Starting phenix.real_space_refine on Sat Feb 17 21:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekq_28210/02_2024/8ekq_28210_updated.pdb" } resolution = 2.6 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= 1.000 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 8 5.49 5 S 108 5.16 5 C 13020 2.51 5 N 3264 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 384": "OE1" <-> "OE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 384": "OE1" <-> "OE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D ARG 490": "NH1" <-> "NH2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D GLU 701": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19864 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4896 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4896 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4896 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4896 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.60, per 1000 atoms: 0.53 Number of scatterers: 19864 At special positions: 0 Unit cell: (136.51, 136.51, 108.04, 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 108 16.00 P 8 15.00 O 3464 8.00 N 3264 7.00 C 13020 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: 7.87 Conformation dependent library (CDL) restraints added in 3.7 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 4 sheets defined 57.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'A' and resid 77 through 84 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 101 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 136 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 230 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 388 Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 430 through 465 removed outlier: 7.223A pdb=" N LEU A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.854A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.630A pdb=" N LEU A 512 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (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 533 No H-bonds generated for 'chain 'A' and resid 530 through 533' Processing helix chain 'A' and resid 537 through 559 Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 619 through 648 removed outlier: 4.017A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 673 removed outlier: 4.280A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.578A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 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 101 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 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 255 Processing helix chain 'B' and resid 261 through 281 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 322 through 326 Proline residue: B 325 - end of helix No H-bonds generated for 'chain 'B' and resid 322 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 430 through 465 removed outlier: 7.223A pdb=" N LEU B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.854A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.630A pdb=" N LEU B 512 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 3.632A 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 530 through 533 No H-bonds generated for 'chain 'B' and resid 530 through 533' Processing helix chain 'B' and resid 537 through 559 Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 619 through 648 removed outlier: 4.017A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 673 removed outlier: 4.280A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.578A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 84 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 101 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 136 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 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 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 Processing helix chain 'C' and resid 322 through 326 Proline residue: C 325 - end of helix No H-bonds generated for 'chain 'C' and resid 322 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 430 through 465 removed outlier: 7.223A pdb=" N LEU C 461 " --> pdb=" O TRP C 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.854A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.630A pdb=" N LEU C 512 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (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 Processing helix chain 'C' and resid 593 through 604 Processing helix chain 'C' and resid 619 through 648 removed outlier: 4.017A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 673 removed outlier: 4.280A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.578A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 84 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 101 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' 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 