 0.7382 (tt) REVERT: G 228 GLU cc_start: 0.5871 (tm-30) cc_final: 0.5545 (mt-10) REVERT: G 230 ASN cc_start: 0.7612 (p0) cc_final: 0.7406 (p0) REVERT: G 248 LEU cc_start: 0.8958 (tt) cc_final: 0.8597 (mt) REVERT: A 15 ASN cc_start: 0.6435 (t0) cc_final: 0.5904 (t0) REVERT: A 20 THR cc_start: 0.8895 (m) cc_final: 0.8612 (p) REVERT: A 24 LEU cc_start: 0.8142 (mp) cc_final: 0.7721 (tt) REVERT: A 26 HIS cc_start: 0.7356 (m90) cc_final: 0.6897 (m170) REVERT: C 26 VAL cc_start: 0.8486 (t) cc_final: 0.8273 (p) REVERT: C 40 ASN cc_start: 0.8446 (m110) cc_final: 0.7859 (m-40) REVERT: b 9 SER cc_start: 0.7495 (p) cc_final: 0.7280 (p) REVERT: d 37 GLU cc_start: 0.6501 (mt-10) cc_final: 0.5813 (mt-10) REVERT: d 65 ARG cc_start: 0.7587 (tmt90) cc_final: 0.7335 (mtp180) REVERT: d 77 LEU cc_start: 0.8018 (tt) cc_final: 0.7784 (mt) REVERT: e 15 ASN cc_start: 0.8323 (m110) cc_final: 0.7840 (t0) REVERT: e 49 PHE cc_start: 0.7160 (m-80) cc_final: 0.6227 (m-10) REVERT: i 51 ASN cc_start: 0.6219 (m110) cc_final: 0.5680 (t0) REVERT: i 85 ILE cc_start: 0.8190 (pt) cc_final: 0.7880 (mm) REVERT: H 16 GLU cc_start: 0.5685 (mm-30) cc_final: 0.5264 (mm-30) REVERT: D 432 ILE cc_start: 0.8437 (tt) cc_final: 0.8196 (tt) REVERT: D 494 LEU cc_start: 0.9463 (tp) cc_final: 0.9036 (tp) REVERT: D 515 PHE cc_start: 0.8043 (t80) cc_final: 0.7174 (t80) REVERT: D 587 ILE cc_start: 0.9003 (pt) cc_final: 0.8746 (pt) REVERT: D 602 LEU cc_start: 0.7459 (mm) cc_final: 0.7230 (mm) outliers start: 12 outliers final: 3 residues processed: 941 average time/residue: 0.4815 time to fit residues: 708.8811 Evaluate side-chains 489 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 486 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 30.0000 chunk 269 optimal weight: 40.0000 chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 169 optimal weight: 0.2980 chunk 207 optimal weight: 4.9990 chunk 322 optimal weight: 4.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 301 GLN F 375 ASN F 414 ASN F 492 GLN ** F 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 HIS E 65 ASN E 72 ASN E 153 GLN E 198 GLN E 245 GLN E 298 ASN E 393 GLN E 437 GLN E 442 ASN E 443 ASN E 459 ASN J 16 GLN G 50 ASN G 81 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 221 GLN C 40 ASN C 66 ASN C 70 ASN b 8 HIS b 122 GLN d 15 GLN d 68 GLN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN h 30 GLN ** i 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 52 HIS D 488 ASN ** D 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 36863 Z= 0.427 Angle : 1.153 27.577 52832 Z= 0.695 Chirality : 0.047 1.814 6466 Planarity : 0.013 0.121 4606 Dihedral : 21.535 179.586 12486 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 0.68 % Allowed : 6.33 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3010 helix: -0.36 (0.12), residues: 1484 sheet: -1.22 (0.29), residues: 282 loop : -2.12 (0.16), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 183 HIS 0.014 0.003 HIS d 17 PHE 0.040 0.003 PHE E 77 TYR 0.049 0.003 TYR E 316 ARG 0.019 0.001 ARG G 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 519 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 495 ILE cc_start: 0.8367 (pt) cc_final: 0.8118 (mm) REVERT: E 16 LEU cc_start: 0.8809 (mt) cc_final: 0.8554 (mt) REVERT: E 23 TYR cc_start: 0.7915 (m-80) cc_final: 0.7480 (m-10) REVERT: E 45 CYS cc_start: 0.7787 (p) cc_final: 0.7495 (p) REVERT: E 74 TYR cc_start: 0.8755 (m-80) cc_final: 0.8417 (m-10) REVERT: E 196 LEU cc_start: 0.9141 (mm) cc_final: 0.8529 (tt) REVERT: E 253 SER cc_start: 0.8619 (m) cc_final: 0.8250 (t) REVERT: E 281 LYS cc_start: 0.9142 (mttt) cc_final: 0.8839 (mtmt) REVERT: E 309 TYR cc_start: 0.8117 (m-80) cc_final: 0.7912 (m-80) REVERT: E 339 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8454 (mtpt) REVERT: E 359 ASN cc_start: 0.8260 (m-40) cc_final: 0.7958 (m-40) REVERT: E 447 PHE cc_start: 0.6830 (m-80) cc_final: 0.6444 (m-80) REVERT: J 33 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7919 (mmtt) REVERT: G 228 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6358 (mt-10) REVERT: G 245 GLN cc_start: 0.8450 (tt0) cc_final: 0.8155 (tt0) REVERT: G 248 LEU cc_start: 0.9136 (tt) cc_final: 0.8511 (mp) REVERT: A 19 TYR cc_start: 0.5918 (t80) cc_final: 0.5013 (t80) REVERT: A 121 ILE cc_start: 0.7262 (mm) cc_final: 0.6854 (mm) REVERT: C 36 ASP cc_start: 0.8038 (m-30) cc_final: 0.7838 (m-30) REVERT: d 65 ARG cc_start: 0.7963 (ttt180) cc_final: 0.7541 (mtp180) REVERT: d 86 LYS cc_start: 0.6986 (mptt) cc_final: 0.6669 (mptt) REVERT: e 10 MET cc_start: 0.6695 (tmm) cc_final: 0.6255 (tmm) REVERT: e 49 PHE cc_start: 0.8243 (m-80) cc_final: 0.7999 (m-80) REVERT: f 46 ASP cc_start: 0.8641 (p0) cc_final: 0.8435 (p0) REVERT: f 78 VAL cc_start: 0.9181 (p) cc_final: 0.8927 (m) REVERT: D 519 HIS cc_start: 0.7825 (m90) cc_final: 0.7619 (m90) outliers start: 14 outliers final: 6 residues processed: 529 average time/residue: 0.4460 time to fit residues: 384.8640 Evaluate side-chains 369 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 363 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 219 optimal weight: 0.4980 chunk 88 optimal weight: 30.0000 chunk 322 optimal weight: 0.2980 chunk 348 optimal weight: 40.0000 chunk 287 optimal weight: 40.0000 chunk 320 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 GLN F 432 ASN ** F 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 ASN b 14 ASN e 15 ASN H 17 GLN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 36863 Z= 0.459 Angle : 1.164 27.592 52832 Z= 0.703 Chirality : 0.049 1.822 6466 Planarity : 0.013 0.111 4606 Dihedral : 21.774 178.546 12486 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.49 % Rotamer: Outliers : 0.34 % Allowed : 6.47 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 3010 helix: 0.10 (0.13), residues: 1466 sheet: -1.20 (0.30), residues: 276 loop : -2.06 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 165 HIS 0.011 0.002 HIS D 519 PHE 0.044 0.003 PHE F 307 TYR 0.040 0.003 TYR E 69 ARG 0.029 0.002 ARG E 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 461 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 368 MET cc_start: 0.8314 (mmm) cc_final: 0.8107 (mmm) REVERT: E 26 SER cc_start: 0.9109 (t) cc_final: 0.8595 (p) REVERT: E 194 MET cc_start: 0.7540 (mmt) cc_final: 0.7339 (mmm) REVERT: E 196 LEU cc_start: 0.9196 (mm) cc_final: 0.8790 (tp) REVERT: E 281 LYS cc_start: 0.9204 (mttt) cc_final: 0.8794 (mtmt) REVERT: E 336 MET cc_start: 0.8258 (mmp) cc_final: 0.7979 (mmp) REVERT: J 10 GLN cc_start: 0.8097 (pm20) cc_final: 0.7876 (pm20) REVERT: J 33 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8012 (mmtt) REVERT: G 228 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6417 (mt-10) REVERT: G 288 MET cc_start: 0.8297 (tpp) cc_final: 0.8052 (tpp) REVERT: A 19 TYR cc_start: 0.6129 (t80) cc_final: 0.5724 (t80) REVERT: A 44 ASN cc_start: 0.6680 (m-40) cc_final: 