Starting phenix.real_space_refine (version: dev) on Thu Feb 23 23:08:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qun_14149/02_2023/7qun_14149_trim_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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 Process input model Symmetric amino acids flipped Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 238": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21094 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5236 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 694, 5231 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 648} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 149 Conformer: "B" Number of residues, atoms: 694, 5231 Classifications: {'peptide': 694} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 648} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 21, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 149 bond proxies already assigned to first conformer: 5366 Chain: "B" Number of atoms: 5240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5240 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 19, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 5248 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 693, 5243 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 18, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 693, 5243 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 10, 'GLU:plan': 18, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 5379 Chain: "D" Number of atoms: 5266 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 693, 5255 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 16, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 120 Conformer: "B" Number of residues, atoms: 693, 5255 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 16, 'ASP:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 120 bond proxies already assigned to first conformer: 5384 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 19.48, per 1000 atoms: 0.92 Number of scatterers: 21094 At special positions: 0 Unit cell: (131.52, 111.36, 136.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3786 8.00 N 3598 7.00 C 13570 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.21 Conformation dependent library (CDL) restraints added in 5.5 seconds 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 36 sheets defined 18.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.785A pdb=" N ARG A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 444 through 446 No H-bonds generated for 'chain 'A' and resid 444 through 446' Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 520 through 527 Processing helix chain 'A' and resid 545 through 551 removed outlier: 4.043A pdb=" N LEU A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 626 through 633 removed outlier: 3.764A pdb=" N MET A 630 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 654 removed outlier: 3.551A pdb=" N LYS A 654 " --> pdb=" O ALA A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 Proline residue: A 661 - end of helix Processing helix chain 'A' and resid 681 through 693 removed outlier: 3.758A pdb=" N ARG A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 729 Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.833A pdb=" N ARG B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 545 through 551 removed outlier: 4.065A pdb=" N LEU B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.563A pdb=" N GLU B 573 " --> pdb=" O GLN B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 626 through 633 removed outlier: 3.695A pdb=" N MET B 630 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 Processing helix chain 'B' and resid 656 through 662 Proline residue: B 661 - end of helix Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 712 through 729 Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 472 through 474 No H-bonds generated for 'chain 'C' and resid 472 through 474' Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 545 through 551 removed outlier: 4.206A pdb=" N LEU C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 616 through 619 No H-bonds generated for 'chain 'C' and resid 616 through 619' Processing helix chain 'C' and resid 626 through 633 removed outlier: 3.636A pdb=" N MET C 630 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 654 removed outlier: 3.667A pdb=" N ALA C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 662 Proline residue: C 661 - end of helix Processing helix chain 'C' and resid 681 through 693 removed outlier: 3.582A pdb=" N TYR C 686 " --> pdb=" O GLN C 682 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 693 " --> pdb=" O VAL C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 729 Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 545 through 551 removed outlier: 4.091A pdb=" N LEU D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 574 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 616 through 619 No H-bonds generated for 'chain 'D' and resid 616 through 619' Processing helix chain 'D' and resid 626 through 633 removed outlier: 3.661A pdb=" N MET D 630 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 654 Processing helix chain 'D' and resid 656 through 662 Proline residue: D 661 - end of helix Processing helix chain 'D' and resid 681 through 693 removed outlier: 3.569A pdb=" N TYR D 686 " --> pdb=" O GLN D 682 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 693 " --> pdb=" O VAL D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 729 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 removed outlier: 4.727A pdb=" N ARG A 62 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 28 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N THR