Starting phenix.real_space_refine (version: dev) on Wed Dec 14 07:46:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966_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/6dmu_7966/12_2022/6dmu_7966_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/12_2022/6dmu_7966_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= 0.003 sd= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 632": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 632": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 584": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 632": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 470": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 584": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 632": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 19636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "B" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "C" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4862 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 24, 'TRANS': 582} Chain breaks: 1 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.42, per 1000 atoms: 0.58 Number of scatterers: 19636 At special positions: 0 Unit cell: (135.3, 135.3, 127.6, 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 140 16.00 P 12 15.00 O 3524 8.00 N 3292 7.00 C 12668 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: 8.28 Conformation dependent library (CDL) restraints added in 3.3 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 8 sheets defined 57.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.792A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.135A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.911A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 120 through 127 removed outlier: 4.267A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.766A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 209 through 224 removed outlier: 4.870A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.931A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 303 through 309 removed outlier: 4.056A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 4.392A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 347 removed outlier: 3.760A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 410 removed outlier: 4.461A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Proline residue: A 405 - end of helix removed outlier: 3.991A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 415 No H-bonds generated for 'chain 'A' and resid 412 through 415' Processing helix chain 'A' and resid 423 through 444 removed outlier: 4.165A pdb=" N ILE A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 469 removed outlier: 4.024A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 494 through 510 removed outlier: 4.063A pdb=" N PHE A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.752A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.974A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 607 removed outlier: 4.689A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 46 Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.792A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 93 through 99 removed outlier: 4.134A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.910A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 120 through 127 removed outlier: 4.267A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.766A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 209 through 224 removed outlier: 4.870A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.931A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 303 through 309 removed outlier: 4.056A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.392A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 347 removed outlier: 3.759A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 410 removed outlier: 4.461A pdb=" N ARG B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 403 " --> pdb=" O ILE B 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.992A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 423 through 444 removed outlier: 4.165A pdb=" N ILE B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 429 " --> pdb=" O PHE B 425 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 469 removed outlier: 4.025A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N PHE B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 494 through 510 removed outlier: 4.063A pdb=" N PHE B 504 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 538 removed outlier: 3.752A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.974A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 607 removed outlier: 4.689A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.792A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 93 through 99 removed outlier: 4.135A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.911A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 120 through 127 removed outlier: 4.267A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 176 through 184 removed outlier: 3.765A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 199 through 204 Processing helix chain 'C' and resid 209 through 224 removed outlier: 4.870A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.931A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 303 through 309 removed outlier: 4.056A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 323 removed outlier: 4.392A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.759A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 410 removed outlier: 4.462A pdb=" N ARG C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C 403 " --> pdb=" O ILE C 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Proline residue: C 405 - end of helix removed outlier: 3.992A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 415 