Starting phenix.real_space_refine (version: dev) on Thu Feb 23 07:29:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n9w_0381/02_2023/6n9w_0381_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.002 sd= 0.045 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 Process input model Symmetric amino acids flipped Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "E ARG 363": "NH1" <-> "NH2" Residue "E ARG 370": "NH1" <-> "NH2" Residue "E ARG 487": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 276": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 255": "NH1" <-> "NH2" Residue "H ARG 429": "NH1" <-> "NH2" Residue "H ARG 547": "NH1" <-> "NH2" Residue "H ARG 566": "NH1" <-> "NH2" Residue "H ARG 591": "NH1" <-> "NH2" Residue "H ARG 599": "NH1" <-> "NH2" Residue "H ARG 687": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19576 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3856 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 485} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3678 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2016 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69 SG CYS A 17 37.587 59.298 40.884 1.00181.79 S ATOM 91 SG CYS A 20 39.316 61.484 38.973 1.00181.96 S ATOM 204 SG CYS A 36 40.487 61.058 41.926 1.00161.54 S ATOM 229 SG CYS A 39 37.651 62.302 42.568 1.00174.44 S Time building chain proxies: 11.10, per 1000 atoms: 0.57 Number of scatterers: 19576 At special positions: 0 Unit cell: (111.8, 135.88, 182.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 112 16.00 P 44 15.00 Mg 6 11.99 O 3807 8.00 N 3418 7.00 C 12188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 241 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.83 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 17 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 39 " Number of angles added : 6 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 17 sheets defined 32.3% alpha, 11.5% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.580A pdb=" N CYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.749A pdb=" N GLN A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.816A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 333 " --> pdb=" O TRP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.707A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 removed outlier: 3.634A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 160 through 167 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.608A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.661A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.779A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 378 through 385 removed outlier: 3.795A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 3.604A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 438 through 453 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'C' and resid 272 through 278 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 318 through 331 removed outlier: 4.021A pdb=" N VAL C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.509A pdb=" N GLU C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 3.886A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 3.679A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 438 through 456 Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 294 through 298 Processing helix chain 'D' and resid 318 through 330 removed outlier: 3.534A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 357 Processing helix chain 'D' and resid 372 through 375 No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 378 through 385 removed outlier: 3.646A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'D' and resid 440 through 456 removed outlier: 3.551A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 477 No H-bonds generated for 'chain 'D' and resid 475 through 477' Processing helix chain 'E' and resid 294 through 298 Processing helix chain 'E' and resid 318 through 330 Processing helix chain 'E' and resid 348 through 357 removed outlier: 3.924A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 378 through 383 Processing helix chain 'E' and resid 405 through 414 Processing helix chain 'E' and resid 440 through 456 removed outlier: 3.684A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'H' and resid 39 through 51 Processing helix chain 'H' and resid 65 through 74 removed outlier: 3.626A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 97 removed outlier: 3.611A pdb=" N ARG H 96 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 131 Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 165 through 185 removed outlier: 3.698A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.521A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 245 Processing helix chain 'H' and resid 255 through 258 No H-bonds generated for 'chain 'H' and resid 255 through 258' Processing helix chain 'H' and resid 341 through 347 Processing helix chain 'H' and resid 377 through 399 removed outlier: 3.683A pdb=" N ALA H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 452 No H-bonds generated for 'chain 'H' and resid 449 through 452' Processing helix chain 'H' and resid 480 through 490 removed outlier: 3.542A pdb=" N ALA H 489 " --> pdb=" O ALA H 485 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG H 490 " --> pdb=" O HIS H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 501 Processing helix chain 'H' and resid 505 through 513 Processing helix chain 'H' and resid 518 through 529 removed outlier: 3.566A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 541 No H-bonds generated for 'chain 'H' and resid 538 through 541' Processing helix chain 'H' and resid 545 through 556 Processing helix chain 'H' and resid 562 through 573 Processing helix chain 'H' and resid 606 through 636 removed outlier: 3.645A pdb=" N ALA H 609 " --> pdb=" O PRO H 606 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU H 610 " --> pdb=" O HIS H 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR H 612 " --> pdb=" O ALA H 609 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN H 615 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER H 616 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA H 619 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU H 620 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE H 621 