Starting phenix.real_space_refine on Sat Feb 17 19:10:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_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_7966/02_2024/6dmu_7966_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dmu_7966/02_2024/6dmu_7966_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.14, per 1000 atoms: 0.52 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: 7.14 Conformation dependent library (CDL) restraints added in 3.5 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: 4.22 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: 5.18 Time building geometry restraints manager: 7.74 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: 11094 15.52 - 31.05: 649 31.05 - 46.57: 161 46.57 - 62.10: 16 62.10 - 77.62: 24 Dihedral angle restraints: 11944 sinusoidal: 4852 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 11941 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 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: 0.320 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: 2.670 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 49.900 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 11.539 77.622 7360 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.19 % Allowed : 5.14 % Favored : 94.67 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 613 HIS 0.007 0.001 HIS B 509 PHE 0.014 0.002 PHE B 468 TYR 0.016 0.002 TYR B 162 ARG 0.005 0.001 ARG A 154 *********************** 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 : 2.321 Fit side-chains REVERT: A 255 MET cc_start: 0.7701 (ppp) cc_final: 0.7475 (ppp) REVERT: A 340 MET cc_start: 0.8802 (tpp) cc_final: 0.8477 (tpp) REVERT: A 591 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7989 (tp30) REVERT: B 255 MET cc_start: 0.7620 (ppp) cc_final: 0.7246 (ppp) REVERT: B 482 ILE cc_start: 0.8902 (pp) cc_final: 0.8684 (mt) REVERT: B 591 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7820 (tp30) REVERT: C 255 MET cc_start: 0.7593 (ppp) cc_final: 0.7252 (ppp) REVERT: C 340 MET cc_start: 0.8841 (tpp) cc_final: 0.8448 (tpp) REVERT: C 591 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7796 (tp30) REVERT: D 255 MET cc_start: 0.7678 (ppp) cc_final: 0.7341 (ppp) REVERT: D 340 MET cc_start: 0.8865 (tpp) cc_final: 0.8540 (tpp) REVERT: D 591 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7942 (tp30) outliers start: 4 outliers final: 4 residues processed: 416 average time/residue: 0.3245 time to fit residues: 201.2635 Evaluate side-chains 230 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 226 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 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: 3.9990 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: 3.4388 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20084 Z= 0.241 Angle : 0.667 15.137 27272 Z= 0.337 Chirality : 0.041 0.163 3104 Planarity : 0.005 0.043 3432 Dihedral : 7.444 53.380 2764 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.24 % Allowed : 11.95 % Favored : 84.81 % 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: -2.74 (0.15), residues: 2412 helix: -0.92 (0.14), residues: 1320 sheet: -2.19 (0.41), residues: 88 loop : -3.02 (0.16), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 593 HIS 0.005 0.001 HIS B 509 PHE 0.011 0.001 PHE D 244 TYR 0.015 0.001 TYR A 415 ARG 0.005 0.000 ARG A 470 *********************** 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 304 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 236 time to evaluate : 2.222 Fit side-chains REVERT: A 340 MET cc_start: 0.8778 (tpp) cc_final: 0.8498 (tpp) REVERT: A 539 THR cc_start: 0.9536 (OUTLIER) cc_final: 0.9292 (p) REVERT: A 591 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7902 (tp30) REVERT: B 539 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9232 (p) REVERT: B 591 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7810 (tp30) REVERT: C 340 MET cc_start: 0.8780 (tpp) cc_final: 0.8448 (tpp) REVERT: C 539 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9318 (p) REVERT: C 591 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7809 (tp30) REVERT: D 340 MET cc_start: 0.8806 (tpp) cc_final: 0.8485 (tpp) REVERT: D 539 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9301 (p) REVERT: D 591 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7809 (tp30) outliers start: 68 outliers final: 30 residues processed: 286 average time/residue: 0.2537 time to fit residues: 118.7175 Evaluate side-chains 253 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.4980 chunk 235 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 257 GLN A 310 GLN B 122 HIS B 257 GLN B 310 GLN C 122 HIS C 257 GLN C 310 GLN D 257 GLN D 310 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 20084 Z= 0.321 Angle : 0.701 15.997 27272 Z= 0.349 Chirality : 0.042 0.158 3104 Planarity : 0.005 0.045 3432 Dihedral : 7.017 54.631 2756 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.90 % Allowed : 12.76 % Favored : 83.33 % 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: -2.18 (0.16), residues: 2412 helix: -0.47 (0.14), residues: 1364 sheet: -1.91 (0.43), residues: 84 loop : -2.86 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 