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 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 322 through 326 Proline residue: D 325 - end of helix No H-bonds generated for 'chain 'D' and resid 322 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 430 through 465 removed outlier: 7.223A pdb=" N LEU D 461 " --> pdb=" O TRP D 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.820A 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: 3.854A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.630A pdb=" N LEU D 512 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 3.632A 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 530 through 533 No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing helix chain 'D' and resid 537 through 559 Processing helix chain 'D' and resid 593 through 604 Processing helix chain 'D' and resid 619 through 648 removed outlier: 4.017A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 673 removed outlier: 4.280A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.578A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.876A 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: 5.935A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 687 through 690 removed outlier: 5.935A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 690 removed outlier: 5.935A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 6.966A 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: 5.935A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2532 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: 5.80 Time building geometry restraints manager: 8.53 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: 3072 1.31 - 1.43: 5656 1.43 - 1.56: 11420 1.56 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 20328 Sorted by residual: bond pdb=" C4 PEX A 802 " pdb=" O4 PEX A 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX B 802 " pdb=" O4 PEX B 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX D 802 " pdb=" O4 PEX D 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX C 802 " pdb=" O4 PEX C 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20323 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.36: 500 106.36 - 113.29: 11048 113.29 - 120.22: 7280 120.22 - 127.15: 8436 127.15 - 134.08: 252 Bond angle restraints: 27516 Sorted by residual: angle pdb=" O3 PEX D 802 " pdb=" P1 PEX D 802 " pdb=" O8 PEX D 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX A 802 " pdb=" P1 PEX A 802 " pdb=" O8 PEX A 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX C 802 " pdb=" P1 PEX C 802 " pdb=" O8 PEX C 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX B 802 " pdb=" P1 PEX B 802 " pdb=" O8 PEX B 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.04 -15.30 3.00e+00 1.11e-01 2.60e+01 ... (remaining 27511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 11196 20.59 - 41.17: 692 41.17 - 61.76: 88 61.76 - 82.34: 36 82.34 - 102.93: 16 Dihedral angle restraints: 12028 sinusoidal: 4924 harmonic: 7104 Sorted by residual: dihedral pdb=" CA TRP B 351 " pdb=" C TRP B 351 " pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP A 351 " pdb=" C TRP A 351 " pdb=" N GLU A 352 " pdb=" CA GLU A 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP C 351 " pdb=" C TRP C 351 " pdb=" N GLU C 352 " pdb=" CA GLU C 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 12025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2179 0.040 - 0.080: 724 0.080 - 0.121: 161 0.121 - 0.161: 24 0.161 - 0.201: 16 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA GLN A 414 " pdb=" N GLN A 414 " pdb=" C GLN A 414 " pdb=" CB GLN A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN B 414 " pdb=" N GLN B 414 " pdb=" C GLN B 414 " pdb=" CB GLN B 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN C 414 " pdb=" N GLN C 414 " pdb=" C GLN C 414 " pdb=" CB GLN C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3101 not shown) Planarity restraints: 3384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 660 " -0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP B 660 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 660 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 660 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 660 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 660 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 660 " -0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP A 660 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 660 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 660 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 660 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 660 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 660 " 0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP D 660 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 660 