0.6345 (m-40) REVERT: A 73 MET cc_start: 0.6375 (tpp) cc_final: 0.5945 (tpt) REVERT: C 44 ASP cc_start: 0.7589 (m-30) cc_final: 0.7385 (t0) REVERT: C 157 ASP cc_start: 0.7623 (m-30) cc_final: 0.7022 (p0) REVERT: b 50 GLU cc_start: 0.7764 (pt0) cc_final: 0.7494 (pt0) REVERT: b 91 GLN cc_start: 0.6713 (tp-100) cc_final: 0.6387 (mm-40) REVERT: b 98 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7557 (tm-30) REVERT: d 65 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7297 (mtp-110) REVERT: f 26 ARG cc_start: 0.4357 (ptt-90) cc_final: 0.3945 (mtm110) REVERT: g 12 ASP cc_start: 0.7563 (m-30) cc_final: 0.7198 (m-30) REVERT: h 42 ASP cc_start: 0.6869 (t0) cc_final: 0.6601 (t0) REVERT: H 221 PHE cc_start: 0.5612 (m-80) cc_final: 0.5365 (m-80) REVERT: H 237 ASP cc_start: 0.6719 (m-30) cc_final: 0.5569 (t70) REVERT: D 494 LEU cc_start: 0.9674 (tp) cc_final: 0.9439 (tp) outliers start: 7 outliers final: 3 residues processed: 466 average time/residue: 0.4455 time to fit residues: 339.1763 Evaluate side-chains 361 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 324 optimal weight: 0.9980 chunk 343 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 307 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN E 245 GLN E 298 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN d 12 ASN d 15 GLN d 43 GLN e 15 ASN e 51 ASN h 78 ASN ** i 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 36863 Z= 0.177 Angle : 1.040 26.155 52832 Z= 0.651 Chirality : 0.043 1.870 6466 Planarity : 0.012 0.109 4606 Dihedral : 21.531 179.657 12486 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 3010 helix: 1.00 (0.14), residues: 1464 sheet: -0.73 (0.31), residues: 271 loop : -1.60 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 147 HIS 0.005 0.001 HIS d 17 PHE 0.026 0.002 PHE E 77 TYR 0.024 0.002 TYR b 18 ARG 0.010 0.001 ARG H 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 504 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 446 TYR cc_start: 0.7926 (m-80) cc_final: 0.7588 (m-10) REVERT: E 194 MET cc_start: 0.7690 (mmt) cc_final: 0.7478 (mmm) REVERT: E 281 LYS cc_start: 0.9025 (mttt) cc_final: 0.8746 (mtmt) REVERT: E 336 MET cc_start: 0.7980 (mmp) cc_final: 0.7725 (mmp) REVERT: E 442 ASN cc_start: 0.8784 (t0) cc_final: 0.8429 (t0) REVERT: J 33 LYS cc_start: 0.8214 (mtmt) cc_final: 0.8006 (mmtt) REVERT: G 288 MET cc_start: 0.8056 (tpp) cc_final: 0.7727 (tpp) REVERT: A 12 ARG cc_start: 0.7647 (pmt-80) cc_final: 0.7403 (pmt-80) REVERT: A 19 TYR cc_start: 0.6278 (t80) cc_final: 0.6054 (t80) REVERT: A 44 ASN cc_start: 0.6595 (m-40) cc_final: 0.6304 (m-40) REVERT: A 73 MET cc_start: 0.6197 (tpp) cc_final: 0.5825 (tpt) REVERT: C 161 GLU cc_start: 0.7642 (tt0) cc_final: 0.7218 (tm-30) REVERT: C 183 TRP cc_start: 0.8957 (m-10) cc_final: 0.8305 (m-10) REVERT: b 21 ARG cc_start: 0.8957 (ttm-80) cc_final: 0.8718 (ttp80) REVERT: b 98 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7427 (tm-30) REVERT: d 86 LYS cc_start: 0.6730 (mptt) cc_final: 0.6314 (mptt) REVERT: d 90 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7630 (mmt90) REVERT: e 49 PHE cc_start: 0.8203 (m-80) cc_final: 0.8001 (m-80) REVERT: g 12 ASP cc_start: 0.7439 (m-30) cc_final: 0.7109 (m-30) REVERT: h 42 ASP cc_start: 0.6761 (t0) cc_final: 0.6399 (t0) REVERT: h 68 LEU cc_start: 0.9153 (mt) cc_final: 0.8472 (mt) REVERT: H 221 PHE cc_start: 0.5683 (m-80) cc_final: 0.5457 (m-80) REVERT: D 494 LEU cc_start: 0.9645 (tp) cc_final: 0.9332 (tp) REVERT: D 507 ASP cc_start: 0.7943 (m-30) cc_final: 0.7638 (m-30) outliers start: 2 outliers final: 1 residues processed: 505 average time/residue: 0.4196 time to fit residues: 348.9698 Evaluate side-chains 380 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 9.9990 chunk 194 optimal weight: 0.0020 chunk 4 optimal weight: 40.0000 chunk 255 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 292 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 175 optimal weight: 10.0000 chunk 307 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN E 51 GLN E 245 GLN E 298 ASN ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN b 91 GLN d 41 ASN d 43 GLN H 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.6387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 36863 Z= 0.492 Angle : 1.178 28.129 52832 Z= 0.710 Chirality : 0.049 1.796 6466 Planarity : 0.013 0.110 4606 Dihedral : 21.721 178.899 12486 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.04 % Favored : 92.86 % Rotamer: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3010 helix: 0.49 (0.13), residues: 1473 sheet: -0.96 (0.31), residues: 268 loop : -1.90 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 147 HIS 0.011 0.002 HIS d 17 PHE 0.048 0.003 PHE F 307 TYR 0.038 0.003 TYR b 18 ARG 0.009 0.001 ARG h 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 428 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 437 MET cc_start: 0.7272 (tpt) cc_final: 0.6967 (tpp) REVERT: F 446 TYR cc_start: 0.7921 (m-80) cc_final: 0.7685 (m-80) REVERT: E 26 SER cc_start: 0.9183 (t) cc_final: 0.8584 (p) REVERT: E 99 GLN cc_start: 0.7514 (mm110) cc_final: 0.7099 (mp10) REVERT: E 194 MET cc_start: 0.8034 (mmt) cc_final: 0.7779 (mmm) REVERT: E 207 GLU cc_start: 0.7649 (tp30) cc_final: 0.7413 (tp30) REVERT: E 281 LYS cc_start: 0.9227 (mttt) cc_final: 0.8797 (mtmt) REVERT: G 87 ASP cc_start: 0.7560 (m-30) cc_final: 0.7158 (m-30) REVERT: G 228 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6400 (mt-10) REVERT: G 288 MET cc_start: 0.8279 (tpp) cc_final: 0.7999 (tpp) REVERT: C 157 ASP cc_start: 0.7747 (m-30) cc_final: 0.7011 (p0) REVERT: b 40 HIS cc_start: 0.7773 (m-70) cc_final: 0.7547 (m170) REVERT: b 98 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7587 (tm-30) REVERT: e 10 MET cc_start: 0.6559 (tmm) cc_final: 0.5945 (ttt) REVERT: f 26 ARG cc_start: 0.4852 (ptt-90) cc_final: 0.4648 (mtm110) REVERT: h 36 MET cc_start: 0.7927 (ttp) cc_final: 0.7711 (ptm) REVERT: H 16 GLU cc_start: 0.5810 (tp30) cc_final: 0.5610 (tp30) REVERT: D 494 LEU cc_start: 0.9608 (tp) cc_final: 0.9385 (tp) REVERT: D 609 GLU cc_start: 0.7278 (pm20) cc_final: 0.6715 (pm20) outliers start: 2 outliers final: 0 residues processed: 430 average time/residue: 0.4389 time to fit residues: 314.4858 Evaluate side-chains 338 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 343 optimal weight: 0.9980 chunk 285 optimal weight: 40.0000 chunk 159 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 ASN b 14 ASN d 12 ASN d 43 GLN ** i 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36863 Z= 0.184 Angle : 1.047 26.223 52832 Z= 0.654 Chirality : 0.043 1.877 6466 Planarity : 0.012 0.108 4606 Dihedral : 21.506 179.848 12486 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 3010 helix: 1.18 (0.14), residues: 1466 sheet: -0.80 (0.32), residues: 262 loop : -1.56 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP h 26 HIS 0.005 