593 HIS 0.005 0.001 HIS B 509 PHE 0.013 0.002 PHE C 244 TYR 0.014 0.002 TYR D 623 ARG 0.008 0.001 ARG A 470 *********************** 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 304 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 222 time to evaluate : 2.327 Fit side-chains REVERT: A 340 MET cc_start: 0.8787 (tpp) cc_final: 0.8524 (tpp) REVERT: A 539 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9350 (p) REVERT: A 591 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7931 (tp30) REVERT: A 592 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9041 (tp) REVERT: B 294 GLU cc_start: 0.7864 (pt0) cc_final: 0.7657 (pt0) REVERT: B 591 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7902 (tp30) REVERT: B 592 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9004 (tp) REVERT: C 255 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7119 (tmm) REVERT: C 294 GLU cc_start: 0.7869 (pt0) cc_final: 0.7655 (pt0) REVERT: C 340 MET cc_start: 0.8751 (tpp) cc_final: 0.8450 (tpp) REVERT: C 591 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7898 (tp30) REVERT: C 592 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.8991 (tp) REVERT: D 340 MET cc_start: 0.8749 (tpp) cc_final: 0.8502 (tpp) REVERT: D 591 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7931 (tp30) REVERT: D 592 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9063 (tp) outliers start: 82 outliers final: 48 residues processed: 277 average time/residue: 0.2582 time to fit residues: 117.1648 Evaluate side-chains 267 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 213 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 597 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- 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 B 509 HIS 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: 0.8452 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20084 Z= 0.147 Angle : 0.599 15.487 27272 Z= 0.290 Chirality : 0.038 0.160 3104 Planarity : 0.004 0.038 3432 Dihedral : 6.625 55.484 2756 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.38 % Allowed : 13.95 % Favored : 82.67 % 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: -1.69 (0.16), residues: 2412 helix: 0.03 (0.15), residues: 1316 sheet: -1.53 (0.44), residues: 88 loop : -2.69 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 583 HIS 0.003 0.001 HIS D 509 PHE 0.011 0.001 PHE B 72 TYR 0.013 0.001 TYR A 623 ARG 0.009 0.000 ARG A 470 *********************** 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 318 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 247 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7170 (tmm) REVERT: A 340 MET cc_start: 0.8697 (tpp) cc_final: 0.8311 (tpp) REVERT: A 591 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7673 (tp30) REVERT: A 592 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8960 (tp) REVERT: B 255 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7055 (tmm) REVERT: B 591 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7652 (tp30) REVERT: B 592 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8919 (tp) REVERT: C 255 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7038 (tmm) REVERT: C 340 MET cc_start: 0.8644 (tpp) cc_final: 0.8220 (tpp) REVERT: C 418 GLN cc_start: 0.8311 (pt0) cc_final: 0.8040 (mt0) REVERT: C 591 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7680 (tp30) REVERT: C 592 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.8911 (tp) REVERT: D 255 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.7057 (tmm) REVERT: D 340 MET cc_start: 0.8679 (tpp) cc_final: 0.8274 (tpp) REVERT: D 418 GLN cc_start: 0.8273 (pt0) cc_final: 0.7995 (mt0) REVERT: D 591 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7675 (tp30) REVERT: D 592 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8948 (tp) outliers start: 71 outliers final: 35 residues processed: 296 average time/residue: 0.2605 time to fit residues: 126.2271 Evaluate side-chains 256 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 213 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 D 257 GLN D 310 GLN D 572 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20084 Z= 0.257 Angle : 0.669 16.563 27272 Z= 0.323 Chirality : 0.041 0.172 3104 Planarity : 0.004 0.039 3432 Dihedral : 6.727 57.821 2756 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.81 % Allowed : 15.24 % Favored : 80.95 % 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: -1.46 (0.17), residues: 2412 helix: 0.12 (0.14), residues: 1356 sheet: -1.02 (0.48), residues: 84 loop : -2.59 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 593 HIS 0.004 0.001 HIS D 509 PHE 0.012 0.001 PHE C 72 TYR 0.014 0.001 TYR C 623 ARG 0.006 0.000 ARG A 470 *********************** 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 293 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 213 time to evaluate : 2.237 Fit side-chains REVERT: A 255 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7238 (tmm) REVERT: A 340 MET cc_start: 0.8702 (tpp) cc_final: 0.8379 (tpp) REVERT: A 483 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 591 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7828 (tp30) REVERT: A 592 