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 660 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 660 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 660 " 0.009 2.00e-02 2.50e+03 ... (remaining 3381 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3959 2.78 - 3.31: 18285 3.31 - 3.84: 34032 3.84 - 4.37: 40391 4.37 - 4.90: 67634 Nonbonded interactions: 164301 Sorted by model distance: nonbonded pdb=" N GLU C 495 " pdb=" OE1 GLU C 495 " model vdw 2.245 2.520 nonbonded pdb=" N GLU D 495 " pdb=" OE1 GLU D 495 " model vdw 2.245 2.520 nonbonded pdb=" N GLU A 495 " pdb=" OE1 GLU A 495 " model vdw 2.245 2.520 nonbonded pdb=" N GLU B 495 " pdb=" OE1 GLU B 495 " model vdw 2.245 2.520 nonbonded pdb=" NH2 ARG A 369 " pdb=" OD2 ASP A 469 " model vdw 2.307 2.520 ... (remaining 164296 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: 0.010 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 16.620 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 54.460 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.004 0.071 20328 Z= 0.259 Angle : 0.845 16.027 27516 Z= 0.404 Chirality : 0.043 0.201 3104 Planarity : 0.006 0.077 3384 Dihedral : 14.355 102.928 7428 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.18 (0.16), residues: 2376 helix: 0.15 (0.12), residues: 1472 sheet: 1.19 (0.50), residues: 112 loop : -0.59 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 660 HIS 0.010 0.001 HIS D 165 PHE 0.018 0.002 PHE B 311 TYR 0.023 0.002 TYR B 412 ARG 0.017 0.001 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.365 Fit side-chains REVERT: A 286 GLN cc_start: 0.7548 (mt0) cc_final: 0.7268 (mm-40) REVERT: A 370 HIS cc_start: 0.8370 (p90) cc_final: 0.8154 (p-80) REVERT: A 671 MET cc_start: 0.8907 (mtm) cc_final: 0.8698 (mtm) REVERT: A 687 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6894 (mtp180) REVERT: B 286 GLN cc_start: 0.7568 (mt0) cc_final: 0.7288 (mm-40) REVERT: B 370 HIS cc_start: 0.8374 (p90) cc_final: 0.8158 (p-80) REVERT: B 671 MET cc_start: 0.8906 (mtm) cc_final: 0.8700 (mtm) REVERT: B 687 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6892 (mtp180) REVERT: C 286 GLN cc_start: 0.7563 (mt0) cc_final: 0.7287 (mm-40) REVERT: C 370 HIS cc_start: 0.8373 (p90) cc_final: 0.8154 (p-80) REVERT: C 671 MET cc_start: 0.8908 (mtm) cc_final: 0.8701 (mtm) REVERT: C 687 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6887 (mtp180) REVERT: D 286 GLN cc_start: 0.7545 (mt0) cc_final: 0.7268 (mm-40) REVERT: D 370 HIS cc_start: 0.8373 (p90) cc_final: 0.8155 (p-80) REVERT: D 671 MET cc_start: 0.8907 (mtm) cc_final: 0.8700 (mtm) REVERT: D 687 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6887 (mtp180) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 1.2886 time to fit residues: 550.1346 Evaluate side-chains 302 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 2.125 ------------------------------------------------------------------------------- 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: 0.0970 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 165 HIS A 294 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 165 HIS B 294 GLN C 165 HIS C 294 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 294 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20328 Z= 0.218 Angle : 0.515 7.853 27516 Z= 0.262 Chirality : 0.037 0.131 3104 Planarity : 0.005 0.037 3384 Dihedral : 9.796 81.124 2876 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.89 % Allowed : 7.05 % Favored : 91.05 % 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: 0.95 (0.17), residues: 2376 helix: 1.15 (0.13), residues: 1476 sheet: 1.42 (0.49), residues: 112 loop : -0.36 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 660 HIS 0.008 0.001 HIS B 165 PHE 0.012 0.001 PHE D 311 TYR 0.021 0.002 TYR B 471 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 308 time to evaluate : 2.207 Fit side-chains REVERT: A 137 MET cc_start: 0.6801 (tpt) cc_final: 0.6578 (tpp) REVERT: A 163 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: A 352 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7448 (tp30) REVERT: A 687 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6857 (mtp180) REVERT: B 137 MET cc_start: 0.6798 (tpt) cc_final: 0.6577 (tpp) REVERT: B 163 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: B 352 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7474 (tp30) REVERT: B 687 ARG cc_start: 0.7082 (mtm180) cc_final: 0.6852 (mtp180) REVERT: C 137 MET cc_start: 0.6795 (tpt) cc_final: 0.6576 (tpp) REVERT: C 352 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7470 (tp30) REVERT: C 687 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6849 (mtp180) REVERT: D 137 MET cc_start: 0.6810 (tpt) cc_final: 0.6593 (tpp) REVERT: D 352 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7471 (tp30) REVERT: D 687 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6848 (mtp180) outliers start: 40 outliers final: 15 residues processed: 326 average time/residue: 1.2394 time to fit residues: 457.8485 Evaluate side-chains 295 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 278 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.0870 chunk 181 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 194 optimal weight: 0.3980 chunk 216 optimal weight: 2.9990 chunk 74 optimal weight: 0.0070 chunk 175 optimal weight: 2.