A 51 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU A 26 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 96 removed outlier: 6.723A pdb=" N LEU A 106 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER A 94 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 104 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU A 125 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 153 through 155 Processing sheet with id= D, first strand: chain 'A' and resid 244 through 247 Processing sheet with id= E, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.638A pdb=" N LEU A 333 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 343 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP A 335 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 341 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 375 through 382 Processing sheet with id= G, first strand: chain 'A' and resid 409 through 416 removed outlier: 6.855A pdb=" N VAL A 421 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 415 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 435 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER A 451 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHE A 437 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 449 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 461 through 469 removed outlier: 3.506A pdb=" N GLU A 485 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY A 586 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 606 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY A 585 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 608 " --> pdb=" O GLY A 585 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N VAL A 609 " --> pdb=" O PRO A 666 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 668 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 67 through 71 Processing sheet with id= J, first strand: chain 'B' and resid 86 through 88 removed outlier: 4.656A pdb=" N ARG B 62 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG B 42 " --> pdb=" O HIS B 71 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 28 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 51 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LEU B 26 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.681A pdb=" N LEU B 93 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 108 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLU B 91 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= M, first strand: chain 'B' and resid 244 through 247 Processing sheet with id= N, first strand: chain 'B' and resid 301 through 303 removed outlier: 6.617A pdb=" N LEU B 333 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL B 343 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ASP B 335 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR B 341 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 375 through 382 Processing sheet with id= P, first strand: chain 'B' and resid 409 through 416 removed outlier: 6.841A pdb=" N VAL B 421 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 415 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 435 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER B 451 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE B 437 " --> pdb=" O TRP B 449 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TRP B 449 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 461 through 469 removed outlier: 3.501A pdb=" N GLU B 485 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLY B 586 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA B 606 " --> pdb=" O LEU B 583 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY B 585 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 608 " --> pdb=" O GLY B 585 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 67 through 71 Processing sheet with id= S, first strand: chain 'C' and resid 86 through 88 removed outlier: 4.853A pdb=" N ARG C 62 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG C 42 " --> pdb=" O HIS C 71 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 28 " --> pdb=" O GLU C 49 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR C 51 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU C 26 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 91 through 96 removed outlier: 6.756A pdb=" N LEU C 106 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER C 94 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA C 104 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 96 " --> pdb=" O MET C 102 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N MET C 102 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU C 125 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS C 129 " --> pdb=" O GLU C 125 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 153 through 155 Processing sheet with id= V, first strand: chain 'C' and resid 244 through 247 Processing sheet with id= W, first strand: chain 'C' and resid 301 through 303 removed outlier: 6.454A pdb=" N LEU C 333 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL C 343 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP C 335 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR C 341 " --> pdb=" O ASP C 335 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 375 through 382 Processing sheet with id= Y, first strand: chain 'C' and resid 409 through 416 removed outlier: 6.858A pdb=" N VAL C 421 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE C 415 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 435 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER C 451 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N PHE C 437 " --> pdb=" O TRP C 449 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TRP C 