Starting phenix.real_space_refine on Mon Mar 18 02:14:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffl_29046/03_2024/8ffl_29046_updated.pdb" } resolution = 3.47 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= 0.000 sd= 0.004 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 4 5.49 5 S 110 5.16 5 C 12910 2.51 5 N 3263 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "D GLU 685": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19683 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4864 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 582} Chain breaks: 7 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4884 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 585} Chain breaks: 7 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4903 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4892 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 585} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'PHE:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.23, per 1000 atoms: 0.52 Number of scatterers: 19683 At special positions: 0 Unit cell: (129.47, 128.4, 110.21, 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 110 16.00 P 4 15.00 O 3396 8.00 N 3263 7.00 C 12910 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: 7.67 Conformation dependent library (CDL) restraints added in 3.4 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 119 helices and 4 sheets defined 59.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 322 through 326 Proline residue: A 325 - end of helix No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 378 through 413 removed outlier: 5.257A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 465 removed outlier: 7.055A pdb=" N LEU A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 492 removed outlier: 7.049A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 518 removed outlier: 3.541A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 520 through 523 No H-bonds generated for 'chain 'A' and resid 520 through 523' Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.658A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 619 through 650 removed outlier: 4.090A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 673 removed outlier: 4.465A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.619A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.638A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 321 through 326 Proline residue: B 325 - end of helix Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 390 through 412 Processing helix chain 'B' and resid 430 through 465 removed outlier: 7.156A pdb=" N LEU B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N PHE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 471 through 492 Processing helix chain 'B' and resid 495 through 518 Proline residue: B 499 - end of helix removed outlier: 3.566A pdb=" N TYR B 515 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 523 No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 529 through 559 removed outlier: 5.578A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.783A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 671 Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.883A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 378 through 412 removed outlier: 5.464A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 465 removed outlier: 7.004A pdb=" N LEU C 461 " --> pdb=" O TRP C 457 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 Processing helix chain 'C' and resid 495 through 518 removed outlier: 3.968A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.624A pdb=" N TYR C 515 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 530 through 533 No H-bonds generated for 'chain 'C' and resid 530 through 533' Processing helix chain 'C' and resid 537 through 559 removed outlier: 4.300A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 604 Processing helix chain 'C' and resid 619 through 649 removed outlier: 3.715A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 673 removed outlier: 4.400A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.771A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 109 through 111 No H-bonds generated for 'chain 'D' and resid 109 through 111' Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 280 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 321 through 326 Proline residue: D 325 - end of helix Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.127A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 413 removed outlier: 5.257A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 465 removed outlier: 7.138A pdb=" N LEU D 461 " --> pdb=" O TRP D 457 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 removed outlier: 4.197A pdb=" N PHE D 476 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 518 removed outlier: 4.313A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.516A pdb=" N TYR D 515 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 523 No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 528 through 559 removed outlier: 3.561A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 Processing helix chain 'D' and resid 619 through 650 removed outlier: 3.963A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 671 Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.676A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 687 through 690 removed outlier: 6.022A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.115A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 692 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 690 removed outlier: 6.105A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 687 through 690 removed outlier: 6.034A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) 956 hydrogen bonds defined for protein. 