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE H 626 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR H 629 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET H 632 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL H 634 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU H 635 " --> pdb=" O MET H 632 " (cutoff:3.500A) Processing helix chain 'H' and resid 663 through 683 removed outlier: 4.409A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 34 through 36 removed outlier: 3.515A pdb=" N ASN A 26 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 13 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 removed outlier: 7.724A pdb=" N VAL A 176 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL A 154 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 201 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL A 155 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 203 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 528 through 534 removed outlier: 7.009A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.700A pdb=" N SER B 120 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.560A pdb=" N VAL B 154 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLN B 201 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL B 155 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 203 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 532 through 534 removed outlier: 6.490A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 498 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 542 through 544 removed outlier: 6.820A pdb=" N VAL C 516 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR C 532 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 514 " --> pdb=" O TYR C 532 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU C 460 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 310 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL C 462 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 514 through 521 removed outlier: 6.503A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 460 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL D 310 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 462 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N SER D 312 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N CYS D 464 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 528 through 533 removed outlier: 6.695A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU E 502 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 460 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL E 310 " --> pdb=" O LEU E 460 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 462 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 2 through 4 Processing sheet with id= L, first strand: chain 'H' and resid 56 through 58 Processing sheet with id= M, first strand: chain 'H' and resid 264 through 267 Processing sheet with id= N, first strand: chain 'H' and resid 419 through 421 Processing sheet with id= O, first strand: chain 'H' and resid 692 through 697 removed outlier: 6.344A pdb=" N GLY H 659 " --> pdb=" O TYR H 648 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYR H 648 " --> pdb=" O GLY H 659 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 592 through 594 Processing sheet with id= Q, first strand: chain 'H' and resid 574 through 579 removed outlier: 4.352A pdb=" N GLU H 575 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LYS H 587 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER H 577 " --> pdb=" O GLN H 585 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN H 585 " --> pdb=" O SER H 577 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q 543 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 8.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3269 1.31 - 1.44: 5246 1.44 - 1.57: 11184 1.57 - 1.69: 80 1.69 - 1.82: 182 Bond restraints: 19961 Sorted by residual: bond pdb=" C4' DOC P 6 " pdb=" C3' DOC P 6 " ideal model delta sigma weight residual 1.334 1.518 -0.184 2.00e-02 2.50e+03 8.44e+01 bond pdb=" C4' DOC P 6 " pdb=" O4' DOC P 6 " ideal model delta sigma weight residual 1.609 1.438 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" O4' DOC P 6 " pdb=" C1' DOC P 6 " ideal model delta sigma weight residual 1.268 1.418 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C4 DOC P 6 " pdb=" N4 DOC P 6 " ideal model delta sigma weight residual 1.494 1.349 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C5 DOC P 6 " pdb=" C6 DOC P 6 " ideal model delta sigma weight residual 1.494 1.380 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 19956 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.87: 404 105.87 - 112.97: 10576 112.97 - 120.08: 7373 120.08 - 127.18: 8438 127.18 - 134.28: 242 Bond angle restraints: 27033 Sorted by residual: angle pdb=" N ASP A 352 " pdb=" CA ASP A 352 " pdb=" C ASP A 352 " ideal model delta sigma weight residual 110.97 106.23 4.74 1.09e+00 8.42e-01 1.89e+01 angle pdb=" N ILE H 464 " pdb=" CA ILE H 464 " pdb=" C ILE H 464 " ideal model delta sigma weight residual 113.53 109.28 4.25 9.80e-01 1.04e+00 1.88e+01 angle pdb=" N HIS A 357 " pdb=" CA HIS A 357 " pdb=" C HIS A 357 " ideal model delta sigma weight residual 111.75 117.21 -5.46 1.28e+00 6.10e-01 1.82e+01 angle pdb=" C ASP A 352 " pdb=" CA ASP A 352 " pdb=" CB ASP A 352 " ideal model delta sigma weight residual 110.96 117.41 -6.45 1.54e+00 4.22e-01 1.75e+01 angle pdb=" N PHE E 289 " pdb=" CA PHE E 289 " pdb=" C PHE E 289 " ideal model delta sigma weight residual 110.20 116.70 -6.50 1.58e+00 4.01e-01 1.69e+01 ... (remaining 27028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 11578 35.27 - 70.55: 176 70.55 - 105.82: 21 105.82 - 141.09: 4 141.09 - 176.36: 8 Dihedral angle restraints: 11787 sinusoidal: 4986 harmonic: 6801 Sorted by residual: dihedral pdb=" C2 TTP B 700 " pdb=" C1' TTP B 700 " pdb=" N1 TTP B 700 " pdb=" O4' TTP B 700 " ideal model delta sinusoidal sigma weight residual -58.32 118.05 -176.36 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' TTP C 700 " pdb=" O5' TTP C 700 " pdb=" PA TTP C 700 " pdb=" O3A TTP C 700 " ideal model delta sinusoidal sigma weight residual 179.97 -5.73 -174.