No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 423 through 444 removed outlier: 4.164A pdb=" N ILE C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE C 429 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 469 removed outlier: 4.024A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 488 Processing helix chain 'C' and resid 494 through 510 removed outlier: 4.063A pdb=" N PHE C 504 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 removed outlier: 3.753A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.973A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 585 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 607 removed outlier: 4.688A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.792A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 93 through 99 removed outlier: 4.135A pdb=" N LEU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.911A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 120 through 127 removed outlier: 4.267A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 Processing helix chain 'D' and resid 166 through 173 Processing helix chain 'D' and resid 176 through 184 removed outlier: 3.766A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 199 through 204 Processing helix chain 'D' and resid 209 through 224 removed outlier: 4.870A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.931A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 303 through 309 removed outlier: 4.056A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 323 removed outlier: 4.393A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 347 removed outlier: 3.759A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 410 removed outlier: 4.461A pdb=" N ARG D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 387 " --> pdb=" O ASN D 383 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.992A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 415 No H-bonds generated for 'chain 'D' and resid 412 through 415' Processing helix chain 'D' and resid 423 through 444 removed outlier: 4.165A pdb=" N ILE D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 469 removed outlier: 4.025A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE D 468 " --> pdb=" O SER D 464 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 488 Processing helix chain 'D' and resid 494 through 510 removed outlier: 4.063A pdb=" N PHE D 504 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 removed outlier: 3.753A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 565 Processing helix chain 'D' and resid 569 through 587 removed outlier: 3.973A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 585 " --> pdb=" O THR D 581 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 607 removed outlier: 4.689A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 264 through 266 removed outlier: 3.527A pdb=" N HIS A 265 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= C, first strand: chain 'B' and resid 264 through 266 removed outlier: 3.527A pdb=" N HIS B 265 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 352 through 354 Processing sheet with id= E, first strand: chain 'C' and resid 264 through 266 removed outlier: 3.527A pdb=" N HIS C 265 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 352 through 354 Processing sheet with id= G, first strand: chain 'D' and resid 264 through 266 removed outlier: 3.528A pdb=" N HIS D 265 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 352 through 354 764 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 8.80 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: 3124 1.31 - 1.44: 5444 1.44 - 1.57: 11268 1.57 - 1.69: 20 1.69 - 1.82: 228 Bond restraints: 20084 Sorted by residual: bond pdb=" C GLU C 113 " pdb=" N PRO C 114 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.71e+00 bond pdb=" C GLU A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.71e+00 bond pdb=" C GLU D 113 " pdb=" N PRO D 114 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.66e+00 bond pdb=" C GLU B 113 " pdb=" N PRO B 114 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.55e+00 bond pdb=" CA THR C 311 " pdb=" C THR C 311 " ideal model delta sigma weight residual 1.521 1.539 -0.018 1.14e-02 7.69e+03 2.42e+00 ... (remaining 20079 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.44: 412 105.44 - 112.60: 10125 112.60 - 119.76: 7223 119.76 - 126.92: 9255 126.92 - 134.07: 257 Bond angle restraints: 27272 Sorted by residual: angle pdb=" C VAL D 451 " pdb=" N VAL D 452 " pdb=" CA VAL D 452 " ideal model delta sigma weight residual 120.33 124.53 -4.20 8.00e-01 1.56e+00 2.75e+01 angle pdb=" C VAL A 451 " pdb=" N VAL A 452 " pdb=" CA VAL A 452 " ideal model delta sigma weight residual 120.33 124.46 -4.13 8.00e-01 1.56e+00 2.66e+01 angle pdb=" C VAL B 451 " pdb=" N VAL B 452 " pdb=" CA VAL B 452 " ideal model delta sigma weight residual 120.33 124.45 -4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" C VAL C 451 " pdb=" N VAL C 452 " pdb=" CA VAL C 452 " ideal model delta sigma weight residual 120.33 124.41 -4.08 8.00e-01 1.56e+00 2.61e+01 angle pdb=" CA ARG D 363 " pdb=" CB ARG D 363 " pdb=" CG ARG D 363 " ideal model delta sigma weight residual 114.10 121.51 -7.41 2.00e+00 2.50e-01 1.37e+01 ... (remaining 27267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 11054 15.52 - 31.05: 637 31.05 - 46.57: 181 46.57 - 62.10: 8 62.10 - 77.62: 24 Dihedral angle restraints: 11904 sinusoidal: 4812 harmonic: 7092 Sorted by residual: dihedral pdb=" CA GLY C 626 " pdb=" C GLY C 626 " pdb=" N ASP C 627 " pdb=" CA ASP C 627 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY A 626 " pdb=" C GLY A 626 " pdb=" N ASP A 627 " pdb=" CA ASP A 627 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA GLY D 626 " pdb=" C GLY D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 11901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2241 0.056 - 0.112: 686 0.112 - 0.168: 