2592 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: 6.06 Time building geometry restraints manager: 8.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3391 1.33 - 1.45: 5396 1.45 - 1.57: 11195 1.57 - 1.70: 8 1.70 - 1.82: 168 Bond restraints: 20158 Sorted by residual: bond pdb=" CG MET C 640 " pdb=" SD MET C 640 " ideal model delta sigma weight residual 1.803 1.765 0.038 2.50e-02 1.60e+03 2.29e+00 bond pdb=" CA CYS D 282 " pdb=" CB CYS D 282 " ideal model delta sigma weight residual 1.525 1.534 -0.009 8.30e-03 1.45e+04 1.23e+00 bond pdb=" CB ASN C 639 " pdb=" CG ASN C 639 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.00e+00 bond pdb=" CB PRO A 283 " pdb=" CG PRO A 283 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.98e-01 bond pdb=" CA ASN C 639 " pdb=" CB ASN C 639 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.85e-01 ... (remaining 20153 not shown) Histogram of bond angle deviations from ideal: 93.21 - 101.38: 51 101.38 - 109.55: 1539 109.55 - 117.73: 13442 117.73 - 125.90: 11895 125.90 - 134.07: 395 Bond angle restraints: 27322 Sorted by residual: angle pdb=" N VAL A 649 " pdb=" CA VAL A 649 " pdb=" C VAL A 649 " ideal model delta sigma weight residual 112.80 107.63 5.17 1.15e+00 7.56e-01 2.02e+01 angle pdb=" CB MET A 433 " pdb=" CG MET A 433 " pdb=" SD MET A 433 " ideal model delta sigma weight residual 112.70 122.04 -9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 112.29 109.71 2.58 9.40e-01 1.13e+00 7.52e+00 angle pdb=" CA MET B 404 " pdb=" CB MET B 404 " pdb=" CG MET B 404 " ideal model delta sigma weight residual 114.10 109.41 4.69 2.00e+00 2.50e-01 5.50e+00 angle pdb=" N CYS C 678 " pdb=" CA CYS C 678 " pdb=" C CYS C 678 " ideal model delta sigma weight residual 107.23 111.10 -3.87 1.67e+00 3.59e-01 5.38e+00 ... (remaining 27317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10725 17.99 - 35.98: 881 35.98 - 53.97: 176 53.97 - 71.97: 55 71.97 - 89.96: 13 Dihedral angle restraints: 11850 sinusoidal: 4769 harmonic: 7081 Sorted by residual: dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLY B 210 " pdb=" CA GLY B 210 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2073 0.030 - 0.060: 731 0.060 - 0.089: 217 0.089 - 0.119: 71 0.119 - 0.149: 3 Chirality restraints: 3095 Sorted by residual: chirality pdb=" CA MET B 404 " pdb=" N MET B 404 " pdb=" C MET B 404 " pdb=" CB MET B 404 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CB VAL B 84 " pdb=" CA VAL B 84 " pdb=" CG1 VAL B 84 " pdb=" CG2 VAL B 84 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA VAL A 649 " pdb=" N VAL A 649 " pdb=" C VAL A 649 " pdb=" CB VAL A 649 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 3092 not shown) Planarity restraints: 3358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 282 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 283 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 649 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.94e+00 pdb=" C VAL A 649 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 649 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN A 650 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 212 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 213 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.019 5.00e-02 4.00e+02 ... (remaining 3355 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1437 2.74 - 3.28: 19863 3.28 - 3.82: 33026 3.82 - 4.36: 39436 4.36 - 4.90: 68429 Nonbonded interactions: 162191 Sorted by model distance: nonbonded pdb=" OE1 GLU C 113 " pdb=" OG1 THR C 116 " model vdw 2.199 2.440 nonbonded pdb=" O PRO D 325 " pdb=" NH2 ARG D 702 " model vdw 2.271 2.520 nonbonded pdb=" OG1 THR D 604 " pdb=" OH TYR D 629 " model vdw 2.276 2.440 nonbonded pdb=" OG SER D 646 " pdb=" OE2 GLU D 647 " model vdw 2.277 2.440 nonbonded pdb=" O PRO C 325 " pdb=" NH2 ARG C 702 " model vdw 2.286 2.520 ... (remaining 162186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 89 or (resid 90 and (name N or name CA or name \ C or name O or name CB )) or resid 91 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 414 or (resid 429 and \ (name N or name CA or name C or name O or name CB )) or resid 430 through 463 o \ r (resid 464 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 65 through 494 or (resid 495 and (name N or name CA or name C or name O or name \ CB )) or resid 496 through 530 or (resid 531 and (name N or name CA or name C or \ name O or name CB )) or resid 532 through 534 or (resid 535 and (name N or name \ CA or name C or name O or name CB )) or resid 536 through 611 or (resid 612 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 48 through 720 or resid 801)) selection = (chain 'B' and (resid 31 through 45 or