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.8957 (tp) REVERT: A 625 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 255 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: B 591 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7777 (tp30) REVERT: B 592 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.8965 (tp) REVERT: B 625 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8191 (mm) REVERT: C 98 LEU cc_start: 0.8434 (tt) cc_final: 0.8147 (mp) REVERT: C 255 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.7074 (tmm) REVERT: C 340 MET cc_start: 0.8687 (tpp) cc_final: 0.8342 (tpp) REVERT: C 418 GLN cc_start: 0.8276 (pt0) cc_final: 0.8059 (mt0) REVERT: C 591 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7770 (tp30) REVERT: C 592 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8965 (tp) REVERT: C 625 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8184 (mm) REVERT: D 255 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7185 (tmm) REVERT: D 340 MET cc_start: 0.8711 (tpp) cc_final: 0.8380 (tpp) REVERT: D 591 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7853 (tp30) outliers start: 80 outliers final: 58 residues processed: 270 average time/residue: 0.2402 time to fit residues: 108.6569 Evaluate side-chains 275 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 207 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 564 ILE 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: 3.9990 chunk 45 optimal weight: 4.9990 chunk 136 optimal weight: 0.0670 chunk 57 optimal weight: 7.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- 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 572 ASN D 257 GLN D 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20084 Z= 0.152 Angle : 0.615 16.506 27272 Z= 0.291 Chirality : 0.038 0.170 3104 Planarity : 0.004 0.039 3432 Dihedral : 6.569 59.664 2756 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.43 % Allowed : 16.24 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2412 helix: 0.37 (0.15), residues: 1344 sheet: -0.58 (0.51), residues: 84 loop : -2.57 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 583 HIS 0.003 0.001 HIS C 509 PHE 0.009 0.001 PHE B 574 TYR 0.013 0.001 TYR B 621 ARG 0.006 0.000 ARG A 470 *********************** 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 307 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 235 time to evaluate : 2.345 Fit side-chains revert: symmetry clash REVERT: A 340 MET cc_start: 0.8645 (tpp) cc_final: 0.8281 (tpp) REVERT: A 365 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8710 (tp) REVERT: A 483 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 591 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7662 (tp30) REVERT: B 418 GLN cc_start: 0.8448 (mt0) cc_final: 0.8228 (mt0) REVERT: B 515 GLU cc_start: 0.8244 (mp0) cc_final: 0.7884 (mp0) REVERT: B 591 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7659 (tp30) REVERT: B 592 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8890 (tp) REVERT: C 340 MET cc_start: 0.8635 (tpp) cc_final: 0.8243 (tpp) REVERT: C 515 GLU cc_start: 0.8174 (mp0) cc_final: 0.7880 (mp0) REVERT: C 591 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7644 (tp30) REVERT: C 592 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 340 MET cc_start: 0.8652 (tpp) cc_final: 0.8277 (tpp) REVERT: D 365 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8689 (tp) REVERT: D 390 LEU cc_start: 0.9034 (mm) cc_final: 0.8660 (mt) REVERT: D 515 GLU cc_start: 0.8171 (mp0) cc_final: 0.7963 (mp0) REVERT: D 591 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7619 (tp30) REVERT: D 625 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8022 (mm) outliers start: 72 outliers final: 45 residues processed: 287 average time/residue: 0.2482 time to fit residues: 118.0648 Evaluate side-chains 275 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.0670 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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 C 509 HIS D 257 GLN D 310 GLN D 509 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20084 Z= 0.238 Angle : 0.656 16.956 27272 Z= 0.314 Chirality : 0.040 0.185 3104 Planarity : 0.004 0.041 3432 Dihedral : 6.688 59.551 2756 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.05 % Allowed : 16.86 % Favored : 80.10 % 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: -1.13 (0.17), residues: 2412 helix: 0.44 (0.15), residues: 1352 sheet: -0.58 (0.51), residues: 84 loop : -2.54 (0.17), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 583 HIS 0.003 0.001 HIS B 582 PHE 0.015 0.001 PHE B 553 TYR 0.018 0.001 TYR D 415 ARG 0.005 0.000 ARG A 470 *********************** 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 287 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 223 time to evaluate : 2.242 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.7982 (tpp) cc_final: 0.7757 (tpt) REVERT: A 340 MET cc_start: 0.8693 (tpp) cc_final: 0.8348 (tpp) REVERT: A 365 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 591 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7792 (tp30) REVERT: A 625 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8136 (mm) REVERT: B 418 GLN