156 0.168 - 0.224: 13 0.224 - 0.280: 8 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA THR C 311 " pdb=" N THR C 311 " pdb=" C THR C 311 " pdb=" CB THR C 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3101 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 206 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.37e+00 pdb=" N PRO B 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 206 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 206 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO D 207 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " 0.032 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 6320 2.86 - 3.37: 18395 3.37 - 3.88: 28910 3.88 - 4.39: 30085 4.39 - 4.90: 52866 Nonbonded interactions: 136576 Sorted by model distance: nonbonded pdb=" O GLY D 422 " pdb=" ND1 HIS D 426 " model vdw 2.348 2.520 nonbonded pdb=" O GLY C 422 " pdb=" ND1 HIS C 426 " model vdw 2.348 2.520 nonbonded pdb=" O GLY A 422 " pdb=" ND1 HIS A 426 " model vdw 2.349 2.520 nonbonded pdb=" O GLY B 422 " pdb=" ND1 HIS B 426 " model vdw 2.349 2.520 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.465 2.440 ... (remaining 136571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 140 5.16 5 C 12668 2.51 5 N 3292 2.21 5 O 3524 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: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 3.370 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.160 Process input model: 51.010 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.006 0.068 20084 Z= 0.364 Angle : 0.992 8.954 27272 Z= 0.530 Chirality : 0.056 0.280 3104 Planarity : 0.007 0.058 3432 Dihedral : 11.623 77.622 7320 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.13), residues: 2412 helix: -2.49 (0.10), residues: 1380 sheet: -2.69 (0.37), residues: 88 loop : -3.28 (0.15), residues: 944 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 412 time to evaluate : 2.223 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 416 average time/residue: 0.3071 time to fit residues: 191.3514 Evaluate side-chains 229 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1607 time to fit residues: 4.3374 ------------------------------------------------------------------------------- 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: 4.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 0.1980 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 310 GLN B 257 GLN B 310 GLN C 257 GLN C 310 GLN D 257 GLN D 310 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20084 Z= 0.253 Angle : 0.677 15.130 27272 Z= 0.342 Chirality : 0.041 0.163 3104 Planarity : 0.005 0.044 3432 Dihedral : 7.145 51.112 2716 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 3.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.15), residues: 2412 helix: -0.88 (0.14), residues: 1324 sheet: -2.31 (0.40), residues: 88 loop : -3.02 (0.16), residues: 1000 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 237 time to evaluate : 2.386 Fit side-chains outliers start: 68 outliers final: 29 residues processed: 285 average time/residue: 0.2618 time to fit residues: 121.6202 Evaluate side-chains 247 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 2.331 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1786 time to fit residues: 12.5530 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 157 HIS A 257 GLN A 310 GLN B 122 HIS B 157 HIS B 257 GLN B 310 GLN C 122 HIS C 157 HIS C 257 GLN C 310 GLN D 122 HIS D 157 HIS D 257 GLN D 310 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 20084 Z= 0.382 Angle : 0.762 16.141 27272 Z= 0.381 Chirality : 0.044 0.160 3104 Planarity : 0.005 0.042 3432 Dihedral : 7.197 51.909 2716 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2412 helix: -0.44 (0.14), residues: 1360 sheet: -2.13 (0.41), residues: 84 loop : -2.90 (0.17), residues: 968 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 216 time to evaluate : 2.388 Fit side-chains outliers start: 57 outliers final: 32 residues processed: 264 average time/residue: 0.2523 time to fit residues: 110.6650 Evaluate side-chains 233 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1683 time to fit residues: 13.2868 ------------------------------------------------------------------------------- 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: 0.0270 chunk 164 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 310 GLN B 310 GLN B 509 HIS B 572 ASN C 310 GLN C 572 ASN D 257 GLN D 310 GLN D 572 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 20084 Z= 0.144 Angle : 0.609 15.407 27272 Z= 0.293 Chirality : 0.038 0.151 3104 Planarity : 0.004 0.041 3432 Dihedral : 6.792 59.610 2716 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2412 helix: 0.05 (0.15), residues: 1320 sheet: -1.86 (0.41), residues: 88 loop : -2.59 (0.17), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 2.174 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 283 average time/residue: 0.2619 time to fit residues: 121.0848 Evaluate side-chains 232 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 217 time to evaluate : 2.310 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1779 time to fit residues: 8.2204 ------------------------------------------------------------------------------- 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: 5.9990 chunk 131 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 310 GLN D 257 GLN D 310 GLN D 509 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20084 Z= 0.262 Angle : 0.678 16.358 27272 Z= 0.327 Chirality : 0.041 0.169 3104 Planarity : 0.004 0.041 3432 Dihedral : 6.695 56.952 2716 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2412 helix: 0.22 (0.14), residues: 1348 sheet: -1.45 (0.44), residues: 84 loop : -2.58 (0.17), residues: 980 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 220 time to evaluate : 2.563 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 243 average time/residue: 0.2648 time to fit residues: 107.3002 Evaluate side-chains 224 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 207 time to evaluate : 3.400 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2233 time to fit residues: 10.4490 ------------------------------------------------------------------------------- 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: 1.