Starting phenix.real_space_refine on Mon Mar 18 09:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/03_2024/8eks_28212_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.065 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 112 5.16 5 C 13364 2.51 5 N 3440 2.21 5 O 3564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 91": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 672": "OE1" <-> "OE2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 672": "OE1" <-> "OE2" Residue "B GLU 708": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C GLU 672": "OE1" <-> "OE2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D GLU 672": "OE1" <-> "OE2" Residue "D GLU 708": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20484 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5086 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5086 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5086 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5086 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 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: 10.86, per 1000 atoms: 0.53 Number of scatterers: 20484 At special positions: 0 Unit cell: (138.03, 138.03, 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 112 16.00 P 4 15.00 O 3564 8.00 N 3440 7.00 C 13364 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: 7.91 Conformation dependent library (CDL) restraints added in 3.3 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 4 sheets defined 57.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 134 through 145 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.507A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) 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 230 Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.591A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.602A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) 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 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 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 388 Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 429 through 458 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.821A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 Processing helix chain 'A' and resid 495 through 518 removed outlier: 3.567A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.724A pdb=" N VAL A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 503 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 504 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 508 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) 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 561 removed outlier: 3.779A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 619 through 650 Processing helix chain 'A' and resid 656 through 673 removed outlier: 3.837A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.642A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.545A 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 89 through 92 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 134 through 145 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.507A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.591A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.602A 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 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' 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 429 through 458 Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.821A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 Processing helix chain 'B' and resid 495 through 518 removed outlier: 3.567A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.724A pdb=" N VAL B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 503 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 504 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 508 " --> pdb=" O LEU B 505 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (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 530 through 561 removed outlier: 3.779A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 619 through 650 Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.837A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.642A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 134 through 145 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.507A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.591A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.602A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) 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 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 388 Processing helix chain 'C' and resid 390 through 412 Processing helix chain 'C' and resid 429 through 458 Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.821A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 Processing helix chain 'C' and resid 495 through 518 removed outlier: 3.567A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.724A pdb=" N VAL C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 503 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 504 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 508 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (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 561 removed outlier: 3.779A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 604 Processing helix chain 'C' and resid 619 through 650 Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.837A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.642A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.545A 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 89 through 92 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 134 through 145 Proline residue: D 138 - end of helix Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.507A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) 