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 673 ASN B 294 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20328 Z= 0.216 Angle : 0.499 8.738 27516 Z= 0.252 Chirality : 0.037 0.133 3104 Planarity : 0.004 0.034 3384 Dihedral : 9.625 76.752 2876 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.70 % Allowed : 8.43 % Favored : 89.87 % 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: 1.20 (0.17), residues: 2376 helix: 1.38 (0.14), residues: 1476 sheet: 1.44 (0.49), residues: 112 loop : -0.32 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 660 HIS 0.005 0.001 HIS D 165 PHE 0.013 0.001 PHE D 394 TYR 0.020 0.002 TYR D 471 ARG 0.003 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 2.419 Fit side-chains REVERT: A 163 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: A 352 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7455 (tp30) REVERT: B 108 ASP cc_start: 0.6949 (m-30) cc_final: 0.6748 (m-30) REVERT: B 137 MET cc_start: 0.6890 (tpt) cc_final: 0.6673 (tpp) REVERT: B 163 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: B 352 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7477 (tp30) REVERT: B 607 MET cc_start: 0.8570 (mtp) cc_final: 0.8359 (mtp) REVERT: C 137 MET cc_start: 0.6887 (tpt) cc_final: 0.6671 (tpp) REVERT: C 352 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7481 (tp30) REVERT: C 663 GLN cc_start: 0.8964 (mt0) cc_final: 0.8761 (mt0) REVERT: D 352 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7480 (tp30) REVERT: D 531 LYS cc_start: 0.6986 (ttmt) cc_final: 0.5557 (tptm) outliers start: 36 outliers final: 15 residues processed: 329 average time/residue: 1.2993 time to fit residues: 483.1005 Evaluate side-chains 312 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 0.0040 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 0.0470 chunk 62 optimal weight: 5.9990 overall best weight: 1.3894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN B 370 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN C 133 ASN C 370 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 294 GLN D 370 HIS ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20328 Z= 0.226 Angle : 0.489 9.558 27516 Z= 0.251 Chirality : 0.038 0.133 3104 Planarity : 0.004 0.032 3384 Dihedral : 9.414 75.056 2876 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.99 % Allowed : 9.56 % Favored : 88.45 % 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: 1.29 (0.17), residues: 2376 helix: 1.46 (0.14), residues: 1472 sheet: 1.37 (0.49), residues: 112 loop : -0.28 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 660 HIS 0.005 0.001 HIS B 165 PHE 0.014 0.001 PHE B 394 TYR 0.021 0.002 TYR C 471 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 298 time to evaluate : 2.345 Fit side-chains REVERT: A 137 MET cc_start: 0.7187 (tpt) cc_final: 0.6792 (tpp) REVERT: A 163 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: A 531 LYS cc_start: 0.7004 (ttmt) cc_final: 0.5598 (tptm) REVERT: B 108 ASP cc_start: 0.6966 (m-30) cc_final: 0.6766 (m-30) REVERT: B 137 MET cc_start: 0.6884 (tpt) cc_final: 0.6683 (tpp) REVERT: B 163 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: B 531 LYS cc_start: 0.6984 (ttmt) cc_final: 0.5593 (tptm) REVERT: C 137 MET cc_start: 0.6880 (tpt) cc_final: 0.6677 (tpp) REVERT: C 531 LYS cc_start: 0.7006 (ttmt) cc_final: 0.5598 (tptm) REVERT: D 137 MET cc_start: 0.7201 (tpt) cc_final: 0.6804 (tpp) REVERT: D 531 LYS cc_start: 0.6997 (ttmt) cc_final: 0.5580 (tptm) outliers start: 42 outliers final: 29 residues processed: 322 average time/residue: 1.3185 time to fit residues: 478.6949 Evaluate side-chains 317 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 286 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU 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: 3.9990 chunk 3 optimal weight: 0.0670 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN B 294 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20328 Z= 0.273 Angle : 0.516 8.235 27516 Z= 0.264 Chirality : 0.039 0.140 3104 Planarity : 0.004 0.036 3384 Dihedral : 9.697 73.910 2876 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.32 % Allowed : 10.32 % Favored : 87.36 % 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: 1.17 (0.17), residues: 2376 helix: 1.36 (0.14), residues: 1472 sheet: 1.39 (0.49), residues: 112 loop : -0.