cc_start: 0.8499 (mt0) cc_final: 0.8205 (mt0) REVERT: B 515 GLU cc_start: 0.8183 (mp0) cc_final: 0.7963 (mp0) REVERT: B 591 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7764 (tp30) REVERT: B 592 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.8915 (tp) REVERT: B 625 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8141 (mm) REVERT: C 340 MET cc_start: 0.8680 (tpp) cc_final: 0.8313 (tpp) REVERT: C 515 GLU cc_start: 0.8144 (mp0) cc_final: 0.7942 (mp0) REVERT: C 591 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7744 (tp30) REVERT: C 592 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8912 (tp) REVERT: C 625 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8115 (mm) REVERT: D 340 MET cc_start: 0.8716 (tpp) cc_final: 0.8359 (tpp) REVERT: D 365 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8674 (tp) REVERT: D 390 LEU cc_start: 0.9072 (mm) cc_final: 0.8703 (mt) REVERT: D 591 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7768 (tp30) REVERT: D 625 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8011 (mm) outliers start: 64 outliers final: 50 residues processed: 272 average time/residue: 0.2465 time to fit residues: 111.3951 Evaluate side-chains 269 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 625 LEU 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: 0.0570 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 509 HIS B 157 HIS C 157 HIS D 157 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20084 Z= 0.267 Angle : 0.694 17.090 27272 Z= 0.333 Chirality : 0.041 0.186 3104 Planarity : 0.004 0.041 3432 Dihedral : 6.800 59.621 2756 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.14 % Allowed : 17.52 % Favored : 79.33 % 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: -1.09 (0.17), residues: 2412 helix: 0.48 (0.15), residues: 1348 sheet: -0.67 (0.49), residues: 84 loop : -2.51 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.004 0.001 HIS A 509 PHE 0.009 0.001 PHE C 244 TYR 0.015 0.001 TYR C 623 ARG 0.005 0.000 ARG A 470 *********************** 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 280 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 214 time to evaluate : 2.432 Fit side-chains REVERT: A 340 MET cc_start: 0.8719 (tpp) cc_final: 0.8398 (tpp) REVERT: A 365 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8695 (tp) REVERT: A 447 MET cc_start: 0.8380 (mtt) cc_final: 0.8115 (mtt) REVERT: A 483 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8346 (tm-30) REVERT: A 591 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7822 (tp30) REVERT: A 625 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8003 (mm) REVERT: B 418 GLN cc_start: 0.8502 (mt0) cc_final: 0.8240 (mt0) REVERT: B 515 GLU cc_start: 0.8179 (mp0) cc_final: 0.7964 (mp0) REVERT: B 591 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7850 (tp30) REVERT: B 592 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8954 (tp) REVERT: B 625 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8128 (mm) REVERT: C 340 MET cc_start: 0.8701 (tpp) cc_final: 0.8358 (tpp) REVERT: C 447 MET cc_start: 0.8356 (mtt) cc_final: 0.8103 (mtt) REVERT: C 591 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7849 (tp30) REVERT: C 592 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8964 (tp) REVERT: C 625 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8095 (mm) REVERT: D 340 MET cc_start: 0.8711 (tpp) cc_final: 0.8387 (tpp) REVERT: D 365 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8665 (tp) REVERT: D 390 LEU cc_start: 0.9106 (mm) cc_final: 0.8719 (mt) REVERT: D 447 MET cc_start: 0.8365 (mtt) cc_final: 0.8108 (mtt) REVERT: D 591 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7806 (tp30) REVERT: D 625 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8088 (mm) outliers start: 66 outliers final: 54 residues processed: 264 average time/residue: 0.2464 time to fit residues: 109.4263 Evaluate side-chains 272 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 0.2980 chunk 202 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 129 optimal weight: 0.0980 chunk 93 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 0.3980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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: 0.8491 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20084 Z= 0.183 Angle : 0.645 17.400 27272 Z= 0.305 Chirality : 0.039 0.186 3104 Planarity : 0.004 0.041 3432 Dihedral : 6.606 59.909 2756 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.81 % Allowed : 18.05 % Favored : 79.14 % 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: -0.96 (0.17), residues: 2412 helix: 0.54 (0.15), residues: 1356 sheet: -0.44 (0.50), residues: 84 loop : -2.42 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 583 HIS 0.002 0.001 HIS D 582 PHE 0.009 0.001 PHE B 553 TYR 0.016 0.001 TYR B 415 ARG 0.005 0.000 ARG A 470 *********************** 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 283 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 224 time to evaluate : 2.040 Fit side-chains REVERT: A 340 MET cc_start: 0.8652 (tpp) cc_final: 0.8297 (tpp) REVERT: A 365 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 447 MET cc_start: 