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 230 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.591A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.602A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) 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 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 369 through 372 No H-bonds generated for 'chain 'D' and resid 369 through 372' Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 390 through 412 Processing helix chain 'D' and resid 429 through 458 Processing helix chain 'D' and resid 460 through 465 removed outlier: 3.821A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 Processing helix chain 'D' and resid 495 through 518 removed outlier: 3.567A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.724A pdb=" N VAL D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 503 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER D 504 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 508 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (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 530 through 561 removed outlier: 3.779A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 Processing helix chain 'D' and resid 619 through 650 Processing helix chain 'D' and resid 656 through 673 removed outlier: 3.837A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.642A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG A 702 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 690 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 704 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 688 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 702 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS C 690 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 704 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU C 688 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 702 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS D 690 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS D 704 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU D 688 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2628 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: 5.82 Time building geometry restraints manager: 8.60 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: 3192 1.31 - 1.44: 5876 1.44 - 1.56: 11736 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20984 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 20979 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.66: 568 106.66 - 113.50: 11392 113.50 - 120.33: 7404 120.33 - 127.17: 8792 127.17 - 134.01: 272 Bond angle restraints: 28428 Sorted by residual: angle pdb=" O3 PEX C 801 " pdb=" P1 PEX C 801 " pdb=" O8 PEX C 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX A 801 " pdb=" P1 PEX A 801 " pdb=" O8 PEX A 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 113.07 107.22 5.85 1.37e+00 5.33e-01 1.82e+01 ... (remaining 28423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 11896 26.25 - 52.50: 476 52.50 - 78.74: 28 78.74 - 104.99: 20 104.99 - 131.24: 4 Dihedral angle restraints: 12424 sinusoidal: 5116 harmonic: 7308 Sorted by residual: dihedral pdb=" O4 PEX D 801 " pdb=" C2 PEX D 801 " pdb=" C3 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O4 PEX C 801 " pdb=" C2 PEX C 801 " pdb=" C3 PEX C 801 " pdb=" O6 PEX C 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O4 PEX A 801 " pdb=" C2 PEX A 801 " pdb=" C3 PEX A 801 " pdb=" O6 PEX A 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 12421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2668 0.049 - 0.098: 456 0.098 - 0.147: 40 0.147 - 0.196: 4 0.196 - 0.245: 4 Chirality restraints: 3172 Sorted by residual: chirality pdb=" CA ARG D 490 " pdb=" N ARG D 490 " pdb=" C ARG D 490 " pdb=" CB ARG D 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ARG B 490 " pdb=" N ARG B 490 " pdb=" C ARG B 490 " pdb=" CB ARG B 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ARG C 490 " pdb=" N ARG C 490 " pdb=" C ARG C 490 " pdb=" CB ARG C 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3169 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 414 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO D 415 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 414 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO C 415 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 414 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 415 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.021 5.00e-02 4.00e+02 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2516 2.75 - 3.29: 19888 3.29 - 3.83: 33316 3.83 - 4.36: 41456 4.36 - 4.90: 70716 Nonbonded interactions: 167892 Sorted by model distance: nonbonded pdb=" OG SER C 592 " pdb=" OD2 ASP C 595 " model vdw 2.215 2.440 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP A 595 " model vdw 2.215 2.440 nonbonded pdb=" OG SER D 592 " pdb=" OD2 ASP D 595 " model vdw 2.215 2.440 nonbonded pdb=" OG SER B 592 " pdb=" OD2 ASP B 595 " model vdw 2.215 2.440 nonbonded pdb=" O GLY D 131 " pdb=" OG SER D 176 " model vdw 2.293 2.440 ... (remaining 167887 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 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: 1.050 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: 6.260 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 52.680 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 0.003 0.072 20984 Z= 0.178 Angle : 0.617 16.243 28428 Z= 0.309 Chirality : 0.035 0.245 3172 Planarity : 0.004 0.039 3536 Dihedral : 13.549 131.241 7696 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.29 (0.13), residues: 2464 helix: -1.74 (0.09), residues: 1436 sheet: -0.79 (0.48), residues: 120 loop : -0.90 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 101 HIS 0.004 