resid 75 through 143 or (resid 144 and (n \ ame N or name CA or name C or name O or name CB )) or resid 145 through 414 or ( \ resid 429 and (name N or name CA or name C or name O or name CB )) or resid 430 \ through 494 or (resid 495 and (name N or name CA or name C or name O or name CB \ )) or resid 496 through 524 or resid 529 through 530 or (resid 531 and (name N o \ r name CA or name C or name O or name CB )) or resid 532 through 534 or (resid 5 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 536 through \ 598 or (resid 599 and (name N or name CA or name C or name O or name CB )) or r \ esid 600 through 608 or (resid 609 and (name N or name CA or name C or name O or \ name CB )) or resid 610 through 716 or (resid 717 and (name N or name CA or nam \ e C or name O or name CB )) or resid 718 through 720 or resid 801)) selection = (chain 'C' and (resid 31 through 45 or resid 75 through 89 or (resid 90 and (nam \ e N or name CA or name C or name O or name CB )) or resid 91 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 261 or (resid 262 and (name N or name CA or name C or name O o \ r name CB )) or resid 263 through 414 or (resid 429 and (name N or name CA or na \ me C or name O or name CB )) or resid 430 through 463 or (resid 464 and (name N \ or name CA or name C or name O or name CB )) or resid 465 through 494 or (resid \ 495 and (name N or name CA or name C or name O or name CB )) or resid 496 throug \ h 524 or resid 529 through 598 or (resid 599 and (name N or name CA or name C or \ name O or name CB )) or resid 600 through 608 or (resid 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 611 or (resid 612 and \ (name N or name CA or name C or name O or name CB )) or resid 616 through 646 o \ r (resid 647 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 48 through 652 or resid 655 through 720 or resid 801)) selection = (chain 'D' and (resid 31 through 45 or resid 75 through 89 or (resid 90 and (nam \ e N or name CA or name C or name O or name CB )) or resid 91 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 throug \ h 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 463 or (resid 464 and (name N or name CA or name C or name O o \ r name CB )) or resid 465 through 524 or resid 529 through 530 or (resid 531 and \ (name N or name CA or name C or name O or name CB )) or resid 532 through 534 o \ r (resid 535 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 36 through 598 or (resid 599 and (name N or name CA or name C or name O or name \ CB )) or resid 600 through 611 or (resid 612 and (name N or name CA or name C or \ name O or name CB )) or resid 616 through 646 or (resid 647 and (name N or name \ CA or name C or name O or name CB )) or resid 648 through 716 or (resid 717 and \ (name N or name CA or name C or name O or name CB )) or resid 718 through 720 o \ r resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.860 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 52.900 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20158 Z= 0.154 Angle : 0.489 9.340 27322 Z= 0.277 Chirality : 0.035 0.149 3095 Planarity : 0.003 0.053 3358 Dihedral : 14.395 89.956 7262 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.17), residues: 2364 helix: 1.79 (0.14), residues: 1442 sheet: 0.92 (0.54), residues: 116 loop : 0.08 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 657 HIS 0.008 0.001 HIS A 269 PHE 0.015 0.001 PHE C 429 TYR 0.013 0.001 TYR C 98 ARG 0.006 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.977 Fit side-chains REVERT: A 433 MET cc_start: 0.6934 (mmp) cc_final: 0.6481 (ptt) REVERT: B 433 MET cc_start: 0.6629 (ttm) cc_final: 0.6201 (ttp) REVERT: C 289 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8077 (mt-10) REVERT: C 645 MET cc_start: 0.7207 (mtt) cc_final: 0.6980 (mtp) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.2896 time to fit residues: 70.0755 Evaluate side-chains 140 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.0270 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 overall best weight: 3.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS C 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20158 Z= 0.319 Angle : 0.516 6.226 27322 Z= 0.268 Chirality : 0.039 0.144 3095 Planarity : 0.004 0.035 3358 Dihedral : 7.222 67.118 2743 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.19 % Allowed : 7.99 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.58 (0.18), residues: 2364 helix: 1.66 (0.14), residues: 1454 sheet: 0.77 (0.52), residues: 116 loop : 0.07 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 333 HIS 0.008 0.001 HIS A 269 PHE 0.023 0.002 PHE A 540 TYR 0.015 0.001 TYR D 471 ARG 0.004 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.132 Fit side-chains REVERT: B 404 MET cc_start: 0.9062 (mmm) cc_final: 0.8850 (mmt) REVERT: C 519 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7368 (p90) REVERT: C 540 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: C 640 MET cc_start: 0.7513 (tpp) cc_final: 0.7186 (mmt) REVERT: C 644 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8431 (tt) REVERT: C 645 MET cc_start: 0.7232 (mtt) cc_final: 0.7000 (mtp) outliers start: 25 outliers final: 11 residues processed: 165 average time/residue: 0.2820 time to fit residues: 