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C2 TTP C 700 " pdb=" C1' TTP C 700 " pdb=" N1 TTP C 700 " pdb=" O4' TTP C 700 " ideal model delta sinusoidal sigma weight residual -58.32 114.23 -172.55 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 11784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2276 0.053 - 0.105: 542 0.105 - 0.158: 144 0.158 - 0.211: 8 0.211 - 0.263: 9 Chirality restraints: 2979 Sorted by residual: chirality pdb=" C3' TTP E 700 " pdb=" C2' TTP E 700 " pdb=" C4' TTP E 700 " pdb=" O3' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' TTP H 801 " pdb=" C2' TTP H 801 " pdb=" C4' TTP H 801 " pdb=" O3' TTP H 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C3' TTP B 700 " pdb=" C2' TTP B 700 " pdb=" C4' TTP B 700 " pdb=" O3' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2976 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 511 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 147 " -0.010 2.00e-02 2.50e+03 1.19e-02 3.57e+00 pdb=" CG TRP A 147 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 147 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 147 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 147 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 147 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 147 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 147 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 147 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 147 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 511 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.023 5.00e-02 4.00e+02 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 155 2.65 - 3.21: 15807 3.21 - 3.77: 28871 3.77 - 4.34: 39291 4.34 - 4.90: 63778 Nonbonded interactions: 147902 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.082 2.170 nonbonded pdb=" OG SER B 319 " pdb="MG MG B 701 " model vdw 2.113 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.115 2.170 nonbonded pdb=" O1B TTP C 700 " pdb="MG MG C 701 " model vdw 2.119 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.157 2.170 ... (remaining 147897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 65 through 549) selection = (chain 'B' and (resid 65 through 208 or resid 219 through 280 or resid 285 throu \ gh 430 or resid 437 through 549)) } ncs_group { reference = (chain 'C' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545 or resid 700 through 701)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545 or resid 700 through 7 \ 01)) selection = (chain 'E' and (resid 285 through 506 or resid 510 through 545 or resid 700 thro \ ugh 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 44 5.49 5 Mg 6 5.21 5 S 112 5.16 5 C 12188 2.51 5 N 3418 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.140 Check model and map are aligned: 0.000 Process input model: 56.100 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.200 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.184 19961 Z= 0.321 Angle : 0.758 12.177 27033 Z= 0.401 Chirality : 0.050 0.263 2979 Planarity : 0.004 0.048 3346 Dihedral : 13.640 176.363 7432 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.13), residues: 2358 helix: -3.03 (0.11), residues: 831 sheet: -1.21 (0.25), residues: 412 loop : -2.86 (0.15), residues: 1115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 621 time to evaluate : 2.302 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 outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.3632 time to fit residues: 325.9879 Evaluate side-chains 323 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 129 ASN A 145 HIS A 253 GLN A 512 ASN B 67 ASN B 121 GLN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 244 ASN B 296 ASN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN C 296 ASN C 380 GLN C 475 HIS D 278 HIS D 325 GLN D 358 ASN D 512 ASN D 536 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS H 171 ASN H 423 ASN H 432 HIS H 506 HIS H 520 ASN H 558 ASN H 653 HIS H 683 HIS H 704 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19961 Z= 0.200 Angle : 0.628 10.246 27033 Z= 0.312 Chirality : 0.043 0.184 2979 Planarity : 0.004 0.037 3346 Dihedral : 14.762 179.394 2942 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.16), residues: 2358 helix: -1.12 (0.17), residues: 825 sheet: -0.98 (0.26), residues: 411 loop : -2.48 (0.16), residues: 1122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 319 time to evaluate : 2.333 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 outliers start: 53 outliers final: 28 residues processed: 356 average time/residue: 0.3209 time to fit residues: 177.1679 Evaluate side-chains 281 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 253 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1754 time to fit residues: 12.4072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS C 278 HIS ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN H 704 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19961 Z= 0.212 Angle : 0.603 10.480 27033 Z= 0.302 Chirality : 0.043 0.294 2979 Planarity : 0.003 0.033 3346 Dihedral : 14.492 174.956 2942 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.16), residues: 2358 helix: -0.32 (0.18), residues: 843 sheet: -0.83 (0.25), residues: 421 loop : -2.20 (0.17), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 272 time to evaluate : 2.462 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 outliers start: 42 outliers final: 17 residues processed: 300 average time/residue: 0.2921 time to fit residues: 138.6921 Evaluate side-chains 253 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1748 time to fit residues: 8.4270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 30.0000 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 0.0170 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.6422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 465 HIS ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN E 328 GLN ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19961 Z= 0.146 Angle : 0.576 11.323 27033 Z= 0.281 Chirality : 0.042 0.175 2979 Planarity : 0.003 0.038 3346 Dihedral : 14.225 176.904 2942 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2358 helix: 0.06 (0.19), residues: 831 sheet: -0.67 (0.26), residues: 419 loop : -2.02 (0.17), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 2.223 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 outliers start: 30 outliers final: 13 residues processed: 301 average time/residue: 0.3044 time to fit residues: 143.3278 Evaluate side-chains 