0.001 HIS d 17 PHE 0.026 0.001 PHE e 20 TYR 0.016 0.002 TYR b 18 ARG 0.004 0.000 ARG b 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 ILE cc_start: 0.8688 (mt) cc_final: 0.8393 (mt) REVERT: E 80 LEU cc_start: 0.8711 (tp) cc_final: 0.8487 (tt) REVERT: E 189 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8139 (mmm160) REVERT: E 281 LYS cc_start: 0.8936 (mttt) cc_final: 0.8636 (mtmt) REVERT: E 336 MET cc_start: 0.7993 (mmp) cc_final: 0.7715 (mmp) REVERT: E 439 ILE cc_start: 0.8322 (mt) cc_final: 0.7789 (mt) REVERT: J 46 ILE cc_start: 0.7095 (mp) cc_final: 0.6536 (mm) REVERT: G 87 ASP cc_start: 0.7731 (m-30) cc_final: 0.7434 (m-30) REVERT: G 246 ILE cc_start: 0.8737 (pt) cc_final: 0.8180 (mm) REVERT: G 288 MET cc_start: 0.7988 (tpp) cc_final: 0.7464 (tpp) REVERT: C 115 TYR cc_start: 0.7476 (t80) cc_final: 0.7128 (t80) REVERT: C 157 ASP cc_start: 0.7536 (m-30) cc_final: 0.6782 (p0) REVERT: C 161 GLU cc_start: 0.7669 (tt0) cc_final: 0.7329 (tm-30) REVERT: C 183 TRP cc_start: 0.8907 (m-10) cc_final: 0.8246 (m-10) REVERT: b 98 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7510 (tm-30) REVERT: d 15 GLN cc_start: 0.8932 (mt0) cc_final: 0.8189 (mt0) REVERT: d 37 GLU cc_start: 0.8992 (pp20) cc_final: 0.8547 (pp20) REVERT: d 90 ARG cc_start: 0.8192 (mmp80) cc_final: 0.7621 (mmt90) REVERT: e 10 MET cc_start: 0.6445 (tmm) cc_final: 0.5889 (ttt) REVERT: e 49 PHE cc_start: 0.8574 (m-80) cc_final: 0.8355 (m-80) REVERT: h 42 ASP cc_start: 0.6999 (t0) cc_final: 0.6757 (t0) REVERT: H 237 ASP cc_start: 0.6661 (m-30) cc_final: 0.5630 (t70) REVERT: D 494 LEU cc_start: 0.9568 (tp) cc_final: 0.9361 (tp) REVERT: D 515 PHE cc_start: 0.8249 (t80) cc_final: 0.8009 (t80) REVERT: D 519 HIS cc_start: 0.8022 (m90) cc_final: 0.7757 (m170) REVERT: D 601 SER cc_start: 0.8289 (p) cc_final: 0.7859 (p) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.4349 time to fit residues: 339.5701 Evaluate side-chains 372 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 195 optimal weight: 20.0000 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 342 optimal weight: 10.0000 chunk 214 optimal weight: 0.0050 chunk 208 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN E 442 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN b 14 ASN ** i 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 HIS B 38 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36863 Z= 0.220 Angle : 1.048 26.715 52832 Z= 0.655 Chirality : 0.043 1.854 6466 Planarity : 0.012 0.108 4606 Dihedral : 21.387 179.979 12486 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 3010 helix: 1.37 (0.14), residues: 1455 sheet: -0.80 (0.31), residues: 278 loop : -1.49 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 186 HIS 0.006 0.001 HIS d 17 PHE 0.026 0.002 PHE H 221 TYR 0.021 0.002 TYR F 417 ARG 0.005 0.001 ARG i 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 460 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 328 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 443 ILE cc_start: 0.8719 (mt) cc_final: 0.8439 (mt) REVERT: E 29 TYR cc_start: 0.7896 (m-80) cc_final: 0.7599 (m-80) REVERT: E 80 LEU cc_start: 0.8711 (tp) cc_final: 0.8471 (tt) REVERT: E 189 ARG cc_start: 0.8867 (mmm160) cc_final: 0.8199 (mmm160) REVERT: E 194 MET cc_start: 0.7863 (mmm) cc_final: 0.7580 (mmm) REVERT: E 207 GLU cc_start: 0.7606 (tp30) cc_final: 0.7389 (tp30) REVERT: E 281 LYS cc_start: 0.8942 (mttt) cc_final: 0.8641 (mtmt) REVERT: E 336 