75.7978 Evaluate side-chains 154 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 540 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 0.1980 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN B 650 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20158 Z= 0.218 Angle : 0.445 5.919 27322 Z= 0.233 Chirality : 0.036 0.164 3095 Planarity : 0.004 0.038 3358 Dihedral : 7.012 65.231 2743 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.28 % Allowed : 8.66 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.18), residues: 2364 helix: 1.73 (0.14), residues: 1450 sheet: 0.68 (0.51), residues: 116 loop : -0.01 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 333 HIS 0.007 0.001 HIS A 269 PHE 0.022 0.001 PHE A 540 TYR 0.013 0.001 TYR C 98 ARG 0.003 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 2.126 Fit side-chains REVERT: C 182 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8353 (tt) REVERT: C 519 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7406 (p90) REVERT: C 540 PHE cc_start: 0.7791 (m-10) cc_final: 0.7532 (m-80) REVERT: C 644 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8409 (tt) REVERT: C 645 MET cc_start: 0.7367 (mtt) cc_final: 0.7140 (mtp) outliers start: 27 outliers final: 12 residues processed: 166 average time/residue: 0.2989 time to fit residues: 80.0970 Evaluate side-chains 155 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20158 Z= 0.383 Angle : 0.538 7.668 27322 Z= 0.275 Chirality : 0.040 0.181 3095 Planarity : 0.004 0.043 3358 Dihedral : 7.267 59.822 2743 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.67 % Allowed : 10.13 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2364 helix: 1.51 (0.14), residues: 1450 sheet: 0.49 (0.50), residues: 114 loop : -0.16 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 333 HIS 0.008 0.001 HIS A 269 PHE 0.027 0.002 PHE A 540 TYR 0.018 0.002 TYR D 471 ARG 0.004 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 2.280 Fit side-chains REVERT: C 182 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 540 PHE cc_start: 0.7845 (m-10) cc_final: 0.7617 (m-80) REVERT: C 644 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8510 (tt) REVERT: D 493 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6669 (mm-30) outliers start: 35 outliers final: 18 residues processed: 162 average time/residue: 0.2832 time to fit residues: 74.5543 Evaluate side-chains 151 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 7.9990 chunk 131 optimal weight: 0.0570 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20158 Z= 0.199 Angle : 0.439 7.007 27322 Z= 0.229 Chirality : 0.036 0.154 3095 Planarity : 0.004 0.041 3358 Dihedral : 6.980 59.171 2743 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.38 % Allowed : 10.85 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.52 (0.18), residues: 2364 helix: 1.75 (0.14), residues: 1438 sheet: 0.46 (0.50), residues: 114 loop : -0.17 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.019 0.001 PHE A 540 TYR 0.015 0.001 TYR C 98 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 2.339 Fit side-chains REVERT: B 128 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 404 MET cc_start: 0.9139 (mmt) cc_final: 0.8871 (mmt) REVERT: C 182 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8333 (tt) REVERT: C 644 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8511 (tt) outliers start: 29 outliers final: 18 residues processed: 165 average time/residue: 0.2840 time to fit residues: 75.9662 Evaluate side-chains 162 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 6.9990 chunk 208 optimal weight: 0.0060 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 0.0020 overall best weight: 1.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20158 Z= 0.158 Angle : 0.411 8.152 27322 Z= 0.215 Chirality : 0.035 0.154 3095 Planarity : 0.003 0.040 3358 Dihedral : 6.623 58.923 2743 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.52 % Allowed : 10.89 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.66 (0.18), residues: 2364 helix: 1.86 (0.14), residues: 1445 sheet: 0.46 (0.50), residues: 114 loop : -0.12 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.014 0.001 PHE A 540 TYR 0.011 0.001 TYR B 228 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 3.176 Fit side-chains REVERT: A 212 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8856 (mt) REVERT: C 182 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8320 (tt) REVERT: C 289 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8021 (mt-10) REVERT: C 639 ASN cc_start: 0.7804 (t0) cc_final: 0.7466 (t0) outliers start: 32 outliers final: 19 residues processed: 174 average time/residue: 0.3030 time to fit residues: 84.8536 Evaluate side-chains 167 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 539 ARG Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20158 Z= 0.219 Angle : 0.449 8.658 27322 Z= 0.229 Chirality : 0.036 0.167 3095 Planarity : 0.004 0.040 3358 Dihedral : 6.588 59.753 2743 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.52 % Allowed : 10.51 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.18), residues: 2364 helix: 1.83 (0.14), residues: 1443 sheet: 0.44 (0.50), residues: 114 loop : -0.16 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.006 