257 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 244 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1814 time to fit residues: 7.4665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.0050 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 GLN E 358 ASN ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19961 Z= 0.193 Angle : 0.572 8.932 27033 Z= 0.283 Chirality : 0.042 0.159 2979 Planarity : 0.003 0.036 3346 Dihedral : 14.125 179.755 2942 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2358 helix: 0.37 (0.19), residues: 835 sheet: -0.63 (0.26), residues: 411 loop : -1.90 (0.17), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 252 time to evaluate : 2.146 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 outliers start: 24 outliers final: 16 residues processed: 268 average time/residue: 0.2910 time to fit residues: 124.0361 Evaluate side-chains 243 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 227 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2421 time to fit residues: 9.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 0.4980 chunk 136 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 232 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.3980 chunk 19 optimal weight: 0.0030 chunk 76 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 1.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19961 Z= 0.160 Angle : 0.570 9.236 27033 Z= 0.280 Chirality : 0.042 0.154 2979 Planarity : 0.003 0.042 3346 Dihedral : 13.947 176.908 2942 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2358 helix: 0.46 (0.19), residues: 849 sheet: -0.49 (0.27), residues: 407 loop : -1.80 (0.17), residues: 1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 2.351 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 outliers start: 26 outliers final: 16 residues processed: 261 average time/residue: 0.2988 time to fit residues: 124.5522 Evaluate side-chains 245 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 229 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1871 time to fit residues: 8.7945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 0.0370 chunk 131 optimal weight: 0.0010 chunk 195 optimal weight: 0.2980 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.4668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN E 392 HIS E 475 HIS H 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 19961 Z= 0.139 Angle : 0.569 9.596 27033 Z= 0.277 Chirality : 0.042 0.194 2979 Planarity : 0.003 0.042 3346 Dihedral : 13.713 174.089 2942 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2358 helix: 0.52 (0.19), residues: 854 sheet: -0.40 (0.27), residues: 410 loop : -1.72 (0.18), residues: 1094 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 2.374 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 outliers start: 14 outliers final: 9 residues processed: 263 average time/residue: 0.2892 time to fit residues: 122.0914 Evaluate side-chains 244 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1792 time to fit residues: 6.2673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 9.9990 chunk 92 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 ASN H 171 ASN H 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19961 Z= 0.215 Angle : 0.626 14.632 27033 Z= 0.309 Chirality : 0.043 0.170 2979 Planarity : 0.003 0.056 3346 Dihedral : 13.714 169.157 2942 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2358 helix: 0.56 (0.19), residues: 854 sheet: -0.42 (0.27), residues: 409 loop : -1.61 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 236 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 240 average time/residue: 0.3009 time to fit residues: 114.6353 Evaluate side-chains 225 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1769 time to fit residues: 4.5234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.0270 chunk 221 optimal weight: 6.9990 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 66 optimal weight: 0.0270 chunk 194 optimal weight: 0.0040 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 0.3908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN H 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 19961 Z= 0.149 Angle : 0.630 16.103 27033 Z= 0.304 Chirality : 0.042 0.162 2979 Planarity : 0.003 0.043 3346 Dihedral : 13.471 164.757 2942 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.18), residues: 2358 helix: 0.61 (0.19), residues: 853 sheet: -0.28 (0.27), residues: 410 loop : -1.58 (0.18), residues: 1095 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 242 average time/residue: 0.2989 time to fit residues: 115.8102 Evaluate side-chains 234 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 2.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1800 time to fit residues: 3.6948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0170 chunk 227 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 19961 Z= 0.256 Angle : 0.681 15.054 27033 Z= 0.337 Chirality : 0.044 0.185 2979 Planarity : 0.003 0.042 3346 Dihedral : 13.451 155.608 2942 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.18), residues: 2358 helix: 0.56 (0.19), residues: 863 sheet: -0.39 (0.27), residues: 412 loop : -1.52 (0.18), residues: 1083 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 233 average time/residue: 0.2899 time to fit residues: 109.2694 Evaluate side-chains 221 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1767 time to fit residues: 4.3803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 195 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.075914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058323 restraints weight = 84891.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060110 restraints weight = 46130.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061245 restraints weight = 30775.070| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19961 Z= 0.172 Angle : 0.651 14.855 27033 Z= 0.315 Chirality : 0.043 0.168 2979 Planarity : 0.003 0.037 3346 Dihedral : 13.224 152.782 2942 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2358 helix: 0.68 (0.19), residues: 850 sheet: -0.34 (0.27), residues: 410 loop : -1.47 (0.18), residues: 1098 =============================================================================== Job complete usr+sys time: 3901.23 seconds wall clock time: 71 minutes 59.05 seconds (4319.05 seconds total)