0.8387 (mtt) cc_final: 0.8151 (mtt) REVERT: A 483 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 591 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7616 (tp30) REVERT: A 625 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 418 GLN cc_start: 0.8617 (mt0) cc_final: 0.8373 (mt0) REVERT: B 515 GLU cc_start: 0.8187 (mp0) cc_final: 0.7963 (mp0) REVERT: B 591 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7681 (tp30) REVERT: B 592 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8917 (tp) REVERT: C 340 MET cc_start: 0.8621 (tpp) cc_final: 0.8241 (tpp) REVERT: C 447 MET cc_start: 0.8402 (mtt) cc_final: 0.8147 (mtt) REVERT: C 591 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7672 (tp30) REVERT: C 592 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8933 (tp) REVERT: D 340 MET cc_start: 0.8646 (tpp) cc_final: 0.8283 (tpp) REVERT: D 365 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8679 (tp) REVERT: D 390 LEU cc_start: 0.9050 (mm) cc_final: 0.8681 (mt) REVERT: D 447 MET cc_start: 0.8362 (mtt) cc_final: 0.8116 (mtp) REVERT: D 591 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7617 (tp30) REVERT: D 625 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8042 (mm) outliers start: 59 outliers final: 46 residues processed: 267 average time/residue: 0.2534 time to fit residues: 112.2598 Evaluate side-chains 271 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 219 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 439 THR Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN D 257 GLN D 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20084 Z= 0.164 Angle : 0.661 17.160 27272 Z= 0.306 Chirality : 0.038 0.185 3104 Planarity : 0.004 0.044 3432 Dihedral : 6.437 59.925 2756 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.81 % Allowed : 18.24 % Favored : 78.95 % 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: -0.82 (0.17), residues: 2412 helix: 0.64 (0.15), residues: 1356 sheet: -0.24 (0.51), residues: 84 loop : -2.36 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 583 HIS 0.003 0.001 HIS A 582 PHE 0.010 0.001 PHE B 574 TYR 0.012 0.001 TYR A 415 ARG 0.005 0.000 ARG A 470 ********************** 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 294 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 235 time to evaluate : 2.320 Fit side-chains REVERT: A 340 MET cc_start: 0.8664 (tpp) cc_final: 0.8282 (tpp) REVERT: A 365 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 591 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7555 (tp30) REVERT: A 625 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 264 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8365 (ttmt) REVERT: B 418 GLN cc_start: 0.8627 (mt0) cc_final: 0.8424 (mt0) REVERT: B 515 GLU cc_start: 0.8179 (mp0) cc_final: 0.7955 (mp0) REVERT: B 591 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7628 (tp30) REVERT: B 592 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8879 (tp) REVERT: B 625 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8052 (mm) REVERT: C 340 MET cc_start: 0.8646 (tpp) cc_final: 0.8255 (tpp) REVERT: C 447 MET cc_start: 0.8387 (mtt) cc_final: 0.8153 (mtp) REVERT: C 591 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7617 (tp30) REVERT: C 592 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8890 (tp) REVERT: C 625 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7994 (mm) REVERT: D 340 MET cc_start: 0.8657 (tpp) cc_final: 0.8272 (tpp) REVERT: D 390 LEU cc_start: 0.9048 (mm) cc_final: 0.8681 (mt) REVERT: D 447 MET cc_start: 0.8388 (mtt) cc_final: 0.8154 (mtp) REVERT: D 591 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7550 (tp30) REVERT: D 625 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7967 (mm) outliers start: 59 outliers final: 42 residues processed: 282 average time/residue: 0.2607 time to fit residues: 120.8147 Evaluate side-chains 274 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 557 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain D residue 29 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 337 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 0.0040 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 257 GLN D 310 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.084171 restraints weight = 42451.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.086213 restraints weight = 24440.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087469 restraints weight = 17113.681| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20084 Z= 0.183 Angle : 0.646 17.245 27272 Z= 0.304 Chirality : 0.039 0.194 3104 Planarity : 0.004 0.042 3432 Dihedral : 6.377 59.955 2756 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.76 % Allowed : 18.14 % Favored : 79.10 % 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: -0.73 (0.17), residues: 2412 helix: 0.71 (0.15), residues: 1356 sheet: -0.20 (0.52), residues: 84 loop : -2.32 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 583 HIS 0.002 0.001 HIS C 582 PHE 0.008 0.001 PHE B 574 TYR 0.020 0.001 TYR B 621 ARG 0.005 0.000 ARG A 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.32 seconds wall clock time: 59 minutes 27.00 seconds (3567.00 seconds total)