MET cc_start: 0.8048 (mmp) cc_final: 0.7708 (mmp) REVERT: J 46 ILE cc_start: 0.7413 (mp) cc_final: 0.6872 (mm) REVERT: G 87 ASP cc_start: 0.7709 (m-30) cc_final: 0.7476 (m-30) REVERT: A 122 GLU cc_start: 0.5816 (mp0) cc_final: 0.5610 (mp0) REVERT: C 65 GLU cc_start: 0.7418 (mp0) cc_final: 0.6741 (mp0) REVERT: C 157 ASP cc_start: 0.7564 (m-30) cc_final: 0.6780 (p0) REVERT: C 161 GLU cc_start: 0.7654 (tt0) cc_final: 0.7347 (tm-30) REVERT: C 183 TRP cc_start: 0.8980 (m-10) cc_final: 0.8343 (m-10) REVERT: b 98 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7480 (tm-30) REVERT: d 15 GLN cc_start: 0.8933 (mt0) cc_final: 0.8187 (mt0) REVERT: d 37 GLU cc_start: 0.8959 (pp20) cc_final: 0.8258 (pp20) REVERT: d 86 LYS cc_start: 0.6778 (mptt) cc_final: 0.6399 (mptt) REVERT: d 90 ARG cc_start: 0.8108 (mmp80) cc_final: 0.7534 (mmt90) REVERT: e 49 PHE cc_start: 0.8377 (m-80) cc_final: 0.8165 (m-80) REVERT: h 42 ASP cc_start: 0.7057 (t0) cc_final: 0.6786 (t0) REVERT: H 237 ASP cc_start: 0.6618 (m-30) cc_final: 0.5687 (t70) REVERT: D 494 LEU cc_start: 0.9528 (tp) cc_final: 0.9263 (tp) outliers start: 1 outliers final: 0 residues processed: 460 average time/residue: 0.4218 time to fit residues: 324.1987 Evaluate side-chains 374 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 5.9990 chunk 136 optimal weight: 30.0000 chunk 204 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN F 518 ASN E 51 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN E 245 GLN ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** b 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN d 41 ASN d 58 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 36863 Z= 0.269 Angle : 1.068 26.952 52832 Z= 0.663 Chirality : 0.044 1.851 6466 Planarity : 0.012 0.109 4606 Dihedral : 21.389 179.966 12486 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 3010 helix: 1.30 (0.14), residues: 1467 sheet: -0.90 (0.32), residues: 262 loop : -1.52 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 382 HIS 0.006 0.001 HIS d 17 PHE 0.033 0.002 PHE E 77 TYR 0.020 0.002 TYR E 112 ARG 0.006 0.001 ARG b 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 328 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8027 (mm-30) REVERT: F 443 ILE cc_start: 0.8795 (mt) cc_final: 0.8542 (mt) REVERT: F 446 TYR cc_start: 0.7828 (m-10) cc_final: 0.7085 (m-10) REVERT: E 74 TYR cc_start: 0.8848 (m-10) cc_final: 0.8640 (m-10) REVERT: E 80 LEU cc_start: 0.8679 (tp) cc_final: 0.8445 (tt) REVERT: E 281 LYS cc_start: 0.9021 (mttt) cc_final: 0.8714 (mtmt) REVERT: E 439 ILE cc_start: 0.8346 (mt) cc_final: 0.7978 (mt) REVERT: J 46 ILE cc_start: 0.7379 (mp) cc_final: 0.6889 (mm) REVERT: G 281 MET cc_start: 0.7683 (mmp) cc_final: 0.7334 (mmp) REVERT: A 67 ILE cc_start: 0.8418 (tt) cc_final: 0.8208 (mp) REVERT: C 157 ASP cc_start: 0.7849 (m-30) cc_final: 0.6951 (p0) REVERT: C 158 GLU cc_start: 0.6912 (tt0) cc_final: 0.6674 (tt0) REVERT: C 161 GLU cc_start: 0.7801 (tt0) cc_final: 0.7360 (tm-30) REVERT: C 183 TRP cc_start: 0.8963 (m-10) cc_final: 0.8358 (m-10) REVERT: b 98 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7668 (tm-30) REVERT: d 37 GLU cc_start: 0.8937 (pp20) cc_final: 0.8159 (pp20) REVERT: d 86 LYS cc_start: 0.6668 (mptt) cc_final: 0.6337 (mptt) REVERT: f 58 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6089 (mm-30) REVERT: h 10 LEU cc_start: 0.8352 (tp) cc_final: 0.7437 (tt) REVERT: h 42 ASP cc_start: 0.7229 (t0) cc_final: 