0.001 HIS A 251 PHE 0.010 0.001 PHE D 405 TYR 0.005 0.001 TYR C 514 ARG 0.009 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.535 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2999 time to fit residues: 89.7724 Evaluate side-chains 156 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 194 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 20984 Z= 0.485 Angle : 0.631 6.715 28428 Z= 0.316 Chirality : 0.042 0.150 3172 Planarity : 0.005 0.046 3536 Dihedral : 8.151 138.440 2856 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 5.98 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.35 (0.16), residues: 2464 helix: 0.19 (0.13), residues: 1468 sheet: -0.41 (0.57), residues: 84 loop : -0.73 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 677 HIS 0.011 0.002 HIS A 251 PHE 0.021 0.002 PHE C 319 TYR 0.017 0.002 TYR A 271 ARG 0.005 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 2.252 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 172 average time/residue: 0.3462 time to fit residues: 91.3360 Evaluate side-chains 160 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 439 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 225 optimal weight: 0.5980 chunk 243 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20984 Z= 0.202 Angle : 0.454 5.791 28428 Z= 0.226 Chirality : 0.036 0.153 3172 Planarity : 0.003 0.030 3536 Dihedral : 7.832 137.728 2856 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.27 % Allowed : 7.07 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.50 (0.17), residues: 2464 helix: 1.05 (0.14), residues: 1480 sheet: -0.21 (0.58), residues: 84 loop : -0.75 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 677 HIS 0.005 0.001 HIS D 251 PHE 0.010 0.001 PHE B 319 TYR 0.011 0.001 TYR C 544 ARG 0.003 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 2.475 Fit side-chains REVERT: A 433 MET cc_start: 0.7647 (tpt) cc_final: 0.7389 (tpt) REVERT: B 433 MET cc_start: 0.7649 (tpt) cc_final: 0.7393 (tpt) REVERT: C 433 MET cc_start: 0.7645 (tpt) cc_final: 0.7390 (tpt) REVERT: D 433 MET cc_start: 0.7644 (tpt) cc_final: 0.7388 (tpt) outliers start: 28 outliers final: 20 residues processed: 176 average time/residue: 0.3446 time to fit residues: 93.1310 Evaluate side-chains 156 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20984 Z= 0.268 Angle : 0.478 5.639 28428 Z= 0.238 Chirality : 0.037 0.123 3172 Planarity : 0.004 0.029 3536 Dihedral : 7.724 135.982 2856 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.63 % Allowed : 7.07 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.72 (0.17), residues: 2464 helix: 1.28 (0.14), residues: 1480 sheet: -0.13 (0.60), residues: 84 loop : -0.74 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 677 HIS 0.007 0.001 HIS D 251 PHE 0.012 0.001 PHE A 319 TYR 0.011 0.001 TYR C 544 ARG 0.003 0.000 ARG B 684 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 2.523 Fit side-chains REVERT: A 433 MET cc_start: 0.7711 (tpt) cc_final: 0.7477 (tpt) REVERT: B 433 MET cc_start: 0.7712 (tpt) cc_final: 0.7477 (tpt) REVERT: C 433 MET cc_start: 0.7709 (tpt) cc_final: 0.7476 (tpt) REVERT: D 433 MET cc_start: 0.7708 (tpt) cc_final: 0.7473 (tpt) outliers start: 36 outliers final: 16 residues processed: 180 average time/residue: 0.3156 time to fit residues: 90.1822 Evaluate side-chains 160 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 3 optimal weight: 0.0060 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 204 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20984 Z= 0.141 Angle : 0.402 5.166 28428 Z= 0.202 Chirality : 0.034 0.115 3172 Planarity : 0.003 0.029 3536 Dihedral : 7.247 134.594 2856 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.91 % Allowed : 8.88 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.19 (0.17), residues: 2464 helix: 1.67 (0.14), residues: 1484 sheet: 0.12 (0.61), residues: 84 loop : -0.61 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.004 0.001 HIS D 251 PHE 0.006 0.001 PHE A 705 TYR 0.008 0.001 TYR A 544 ARG 0.003 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 2.465 Fit side-chains REVERT: A 433 MET cc_start: 0.7615 (tpt) cc_final: 0.7356 (tpt) REVERT: B 433 MET cc_start: 0.7617 (tpt) cc_final: 0.7362 (tpt) REVERT: C 433 MET cc_start: 0.7614 (tpt) cc_final: 0.7356 (tpt) REVERT: D 433 MET cc_start: 0.7614 (tpt) cc_final: 0.7353 (tpt) outliers start: 20 outliers final: 12 residues processed: 180 average time/residue: 0.3190 time to fit residues: 89.0816 Evaluate side-chains 176 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20984 Z= 0.231 Angle : 0.452 5.355 28428 Z= 0.225 Chirality : 0.036 0.114 3172 Planarity : 0.003 0.028 3536 Dihedral : 7.214 132.146 2856 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 9.60 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2464 helix: 1.69 (0.14), residues: 1484 sheet: 0.06 (0.60), residues: 84 loop : -0.58 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 677 HIS 0.006 0.001 HIS C 251 PHE 0.009 0.001 PHE C 319 TYR 0.011 0.001 TYR C 544 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 2.398 Fit side-chains REVERT: A 41 ARG cc_start: 0.7459 (ttm170) cc_final: 0.6995 (ttt180) REVERT: B 41 ARG cc_start: 0.7458 (ttm170) cc_final: 0.6996 (ttt180) REVERT: C 41 ARG cc_start: 0.7463 (ttm170) cc_final: 0.6996 (ttt180) REVERT: D 41 ARG cc_start: 0.7464 (ttm170) cc_final: 0.6995 (ttt180) outliers start: 28 outliers final: 20 residues processed: 196 average time/residue: 0.3098 time to fit residues: 94.5601 Evaluate side-chains 188 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20984 Z= 0.166 Angle : 0.414 5.258 28428 Z= 0.206 Chirality : 0.035 0.112 3172 Planarity : 0.003 0.030 3536 Dihedral : 7.070 131.737 2856 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.09 % Allowed : 9.96 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.43 (0.17), residues: 