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 310 GLN A 572 ASN B 418 GLN C 509 HIS D 257 GLN D 310 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 20084 Z= 0.151 Angle : 0.629 16.359 27272 Z= 0.295 Chirality : 0.038 0.165 3104 Planarity : 0.004 0.040 3432 Dihedral : 6.354 51.900 2716 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.17), residues: 2412 helix: 0.39 (0.15), residues: 1348 sheet: -1.00 (0.46), residues: 84 loop : -2.56 (0.17), residues: 980 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 2.572 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 257 average time/residue: 0.2752 time to fit residues: 116.8166 Evaluate side-chains 235 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1841 time to fit residues: 7.1026 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 195 optimal weight: 0.0370 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN B 572 ASN D 257 GLN D 310 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 20084 Z= 0.148 Angle : 0.628 16.731 27272 Z= 0.293 Chirality : 0.038 0.256 3104 Planarity : 0.004 0.043 3432 Dihedral : 5.981 52.026 2716 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2412 helix: 0.60 (0.15), residues: 1340 sheet: -0.73 (0.49), residues: 84 loop : -2.44 (0.17), residues: 988 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 2.539 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 259 average time/residue: 0.2619 time to fit residues: 111.5100 Evaluate side-chains 232 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 227 time to evaluate : 2.567 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2155 time to fit residues: 5.1643 ------------------------------------------------------------------------------- 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: 8.9990 chunk 138 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 20084 Z= 0.333 Angle : 0.735 16.463 27272 Z= 0.353 Chirality : 0.042 0.242 3104 Planarity : 0.004 0.043 3432 Dihedral : 6.234 49.739 2716 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2412 helix: 0.51 (0.14), residues: 1360 sheet: -1.08 (0.45), residues: 84 loop : -2.32 (0.18), residues: 968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 2.371 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 222 average time/residue: 0.2603 time to fit residues: 95.5167 Evaluate side-chains 216 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 2.452 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1732 time to fit residues: 7.5714 ------------------------------------------------------------------------------- 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: 2.9990 chunk 221 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 0.0010 chunk 129 optimal weight: 0.0020 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 20084 Z= 0.183 Angle : 0.658 17.350 27272 Z= 0.308 Chirality : 0.039 0.219 3104 Planarity : 0.004 0.043 3432 Dihedral : 6.035 51.768 2716 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2412 helix: 0.66 (0.15), residues: 1340 sheet: -0.91 (0.46), residues: 84 loop : -2.39 (0.17), residues: 988 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 2.149 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 223 average time/residue: 0.2615 time to fit residues: 96.2267 Evaluate side-chains 214 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.711 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2273 time to fit residues: 4.7412 ------------------------------------------------------------------------------- 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: 3.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 0.0870 chunk 239 optimal weight: 7.9990 chunk 220 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 20084 Z= 0.233 Angle : 0.681 17.256 27272 Z= 0.321 Chirality : 0.040 0.212 3104 Planarity : 0.004 0.043 3432 Dihedral : 6.027 50.724 2716 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.17), residues: 2412 helix: 0.63 (0.14), residues: 1360 sheet: -0.95 (0.46), residues: 84 loop : -2.36 (0.17), residues: 968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 211 time to evaluate : 2.270 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 213 average time/residue: 0.2669 time to fit residues: 95.0632 Evaluate side-chains 211 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 207 time to evaluate : 2.505 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1786 time to fit residues: 4.8144 ------------------------------------------------------------------------------- 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: 3.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.0870 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 190 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.085327 restraints weight = 42625.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087489 restraints weight = 24152.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.088957 restraints weight = 16656.127| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 20084 Z= 0.156 Angle : 0.641 17.172 27272 Z= 0.298 Chirality : 0.038 0.198 3104 Planarity : 0.004 0.043 3432 Dihedral : 5.811 53.943 2716 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2412 helix: 0.75 (0.15), residues: 1344 sheet: -0.70 (0.48), residues: 84 loop : -2.31 (0.17), residues: 984 =============================================================================== Job complete usr+sys time: 2984.20 seconds wall clock time: 55 minutes 36.69 seconds (3336.69 seconds total)