449 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 461 through 469 removed outlier: 3.552A pdb=" N GLU C 485 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 606 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLY C 585 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL C 608 " --> pdb=" O GLY C 585 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 67 through 71 Processing sheet with id= AB, first strand: chain 'D' and resid 86 through 88 removed outlier: 4.876A pdb=" N ARG D 62 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 42 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D 28 " --> pdb=" O GLU D 49 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N THR D 51 " --> pdb=" O LEU D 26 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU D 26 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 91 through 96 removed outlier: 6.783A pdb=" N LEU D 106 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER D 94 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA D 104 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU D 125 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 153 through 155 Processing sheet with id= AE, first strand: chain 'D' and resid 244 through 247 Processing sheet with id= AF, first strand: chain 'D' and resid 301 through 303 removed outlier: 6.496A pdb=" N LEU D 333 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL D 343 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP D 335 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR D 341 " --> pdb=" O ASP D 335 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 375 through 382 Processing sheet with id= AH, first strand: chain 'D' and resid 409 through 416 removed outlier: 6.851A pdb=" N VAL D 421 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE D 415 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 435 " --> pdb=" O SER D 451 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER D 451 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE D 437 " --> pdb=" O TRP D 449 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TRP D 449 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 461 through 469 removed outlier: 3.551A pdb=" N GLU D 485 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLY D 586 " --> pdb=" O PRO D 506 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 606 " --> pdb=" O LEU D 583 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLY D 585 " --> pdb=" O ALA D 606 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 608 " --> pdb=" O GLY D 585 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 609 " --> pdb=" O PRO D 666 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 668 " --> pdb=" O VAL D 609 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 67 through 71 744 hydrogen bonds defined for protein. 2105 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: 7.74 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.29: 3368 1.29 - 1.45: 6008 1.45 - 1.60: 12081 1.60 - 1.76: 0 1.76 - 1.91: 212 Bond restraints: 21669 Sorted by residual: bond pdb=" CAM DWZ C 801 " pdb=" OAT DWZ C 801 " ideal model delta sigma weight residual 1.246 1.134 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" CAM DWZ A 801 " pdb=" OAT DWZ A 801 " ideal model delta sigma weight residual 1.246 1.138 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CAM DWZ B 801 " pdb=" OAT DWZ B 801 " ideal model delta sigma weight residual 1.246 1.138 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CAM DWZ D 801 " pdb=" OAT DWZ D 801 " ideal model delta sigma weight residual 1.246 1.140 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CA SER C 587 " pdb=" C SER C 587 " ideal model delta sigma weight residual 1.524 1.573 -0.049 9.50e-03 1.11e+04 2.64e+01 ... (remaining 21664 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.81: 900 106.81 - 113.65: 11684 113.65 - 120.50: 8037 120.50 - 127.34: 8651 127.34 - 134.18: 289 Bond angle restraints: 29561 Sorted by residual: angle pdb=" CA GLY D 589 " pdb=" C GLY D 589 " pdb=" O GLY D 589 " ideal model delta sigma weight residual 120.75 113.30 7.45 1.03e+00 9.43e-01 5.23e+01 angle pdb=" CA GLY D 589 " pdb=" C GLY D 589 " pdb=" N GLY D 590 " ideal model delta sigma weight residual 117.04 123.98 -6.94 9.90e-01 1.02e+00 4.92e+01 angle pdb=" C GLY D 589 " pdb=" N GLY D 590 " pdb=" CA GLY D 590 " ideal model delta sigma weight residual 120.00 127.12 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C GLU C 573 " pdb=" N GLU C 574 " pdb=" CA GLU C 574 " ideal model delta sigma weight residual 122.26 112.80 9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" O VAL C 570 " pdb=" C VAL C 570 " pdb=" N LEU C 571 " ideal model delta sigma weight residual 121.87 115.86 6.01 1.01e+00 9.80e-01 3.54e+01 ... (remaining 29556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11587 17.96 - 35.92: 855 35.92 - 53.88: 209 53.88 - 71.84: 49 71.84 - 89.79: 25 Dihedral angle restraints: 12725 sinusoidal: 4732 harmonic: 7993 Sorted by residual: dihedral pdb=" C LYS B 126 " pdb=" N LYS B 126 " pdb=" CA LYS B 126 " pdb=" CB LYS B 126 " ideal model delta harmonic sigma weight residual -122.60 -131.52 8.92 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C ASP B 559 " pdb=" N ASP B 559 " pdb=" CA ASP B 559 " pdb=" CB ASP B 559 " ideal model delta harmonic sigma weight residual -122.60 -131.37 8.77 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" C SER C 587 " pdb=" N SER C 587 " pdb=" CA SER C 587 " pdb=" CB SER C 587 " ideal model delta harmonic sigma weight residual -122.60 -131.31 8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 12722 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2923 0.075 - 0.149: 359 0.149 - 0.224: 19 0.224 - 0.298: 8 