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 660 HIS 0.005 0.001 HIS D 165 PHE 0.018 0.002 PHE A 394 TYR 0.023 0.002 TYR B 471 ARG 0.003 0.000 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 298 time to evaluate : 2.357 Fit side-chains REVERT: A 163 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: A 407 PHE cc_start: 0.8671 (t80) cc_final: 0.8401 (t80) REVERT: A 531 LYS cc_start: 0.7037 (ttmt) cc_final: 0.5619 (tptm) REVERT: B 163 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7632 (tt0) REVERT: B 407 PHE cc_start: 0.8657 (t80) cc_final: 0.8385 (t80) REVERT: B 531 LYS cc_start: 0.7024 (ttmt) cc_final: 0.5610 (tptm) REVERT: C 137 MET cc_start: 0.6882 (tpt) cc_final: 0.6676 (tpp) REVERT: C 407 PHE cc_start: 0.8675 (t80) cc_final: 0.8403 (t80) REVERT: C 531 LYS cc_start: 0.7063 (ttmt) cc_final: 0.5630 (tptm) REVERT: D 407 PHE cc_start: 0.8677 (t80) cc_final: 0.8410 (t80) REVERT: D 640 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6748 (tmm) outliers start: 49 outliers final: 35 residues processed: 327 average time/residue: 1.3325 time to fit residues: 491.8438 Evaluate side-chains 318 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 280 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 294 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20328 Z= 0.466 Angle : 0.631 9.512 27516 Z= 0.318 Chirality : 0.046 0.160 3104 Planarity : 0.005 0.063 3384 Dihedral : 10.451 72.957 2876 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 10.56 % Favored : 86.22 % 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: 0.80 (0.17), residues: 2376 helix: 1.03 (0.13), residues: 1472 sheet: 1.35 (0.48), residues: 112 loop : -0.41 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 660 HIS 0.006 0.002 HIS D 165 PHE 0.024 0.002 PHE C 394 TYR 0.031 0.003 TYR D 471 ARG 0.004 0.001 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 290 time to evaluate : 2.281 Fit side-chains REVERT: A 113 GLU cc_start: 0.8266 (tt0) cc_final: 0.8029 (tt0) REVERT: A 163 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 407 PHE cc_start: 0.8693 (t80) cc_final: 0.8450 (t80) REVERT: A 640 MET cc_start: 0.6950 (tmm) cc_final: 0.6729 (ttp) REVERT: B 113 GLU cc_start: 0.8239 (tt0) cc_final: 0.8016 (tt0) REVERT: B 163 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: B 407 PHE cc_start: 0.8676 (t80) cc_final: 0.8431 (t80) REVERT: C 113 GLU cc_start: 0.8250 (tt0) cc_final: 0.8027 (tt0) REVERT: D 407 PHE cc_start: 0.8690 (t80) cc_final: 0.8445 (t80) outliers start: 68 outliers final: 42 residues processed: 331 average time/residue: 1.2429 time to fit residues: 466.5829 Evaluate side-chains 317 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 273 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 133 ASN D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20328 Z= 0.185 Angle : 0.496 9.465 27516 Z= 0.247 Chirality : 0.037 0.125 3104 Planarity : 0.004 0.033 3384 Dihedral : 9.366 67.909 2876 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.66 % Allowed : 12.36 % Favored : 85.98 % 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: 1.18 (0.17), residues: 2376 helix: 1.39 (0.14), residues: 1472 sheet: 1.31 (0.49), residues: 112 loop : -0.34 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 660 HIS 0.003 0.001 HIS C 234 PHE 0.016 0.001 PHE B 540 TYR 0.010 0.001 TYR B 162 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 2.330 Fit side-chains REVERT: A 163 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 531 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.5668 (tptm) REVERT: B 113 GLU cc_start: 0.8178 (tt0) cc_final: 0.7973 (tt0) REVERT: B 163 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: B 531 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.5624 (tptm) REVERT: C 137 MET cc_start: 0.7351 (tpp) cc_final: 0.6976 (tpt) REVERT: C 531 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.5666 (tptm) REVERT: D 531 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.5666 (tptm) outliers start: 35 outliers final: 20 residues processed: 307 average time/residue: 1.3049 time to fit residues: 453.1015 Evaluate side-chains 305 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 279 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 531 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 20328 Z= 0.447 Angle : 0.632 10.389 27516 Z= 0.315 Chirality : 0.045 0.156 3104 Planarity : 0.005 0.060 3384 Dihedral : 10.230 66.965 2876 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.04 % Allowed : 12.22 % Favored : 85.75 % 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: 0.81 (0.17), residues: 2376 helix: 1.04 (0.14), residues: 1472 sheet: 1.32 (0.48), residues: 112 loop : -0.41 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 660 HIS 0.006 0.002 HIS A 234 PHE 0.023 0.002 PHE C 394 TYR 0.019 0.003 TYR B 471 ARG 0.003 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 269 time to evaluate : 2.350 Fit side-chains