0.6995 (t0) REVERT: i 61 PHE cc_start: 0.6627 (p90) cc_final: 0.6317 (p90) REVERT: H 237 ASP cc_start: 0.6755 (m-30) cc_final: 0.5622 (t70) REVERT: D 462 ILE cc_start: 0.8986 (mm) cc_final: 0.8777 (mt) REVERT: D 609 GLU cc_start: 0.7372 (pm20) cc_final: 0.6748 (mp0) outliers start: 1 outliers final: 0 residues processed: 448 average time/residue: 0.4162 time to fit residues: 312.4844 Evaluate side-chains 367 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 299 optimal weight: 30.0000 chunk 318 optimal weight: 5.9990 chunk 191 optimal weight: 0.0370 chunk 138 optimal weight: 30.0000 chunk 250 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 288 optimal weight: 20.0000 chunk 301 optimal weight: 30.0000 chunk 317 optimal weight: 3.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 HIS F 375 ASN ** F 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN E 245 GLN ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS b 14 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 36863 Z= 0.346 Angle : 1.106 27.064 52832 Z= 0.679 Chirality : 0.046 1.867 6466 Planarity : 0.012 0.110 4606 Dihedral : 21.512 179.582 12486 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.16), residues: 3010 helix: 1.08 (0.14), residues: 1471 sheet: -0.94 (0.31), residues: 267 loop : -1.71 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 382 HIS 0.009 0.001 HIS C 51 PHE 0.040 0.002 PHE E 77 TYR 0.025 0.002 TYR E 60 ARG 0.008 0.001 ARG b 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 ILE cc_start: 0.8873 (mt) cc_final: 0.8545 (mt) REVERT: E 281 LYS cc_start: 0.9122 (mttt) cc_final: 0.8717 (mtmt) REVERT: E 336 MET cc_start: 0.8088 (mmp) cc_final: 0.7811 (mmt) REVERT: E 346 GLU cc_start: 0.7292 (tt0) cc_final: 0.6980 (tp30) REVERT: J 46 ILE cc_start: 0.7351 (mp) cc_final: 0.6917 (mm) REVERT: C 157 ASP cc_start: 0.7982 (m-30) cc_final: 0.6845 (p0) REVERT: C 158 GLU cc_start: 0.6893 (tt0) cc_final: 0.6690 (tt0) REVERT: b 41 MET cc_start: 0.8563 (ptm) cc_final: 0.8323 (ptm) REVERT: d 86 LYS cc_start: 0.6664 (mptt) cc_final: 0.6332 (mptt) REVERT: f 77 ASN cc_start: 0.8388 (m-40) cc_final: 0.7963 (m-40) REVERT: h 14 GLN cc_start: 0.7838 (tm-30) cc_final: 0.6996 (tm-30) REVERT: h 92 ILE cc_start: 0.9321 (mm) cc_final: 0.9096 (mm) REVERT: i 61 PHE cc_start: 0.6802 (p90) cc_final: 0.6401 (p90) REVERT: H 18 LEU cc_start: 0.8692 (tp) cc_final: 0.8479 (tp) REVERT: H 237 ASP cc_start: 0.6676 (m-30) cc_final: 0.5338 (t70) REVERT: D 462 ILE cc_start: 0.8995 (mm) cc_final: 0.8757 (mt) REVERT: D 609 GLU cc_start: 0.7245 (pm20) cc_final: 0.6739 (mp0) REVERT: B 7 LYS cc_start: 0.4650 (ptpp) cc_final: 0.4241 (tptt) REVERT: B 22 LEU cc_start: 0.8844 (mp) cc_final: 0.8627 (mp) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.4118 time to fit residues: 298.4136 Evaluate side-chains 333 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 0.9990 chunk 337 optimal weight: 5.9990 chunk 205 optimal weight: 0.0470 chunk 159 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 353 optimal weight: 50.0000 chunk 325 optimal weight: 0.6980 chunk 281 optimal weight: 40.0000 chunk 29 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 306 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN F 518 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 HIS b 14 ASN d 41 ASN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36863 Z= 0.189 Angle : 1.056 26.322 52832 Z= 0.656 Chirality : 0.044 1.871 6466 Planarity : 0.012 0.108 4606 Dihedral : 21.363 179.463 12486 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 3010 helix: 1.39 (0.14), residues: 1470 sheet: -0.94 (0.32), residues: 261 loop : -1.51 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 147 HIS 0.005 0.001 HIS d 17 PHE 0.033 0.002 PHE e 49 TYR 0.042 0.002 TYR E 74 ARG 0.006 0.001 ARG E 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6020 Ramachandran restraints generated. 