0.298 - 0.373: 3 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB VAL C 560 " pdb=" CA VAL C 560 " pdb=" CG1 VAL C 560 " pdb=" CG2 VAL C 560 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB VAL C 46 " pdb=" CA VAL C 46 " pdb=" CG1 VAL C 46 " pdb=" CG2 VAL C 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CAB DWZ D 801 " pdb=" CAA DWZ D 801 " pdb=" CAD DWZ D 801 " pdb=" CAE DWZ D 801 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3309 not shown) Planarity restraints: 3785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 120 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE B 120 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE B 120 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 121 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 338 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C THR C 338 " -0.051 2.00e-02 2.50e+03 pdb=" O THR C 338 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG C 339 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 44 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C ARG C 44 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG C 44 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 45 " 0.016 2.00e-02 2.50e+03 ... (remaining 3782 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2892 2.76 - 3.30: 17851 3.30 - 3.83: 33094 3.83 - 4.37: 40455 4.37 - 4.90: 71353 Nonbonded interactions: 165645 Sorted by model distance: nonbonded pdb=" OG SER C 370 " pdb=" OD1 ASP C 372 " model vdw 2.230 2.440 nonbonded pdb=" OG SER D 370 " pdb=" OD1 ASP D 372 " model vdw 2.249 2.440 nonbonded pdb=" O VAL D 217 " pdb=" OG SER D 218 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 370 " pdb=" OD1 ASP A 372 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR C 67 " pdb=" OE1 GLU C 453 " model vdw 2.267 2.440 ... (remaining 165640 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 55 or (resid 56 and (name N or name CA or name C \ or name O or name CB )) or resid 57 through 67 or resid 69 through 88 or (resid \ 89 and (name N or name CA or name C or name O or name CB )) or resid 90 through \ 105 or resid 107 or (resid 108 through 109 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 130 or resid 132 through 292 or (resid \ 293 and (name N or name CA or name C or name O or name CB )) or resid 294 throu \ gh 410 or (resid 411 and (name N or name CA or name C or name O or name CB or na \ me CG )) or resid 412 through 444 or (resid 445 through 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 477 or (resid 478 and \ (name N or name CA or name C or name O or name CB )) or resid 479 through 498 or \ (resid 499 and (name N or name CA or name C or name O or name CB )) or resid 50 \ 0 through 638 or (resid 639 through 642 and (name N or name CA or name C or name \ O or name CB )) or resid 643 through 652 or (resid 653 and (name N or name CA o \ r name C or name O or name CB )) or resid 654 through 663 or (resid 664 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 665 through 693 or (resid 694 and (name N or name CA or name C or nam \ e O or name CB )) or resid 695 through 709 or (resid 710 and (name N or name CA \ or name C or name O or name CB )) or resid 711 through 730 or resid 801)) selection = (chain 'B' and (resid 9 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 67 or res \ id 69 through 105 or resid 107 or (resid 108 through 117 and (name N or name CA \ or name C or name O or name CB )) or resid 118 through 130 or resid 132 through \ 173 or (resid 174 and (name N or name CA or name C or name O or name CB or name \ CG )) or resid 175 through 232 or (resid 233 and (name N or name CA or name C or \ name O or name CB )) or resid 234 through 290 or (resid 291 and (name N or name \ CA or name C or name O or name CB )) or resid 292 or (resid 293 and (name N or \ name CA or name C or name O or name CB )) or resid 294 through 298 or (resid 299 \ and (name N or name CA or name C or name O or name CB )) or resid 300 through 4 \ 10 or (resid 411 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 412 through 416 or (resid 417 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or resid 418 through 444 or (resid 44 \ 5 through 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 through 477 or (resid 478 and (name N or name CA or name C or name O or name \ CB )) or resid 479 through 571 or (resid 572 and (name N or name CA or name C o \ r name O or name CB or name CG )) or (resid 573 through 575 and (name N or name \ CA or name C or name O or name CB )) or resid 576 through 638 or (resid 639 thro \ ugh 642 and (name N or name CA or name C or name O or name CB )) or resid 643 th \ rough 730 or resid 801)) selection = (chain 'C' and (resid 9 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 67 or resid 69 through 95 or (resid \ 96 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 97 through 105 or resid 107 or (resid 108 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 through 130 or resid 132 through 13 \ 8 or (resid 139 and (name N or name CA or name C or name O or name CB )) or resi \ d 140 through 147 or (resid 148 and (name N or name CA or name C or name O or na \ me CB )) or resid 149 through 173 or (resid 174 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 175 through 232 or (resid 233 and ( \ name N or name CA or name C or name O or name CB )) or resid 234 through 290 or \ (resid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 \ or (resid 293 and (name N or name CA or name C or name O or name CB )) or resid \ 294 through 410 or (resid 411 and (name N or name CA or name C or name O or nam \ e CB or name CG )) or resid 412 through 416 or (resid 417 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 418 through 57 \ 4 or (resid 575 and (name N or name CA or name C or name O or name CB )) or resi \ d 576 through 621 or (resid 622 and (name N or name CA or name C or name O or na \ me CB )) or resid 623 through 643 or (resid 644 through 645 and (name N or name \ CA or name C or name O or name CB )) or resid 646 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE )) or resid 665 through 693 or (resid 694 and (name N or name CA or name C or \ name O or name CB )) or resid 695 through 710 or (resid 711 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 712 through 730 or res \ id 801)) selection = (chain 'D' and (resid 9 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 55 or (resid 56 and (n \ ame N or name CA or name C or name O or name CB )) or resid 57 through 67 or res \ id 69 through 95 or (resid 96 and (name N or name CA or name C or name O or name \ CB or name CG )) or resid 97 through 105 or resid 107 through 130 or resid 132 \ through 147 or (resid 148 and (name N or name CA or name C or name O or name CB \ )) or resid 149 through 159 or (resid 160 and (name N or name CA or name C or na \ me O or name CB )) or resid 161 through 173 or (resid 174 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 175 through 232 or (resid \ 233 and (name N or name CA or name C or name O or name CB )) or resid 234 throu \ gh 237 or (resid 238 and (name N or name CA or name C or name O or name CB )) or \ resid 239 through 290 or (resid 291 and (name N or name CA or name C or name O \ or name CB )) or resid 292 through 416 or (resid 417 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD )) or resid 418 through 444 or \ (resid 445 through 446 and (name N or name CA or name C or name O or name CB )) \ or resid 447 through 571 or (resid 572 and (name N or name CA or name C or name \ O or name CB or name CG )) or (resid 573 through 575 and (name N or name CA or n \ ame C or name O or name CB )) or resid 576 through 638 or (resid 639 through 642 \ and (name N or name CA or name C or name O or name CB )) or resid 643 through 6 \ 52 or (resid 653 and (name N or name CA or name C or name O or name CB )) or res \ id 654 through 684 or (resid 685 and (name N or name CA or name C or name O or n \ ame CB )) or resid 686 through 693 or (resid 694 and (name N or name CA or name \ C or name O or name CB )) or resid 695 through 709 or (resid 710 and (name N or \ name CA or name C or name O or name CB )) or (resid 711 and (name N or name CA o \ r name C or name O or name CB or name CG )) or resid 712 through 730 or resid 80 \ 1)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 13570 2.51 5 N 3598 2.21 5 O 3786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.470 Check model and map are aligned: 0.310 Process input model: 65.360 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.005 0.112 21669 Z= 0.310 Angle : 0.718 14.306 29561 Z= 0.413 Chirality : 0.050 0.373 3312 Planarity : 0.004 0.037 3785 Dihedral : 14.589 89.795 7581 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.29 (0.16), residues: 2745 helix: 1.77 (0.25), residues: 467 sheet: 1.02 (0.17), residues: 887 loop : -0.95 (0.16), residues: 1391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 2.643 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 207 average time/residue: 1.6240 time to fit residues: 375.4547 Evaluate side-chains 170 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 2.483 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.7635 time to fit residues: 6.0034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 21669 Z= 0.253 Angle : 0.718 8.861 29561 Z= 0.386 Chirality : 0.051 0.168 3312 Planarity : 0.005 0.040 3785 Dihedral : 5.242 46.133 2988 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.13 (0.16), residues: 2745 helix: 1.37 (0.24), residues: 471 sheet: 1.11 (0.18), residues: 812 loop : -0.99 (0.15), residues: 1462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 2.761 Fit side-chains outliers start: 30 outliers final: 10 residues processed: 178 average time/residue: 1.6340 time to fit residues: 325.6481 Evaluate side-chains 169 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1853 time to fit residues: 5.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 170 optimal weight: 0.0470 chunk 69 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 overall best weight: 2.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21669 Z= 0.231 Angle : 0.685 8.731 29561 Z= 0.370 Chirality : 0.050 0.158 3312 Planarity : 0.005 0.041 3785 Dihedral : 5.253 45.552 2988 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.11 (0.15), residues: 2745 helix: 1.28 (0.24), residues: 471 sheet: 1.04 (0.17), residues: 859 loop : -1.00 (0.15), residues: 1415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 163 time to evaluate : 2.541 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 181 average time/residue: 1.7202 time to fit residues: 348.3296 Evaluate side-chains 172 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.2089 time to fit residues: 5.8263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 168 optimal weight: 0.0070 chunk 251 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 238 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 21669 Z= 0.271 Angle : 0.753 9.425 29561 Z= 0.407 Chirality : 0.052 0.168 3312 Planarity : 0.006 0.054 3785 Dihedral : 5.471 48.991 2988 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.02 (0.15), residues: 2745 helix: 1.18 (0.24), residues: 468 sheet: 1.09 (0.18), residues: 774 loop : -0.99 (0.15), residues: 1503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 165 time to evaluate : 2.623 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 182 average time/residue: 1.7039 time to fit residues: 345.9432 Evaluate side-chains 185 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 10 residues processed: 9 average time/residue: 0.8266 time to fit residues: 12.