REVERT: A 163 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: A 407 PHE cc_start: 0.8674 (t80) cc_final: 0.8424 (t80) REVERT: B 113 GLU cc_start: 0.8217 (tt0) cc_final: 0.7990 (tt0) REVERT: B 137 MET cc_start: 0.7073 (tpt) cc_final: 0.6673 (tpp) REVERT: B 163 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 407 PHE cc_start: 0.8671 (t80) cc_final: 0.8419 (t80) REVERT: C 407 PHE cc_start: 0.8691 (t80) cc_final: 0.8444 (t80) REVERT: D 407 PHE cc_start: 0.8685 (t80) cc_final: 0.8435 (t80) outliers start: 43 outliers final: 35 residues processed: 294 average time/residue: 1.3327 time to fit residues: 449.4109 Evaluate side-chains 306 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 269 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 346 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 chunk 129 optimal weight: 0.0870 chunk 93 optimal weight: 0.3980 chunk 169 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20328 Z= 0.127 Angle : 0.474 9.706 27516 Z= 0.234 Chirality : 0.036 0.116 3104 Planarity : 0.004 0.033 3384 Dihedral : 8.823 63.335 2876 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.90 % Allowed : 13.54 % Favored : 85.56 % 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: 1.35 (0.18), residues: 2376 helix: 1.51 (0.14), residues: 1472 sheet: 1.34 (0.49), residues: 112 loop : -0.23 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 660 HIS 0.003 0.001 HIS B 293 PHE 0.019 0.001 PHE B 540 TYR 0.013 0.001 TYR A 403 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 285 time to evaluate : 2.289 Fit side-chains REVERT: A 163 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: A 531 LYS cc_start: 0.7059 (ttpt) cc_final: 0.5568 (tptm) REVERT: A 640 MET cc_start: 0.7053 (ttp) cc_final: 0.6788 (tmm) REVERT: B 163 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: B 531 LYS cc_start: 0.7050 (ttpt) cc_final: 0.5547 (tptm) REVERT: C 137 MET cc_start: 0.7308 (tpp) cc_final: 0.6913 (tpt) REVERT: C 531 LYS cc_start: 0.7058 (ttpt) cc_final: 0.5566 (tptm) REVERT: D 531 LYS cc_start: 0.7054 (ttpt) cc_final: 0.5566 (tptm) outliers start: 19 outliers final: 11 residues processed: 299 average time/residue: 1.3409 time to fit residues: 452.7944 Evaluate side-chains 291 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 278 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 239 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 370 HIS ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN C 370 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 370 HIS ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20328 Z= 0.412 Angle : 0.618 10.731 27516 Z= 0.307 Chirality : 0.044 0.153 3104 Planarity : 0.005 0.055 3384 Dihedral : 9.850 65.556 2876 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.99 % Allowed : 13.45 % Favored : 85.56 % 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: 0.93 (0.17), residues: 2376 helix: 1.16 (0.14), residues: 1468 sheet: 1.41 (0.48), residues: 112 loop : -0.42 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 660 HIS 0.006 0.002 HIS A 234 PHE 0.022 0.002 PHE B 394 TYR 0.017 0.003 TYR A 403 ARG 0.003 0.000 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 2.293 Fit side-chains REVERT: A 163 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: A 407 PHE cc_start: 0.8677 (t80) cc_final: 0.8437 (t80) REVERT: B 163 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: B 407 PHE cc_start: 0.8668 (t80) cc_final: 0.8424 (t80) REVERT: B 647 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6531 (tp30) REVERT: C 407 PHE cc_start: 0.8681 (t80) cc_final: 0.8438 (t80) REVERT: D 407 PHE cc_start: 0.8662 (t80) cc_final: 0.8421 (t80) outliers start: 21 outliers final: 19 residues processed: 297 average time/residue: 1.3387 time to fit residues: 448.0347 Evaluate side-chains 295 residues out of total 2172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.7980 chunk 202 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.146681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119749 restraints weight = 22004.743| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.35 r_work: 0.3121 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20328 Z= 0.156 Angle : 0.490 10.215 27516 Z= 0.243 Chirality : 0.036 0.121 3104 Planarity : 0.004 0.033 3384 Dihedral : 8.931 63.382 2876 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.95 % Allowed : 13.78 % Favored : 85.27 % 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: 1.25 (0.18), residues: 2376 helix: 1.43 (0.14), residues: 1468 sheet: 1.39 (0.49), residues: 112 loop : -0.31 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 660 HIS 0.004 0.001 HIS B 293 PHE 0.018 0.001 PHE B 540 TYR 0.014 0.001 TYR A 403 ARG 0.003 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7624.61 seconds wall clock time: 136 minutes 4.44 seconds (8164.44 seconds total)