0.001 HIS A 269 PHE 0.017 0.001 PHE A 540 TYR 0.011 0.001 TYR A 544 ARG 0.002 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 2.007 Fit side-chains REVERT: B 404 MET cc_start: 0.9063 (mmt) cc_final: 0.8700 (mmt) REVERT: C 91 GLU cc_start: 0.7615 (mp0) cc_final: 0.7349 (mp0) REVERT: C 182 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 639 ASN cc_start: 0.7753 (t0) cc_final: 0.7422 (t0) REVERT: D 280 ARG cc_start: 0.6642 (ttp-110) cc_final: 0.6420 (mtm110) outliers start: 32 outliers final: 21 residues processed: 174 average time/residue: 0.2938 time to fit residues: 81.3957 Evaluate side-chains 170 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 649 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8409 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20158 Z= 0.208 Angle : 0.440 8.763 27322 Z= 0.225 Chirality : 0.036 0.159 3095 Planarity : 0.003 0.040 3358 Dihedral : 6.509 59.794 2743 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.43 % Allowed : 10.80 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.18), residues: 2364 helix: 1.82 (0.14), residues: 1443 sheet: 0.41 (0.50), residues: 114 loop : -0.15 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.016 0.001 PHE A 540 TYR 0.011 0.001 TYR A 544 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 2.196 Fit side-chains REVERT: A 193 ARG cc_start: 0.8019 (mtm-85) cc_final: 0.7613 (mtp-110) REVERT: A 645 MET cc_start: 0.7901 (ttm) cc_final: 0.7672 (ttm) REVERT: B 404 MET cc_start: 0.9134 (mmt) cc_final: 0.8878 (mmt) REVERT: C 91 GLU cc_start: 0.7567 (mp0) cc_final: 0.7269 (mp0) REVERT: C 182 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (tt) REVERT: D 280 ARG cc_start: 0.6636 (ttp-110) cc_final: 0.6408 (mtm110) outliers start: 30 outliers final: 25 residues processed: 175 average time/residue: 0.2882 time to fit residues: 80.6932 Evaluate side-chains 175 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 9.9990 chunk 215 optimal weight: 0.0870 chunk 129 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20158 Z= 0.136 Angle : 0.412 9.142 27322 Z= 0.212 Chirality : 0.035 0.147 3095 Planarity : 0.003 0.039 3358 Dihedral : 6.223 58.894 2743 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.14 % Allowed : 11.27 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.75 (0.18), residues: 2364 helix: 1.93 (0.14), residues: 1444 sheet: 0.45 (0.50), residues: 114 loop : -0.09 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.016 0.001 PHE A 540 TYR 0.013 0.001 TYR C 98 ARG 0.002 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 2.356 Fit side-chains REVERT: A 645 MET cc_start: 0.7834 (ttm) cc_final: 0.7553 (ttm) REVERT: B 404 MET cc_start: 0.9083 (mmt) cc_final: 0.8844 (mmt) REVERT: C 91 GLU cc_start: 0.7543 (mp0) cc_final: 0.7247 (mp0) REVERT: C 182 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8307 (tt) outliers start: 24 outliers final: 19 residues processed: 168 average time/residue: 0.2742 time to fit residues: 75.0325 Evaluate side-chains 167 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20158 Z= 0.223 Angle : 0.446 9.257 27322 Z= 0.228 Chirality : 0.036 0.157 3095 Planarity : 0.003 0.040 3358 Dihedral : 6.243 58.539 2743 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.33 % Allowed : 11.32 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.67 (0.18), residues: 2364 helix: 1.89 (0.14), residues: 1440 sheet: 0.40 (0.50), residues: 114 loop : -0.13 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.019 0.001 PHE A 540 TYR 0.012 0.001 TYR C 98 ARG 0.002 0.000 ARG D 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 2.114 Fit side-chains REVERT: A 645 MET cc_start: 0.7818 (ttm) cc_final: 0.7598 (ttm) REVERT: B 102 ASN cc_start: 0.6469 (OUTLIER) cc_final: 0.6256 (m-40) REVERT: C 91 GLU cc_start: 0.7561 (mp0) cc_final: 0.7246 (mp0) REVERT: C 182 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8336 (tt) REVERT: D 493 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6547 (mm-30) outliers start: 28 outliers final: 23 residues processed: 168 average time/residue: 0.2787 time to fit residues: 76.2626 Evaluate side-chains 172 residues out of total 2169 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 639 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 486 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 493 GLU Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 195 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095333 restraints weight = 30351.283| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.60 r_work: 0.2949 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20158 Z= 0.182 Angle : 0.433 9.616 27322 Z= 0.222 Chirality : 0.035 0.157 3095 Planarity : 0.003 0.040 3358 Dihedral : 6.157 58.748 2743 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.19 % Allowed : 11.47 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.18), residues: 2364 helix: 1.90 (0.14), residues: 1437 sheet: 0.41 (0.50), residues: 114 loop : -0.11 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.005 0.001 HIS A 269 PHE 0.018 0.001 PHE A 540 TYR 0.012 0.001 TYR C 98 ARG 0.002 0.000 ARG A 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3373.80 seconds wall clock time: 62 minutes 26.53 seconds (3746.53 seconds total)