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 110 optimal weight: 0.0570 chunk 227 optimal weight: 4.9990 chunk 184 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 overall best weight: 1.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 21669 Z= 0.207 Angle : 0.651 8.727 29561 Z= 0.351 Chirality : 0.049 0.151 3312 Planarity : 0.005 0.038 3785 Dihedral : 5.218 44.234 2988 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.10 (0.15), residues: 2745 helix: 1.28 (0.24), residues: 472 sheet: 1.02 (0.17), residues: 859 loop : -1.00 (0.15), residues: 1414 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 2.511 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 185 average time/residue: 1.6760 time to fit residues: 347.5895 Evaluate side-chains 175 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 2.496 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1945 time to fit residues: 4.8864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 267 optimal weight: 0.1980 chunk 221 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21669 Z= 0.231 Angle : 0.689 9.030 29561 Z= 0.372 Chirality : 0.050 0.158 3312 Planarity : 0.005 0.043 3785 Dihedral : 5.302 46.018 2988 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.07 (0.15), residues: 2745 helix: 1.30 (0.24), residues: 465 sheet: 1.07 (0.17), residues: 826 loop : -1.02 (0.15), residues: 1454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.679 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 180 average time/residue: 1.6259 time to fit residues: 327.4446 Evaluate side-chains 179 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 2.353 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 0.4152 time to fit residues: 6.6708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 21669 Z= 0.275 Angle : 0.754 9.480 29561 Z= 0.408 Chirality : 0.052 0.167 3312 Planarity : 0.006 0.054 3785 Dihedral : 5.471 48.857 2988 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.02 (0.15), residues: 2745 helix: 1.13 (0.24), residues: 468 sheet: 1.12 (0.18), residues: 770 loop : -0.98 (0.15), residues: 1507 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 2.260 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 180 average time/residue: 1.6882 time to fit residues: 340.5380 Evaluate side-chains 180 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.3820 time to fit residues: 6.8254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21669 Z= 0.224 Angle : 0.677 8.823 29561 Z= 0.366 Chirality : 0.050 0.155 3312 Planarity : 0.005 0.038 3785 Dihedral : 5.307 45.641 2988 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.04 (0.15), residues: 2745 helix: 1.18 (0.24), residues: 471 sheet: 1.00 (0.17), residues: 859 loop : -1.03 (0.15), residues: 1415 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 2.508 Fit side-chains outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 1.6413 time to fit residues: 325.6787 Evaluate side-chains 180 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.663 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.5827 time to fit residues: 8.0136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 21669 Z= 0.289 Angle : 0.775 9.638 29561 Z= 0.419 Chirality : 0.053 0.172 3312 Planarity : 0.006 0.060 3785 Dihedral : 5.519 49.209 2988 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.01 (0.15), residues: 2745 helix: 1.04 (0.24), residues: 468 sheet: 1.12 (0.18), residues: 768 loop : -0.99 (0.15), residues: 1509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 2.513 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 181 average time/residue: 1.6600 time to fit residues: 337.6943 Evaluate side-chains 182 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 2.342 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 0.2017 time to fit residues: 5.0022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 182 optimal weight: 0.4980 chunk 274 optimal weight: 8.9990 chunk 253 optimal weight: 0.0570 chunk 218 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 169 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 overall best weight: 1.3220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21669 Z= 0.187 Angle : 0.624 8.644 29561 Z= 0.335 Chirality : 0.048 0.146 3312 Planarity : 0.005 0.037 3785 Dihedral : 5.152 42.886 2988 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.12 (0.15), residues: 2745 helix: 1.26 (0.24), residues: 472 sheet: 1.05 (0.17), residues: 858 loop : -0.99 (0.15), residues: 1415 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 2.486 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 177 average time/residue: 1.6991 time to fit residues: 337.4956 Evaluate side-chains 174 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.2081 time to fit residues: 3.8695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 219 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108063 restraints weight = 28054.068| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.17 r_work: 0.3125 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21669 Z= 0.189 Angle : 0.624 8.471 29561 Z= 0.334 Chirality : 0.048 0.147 3312 Planarity : 0.005 0.038 3785 Dihedral : 5.105 42.555 2988 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.15 (0.15), residues: 2745 helix: 1.27 (0.24), residues: 472 sheet: 1.08 (0.17), residues: 858 loop : -0.97 (0.15), residues: 1415 =============================================================================== Job complete usr+sys time: 6773.30 seconds wall clock time: 120 minutes 55.27 seconds (7255.27 seconds total)