3010 Oldfield, 0 Emsley, 3010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 443 ILE cc_start: 0.8811 (mt) cc_final: 0.8611 (mt) REVERT: E 281 LYS cc_start: 0.8923 (mttt) cc_final: 0.8630 (mtmt) REVERT: E 336 MET cc_start: 0.7898 (mmp) cc_final: 0.7522 (mmp) REVERT: E 346 GLU cc_start: 0.7279 (tt0) cc_final: 0.6858 (tp30) REVERT: J 46 ILE cc_start: 0.7296 (mp) cc_final: 0.6887 (mm) REVERT: G 246 ILE cc_start: 0.8768 (pt) cc_final: 0.8205 (mm) REVERT: G 281 MET cc_start: 0.7706 (mmp) cc_final: 0.7050 (mtt) REVERT: C 157 ASP cc_start: 0.7771 (m-30) cc_final: 0.6818 (p0) REVERT: C 158 GLU cc_start: 0.6884 (tt0) cc_final: 0.6653 (tt0) REVERT: C 183 TRP cc_start: 0.8906 (m-10) cc_final: 0.8306 (m-10) REVERT: b 98 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7612 (tm-30) REVERT: d 15 GLN cc_start: 0.8954 (mt0) cc_final: 0.8266 (mt0) REVERT: d 86 LYS cc_start: 0.6585 (mptt) cc_final: 0.6176 (mptt) REVERT: d 90 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7401 (mmt90) REVERT: h 42 ASP cc_start: 0.6864 (t0) cc_final: 0.6623 (t0) REVERT: i 61 PHE cc_start: 0.6706 (p90) cc_final: 0.6164 (p90) REVERT: H 237 ASP cc_start: 0.6589 (m-30) cc_final: 0.5421 (t70) REVERT: D 466 ASN cc_start: 0.7930 (p0) cc_final: 0.7598 (p0) REVERT: D 609 GLU cc_start: 0.7065 (pm20) cc_final: 0.6690 (mp0) REVERT: B 7 LYS cc_start: 0.4877 (ptpp) cc_final: 0.4126 (tptt) outliers start: 1 outliers final: 0 residues processed: 452 average time/residue: 0.4251 time to fit residues: 323.8929 Evaluate side-chains 359 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 0.9980 chunk 300 optimal weight: 30.0000 chunk 86 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 282 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 375 ASN ** F 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN ** G 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 ASN d 41 ASN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.149595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.119462 restraints weight = 108134.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117379 restraints weight = 166012.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118169 restraints weight = 136997.934| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36863 Z= 0.213 Angle : 1.052 26.631 52832 Z= 0.655 Chirality : 0.044 1.864 6466 Planarity : 0.012 0.109 4606 Dihedral : 21.273 179.647 12486 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.91 % Favored : 93.99 % Rotamer: Outliers : 0.10 % Allowed : 0.49 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.89 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 3010 helix: 1.49 (0.14), residues: 1468 sheet: -0.84 (0.31), residues: 267 loop : -1.47 (0.18), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 382 HIS 0.005 0.001 HIS d 17 PHE 0.040 0.002 PHE E 77 TYR 0.035 0.002 TYR E 74 ARG 0.006 0.001 ARG b 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7219.87 seconds wall clock time: 131 minutes 5.79 seconds (7865.79 seconds total)