2464 helix: 1.87 (0.14), residues: 1484 sheet: 0.23 (0.61), residues: 84 loop : -0.54 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 677 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE C 705 TYR 0.009 0.001 TYR C 544 ARG 0.004 0.000 ARG D 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 2.383 Fit side-chains REVERT: A 41 ARG cc_start: 0.7452 (ttm170) cc_final: 0.6993 (ttt180) REVERT: B 41 ARG cc_start: 0.7453 (ttm170) cc_final: 0.6994 (ttt180) REVERT: C 41 ARG cc_start: 0.7453 (ttm170) cc_final: 0.6992 (ttt180) REVERT: D 41 ARG cc_start: 0.7452 (ttm170) cc_final: 0.6991 (ttt180) outliers start: 24 outliers final: 20 residues processed: 188 average time/residue: 0.3198 time to fit residues: 93.5838 Evaluate side-chains 188 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.3980 chunk 95 optimal weight: 0.3980 chunk 142 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 22 optimal weight: 0.0030 chunk 187 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 overall best weight: 0.3648 ------------------------------------------------------------------------------- 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: 0.8203 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20984 Z= 0.108 Angle : 0.380 5.011 28428 Z= 0.190 Chirality : 0.034 0.111 3172 Planarity : 0.003 0.028 3536 Dihedral : 6.843 129.790 2856 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.72 % Allowed : 10.33 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.92 (0.17), residues: 2464 helix: 2.28 (0.14), residues: 1460 sheet: 0.48 (0.61), residues: 84 loop : -0.30 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 677 HIS 0.003 0.001 HIS B 251 PHE 0.005 0.001 PHE A 705 TYR 0.007 0.001 TYR D 271 ARG 0.006 0.000 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 2.401 Fit side-chains REVERT: A 37 SER cc_start: 0.8079 (t) cc_final: 0.7825 (p) REVERT: A 41 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7173 (mmt180) REVERT: B 37 SER cc_start: 0.8076 (t) cc_final: 0.7827 (p) REVERT: B 41 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7171 (mmt180) REVERT: C 37 SER cc_start: 0.8075 (t) cc_final: 0.7825 (p) REVERT: C 41 ARG cc_start: 0.7415 (ttm170) cc_final: 0.7170 (mmt180) REVERT: D 37 SER cc_start: 0.8075 (t) cc_final: 0.7823 (p) REVERT: D 41 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7171 (mmt180) outliers start: 16 outliers final: 12 residues processed: 196 average time/residue: 0.3385 time to fit residues: 101.9538 Evaluate side-chains 192 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 221 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20984 Z= 0.320 Angle : 0.512 5.556 28428 Z= 0.253 Chirality : 0.038 0.117 3172 Planarity : 0.004 0.032 3536 Dihedral : 7.079 126.756 2856 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.91 % Allowed : 10.46 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.35 (0.17), residues: 2464 helix: 1.79 (0.14), residues: 1488 sheet: 0.01 (0.60), residues: 84 loop : -0.53 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 677 HIS 0.008 0.001 HIS C 251 PHE 0.012 0.002 PHE C 311 TYR 0.013 0.002 TYR C 544 ARG 0.005 0.001 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.966 Fit side-chains REVERT: A 41 ARG cc_start: 0.7410 (ttm170) cc_final: 0.6968 (ttt180) REVERT: B 41 ARG cc_start: 0.7411 (ttm170) cc_final: 0.6969 (ttt180) REVERT: C 41 ARG cc_start: 0.7412 (ttm170) cc_final: 0.6971 (ttt180) REVERT: D 41 ARG cc_start: 0.7411 (ttm170) cc_final: 0.6969 (ttt180) outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 0.3242 time to fit residues: 92.4546 Evaluate side-chains 176 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.0370 chunk 143 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 chunk 227 optimal weight: 0.5980 chunk 196 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20984 Z= 0.135 Angle : 0.413 5.447 28428 Z= 0.206 Chirality : 0.034 0.111 3172 Planarity : 0.003 0.029 3536 Dihedral : 6.908 129.228 2856 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.77 % Allowed : 10.82 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.78 (0.17), residues: 2464 helix: 2.16 (0.14), residues: 1460 sheet: 0.26 (0.61), residues: 84 loop : -0.32 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 677 HIS 0.004 0.001 HIS D 251 PHE 0.007 0.001 PHE A 705 TYR 0.009 0.001 TYR C 544 ARG 0.006 0.000 ARG A 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 2.221 Fit side-chains REVERT: A 41 ARG cc_start: 0.7348 (ttm170) cc_final: 0.6891 (ttt180) REVERT: B 41 ARG cc_start: 0.7348 (ttm170) cc_final: 0.6893 (ttt180) REVERT: C 41 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6890 (ttt180) REVERT: D 41 ARG cc_start: 0.7347 (ttm170) cc_final: 0.6890 (ttt180) outliers start: 17 outliers final: 16 residues processed: 189 average time/residue: 0.3263 time to fit residues: 96.1221 Evaluate side-chains 189 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 173 optimal weight: 6.9990 overall best weight: 0.4474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098493 restraints weight = 25084.145| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.64 r_work: 0.2939 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20984 Z= 0.116 Angle : 0.395 5.414 28428 Z= 0.197 Chirality : 0.034 0.111 3172 Planarity : 0.003 0.052 3536 Dihedral : 6.659 125.237 2856 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.04 % Allowed : 10.46 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.07 (0.17), residues: 2464 helix: 2.39 (0.14), residues: 1460 sheet: 0.52 (0.62), residues: 84 loop : -0.22 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 223 HIS 0.002 0.001 HIS D 251 PHE 0.008 0.001 PHE D 519 TYR 0.007 0.001 TYR B 271 ARG 0.014 0.000 ARG C 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.34 seconds wall clock time: 70 minutes 2.02 seconds (4202.02 seconds total)