Starting phenix.real_space_refine on Tue Apr 9 17:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3z_17400/04_2024/8p3z_17400.pdb" } resolution = 3.46 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= -0.001 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11100 2.51 5 N 2740 2.21 5 O 3014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 705": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 570": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 813": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 191": "OE1" <-> "OE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16974 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2874 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 384} Chain breaks: 4 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 390, 2843 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Conformer: "B" Number of residues, atoms: 390, 2843 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 378} Chain breaks: 4 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 bond proxies already assigned to first conformer: 2894 Chain: "C" Number of atoms: 2885 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 2874 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Conformer: "B" Number of residues, atoms: 394, 2874 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 bond proxies already assigned to first conformer: 2925 Chain: "D" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2853 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 Chain: "E" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1373 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE B 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 574 " occ=0.50 residue: pdb=" N APHE C 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 574 " occ=0.50 Time building chain proxies: 11.32, per 1000 atoms: 0.67 Number of scatterers: 16974 At special positions: 0 Unit cell: (117.086, 140.214, 147.441, 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 120 16.00 O 3014 8.00 N 2740 7.00 C 11100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.01 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.05 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.05 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.04 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.04 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: 6.74 Conformation dependent library (CDL) restraints added in 4.3 seconds 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 28 sheets defined 60.5% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 removed outlier: 3.818A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 419' Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.578A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.751A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.611A pdb=" N GLU A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP A 551 " --> pdb=" O PRO A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 547 through 551' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 628 removed outlier: 3.543A pdb=" N ARG A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.627A pdb=" N LEU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 792 through 821 removed outlier: 3.765A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.531A pdb=" N MET B 414 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.913A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.636A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.754A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 545 Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.647A pdb=" N TRP B 578 " --> pdb=" O BPHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 624 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.523A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 823 removed outlier: 3.730A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 823 " --> pdb=" O ARG B 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 removed outlier: 3.801A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 419' Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.639A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.758A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.744A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 626 Processing helix chain 'C' and resid 635 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.635A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.593A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.715A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.809A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.622A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 636 through 642 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.502A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 823 removed outlier: 3.625A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS D 823 " --> pdb=" O ARG D 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 removed outlier: 3.743A pdb=" N LEU E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 104 Processing helix chain 'E' and resid 105 through 124 Processing helix chain 'E' and resid 134 through 161 Processing helix chain 'E' and resid 177 through 210 Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.914A pdb=" N MET F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 105 through 124 Processing helix chain 'F' and resid 133 through 161 removed outlier: 3.586A pdb=" N ALA F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 209 removed outlier: 3.933A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 104 Processing helix chain 'G' and resid 105 through 124 Processing helix chain 'G' and resid 133 through 160 removed outlier: 3.693A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 210 Processing helix chain 'H' and resid 6 through 28 Processing helix chain 'H' and resid 93 through 104 Processing helix chain 'H' and resid 105 through 127 removed outlier: 3.944A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 160 Processing helix chain 'H' and resid 177 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 394 through 399 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.467A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.467A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.824A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.364A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.364A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 394 through 399 Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.450A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.450A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.466A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.594A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.520A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.520A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 77 through 79 Processing sheet with id=AC5, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 38 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AC9, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.780A pdb=" N LYS H 78 " --> pdb=" O THR H 66 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3258 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: 5.53 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2626 1.30 - 1.43: 4979 1.43 - 1.57: 9561 1.57 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 17358 Sorted by residual: bond pdb=" C TYR D 768 " pdb=" N ASP D 769 " ideal model delta sigma weight residual 1.335 1.219 0.116 1.35e-02 5.49e+03 7.35e+01 bond pdb=" C PHE C 584 " pdb=" O PHE C 584 " ideal model delta sigma weight residual 1.237 1.171 0.065 1.19e-02 7.06e+03 3.01e+01 bond pdb=" CA SER C 592 " pdb=" CB SER C 592 " ideal model delta sigma weight residual 1.535 1.469 0.066 1.21e-02 6.83e+03 2.96e+01 bond pdb=" CA SER A 592 " pdb=" CB SER A 592 " ideal model delta sigma weight residual 1.536 1.460 0.077 1.48e-02 4.57e+03 2.67e+01 bond pdb=" CA SER C 788 " pdb=" CB SER C 788 " ideal model delta sigma weight residual 1.533 1.455 0.078 1.60e-02 3.91e+03 2.40e+01 ... (remaining 17353 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.80: 326 105.80 - 113.07: 9287 113.07 - 120.33: 9463 120.33 - 127.60: 4358 127.60 - 134.87: 137 Bond angle restraints: 23571 Sorted by residual: angle pdb=" N GLU C 772 " pdb=" CA GLU C 772 " pdb=" C GLU C 772 " ideal model delta sigma weight residual 113.61 102.70 10.91 1.50e+00 4.44e-01 5.29e+01 angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 113.88 105.63 8.25 1.23e+00 6.61e-01 4.50e+01 angle pdb=" N LEU C 803 " pdb=" CA LEU C 803 " pdb=" C LEU C 803 " ideal model delta sigma weight residual 111.82 104.61 7.21 1.16e+00 7.43e-01 3.87e+01 angle pdb=" N LEU A 803 " pdb=" CA LEU A 803 " pdb=" C LEU A 803 " ideal model delta sigma weight residual 111.82 104.91 6.91 1.16e+00 7.43e-01 3.55e+01 angle pdb=" N SER F 104 " pdb=" CA SER F 104 " pdb=" C SER F 104 " ideal model delta sigma weight residual 110.48 102.21 8.27 1.48e+00 4.57e-01 3.12e+01 ... (remaining 23566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8910 17.67 - 35.33: 858 35.33 - 53.00: 145 53.00 - 70.66: 21 70.66 - 88.33: 13 Dihedral angle restraints: 9947 sinusoidal: 3419 harmonic: 6528 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 22.08 70.92 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 38.19 54.81 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 41.86 51.14 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 9944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1128 0.077 - 0.154: 1084 0.154 - 0.231: 477 0.231 - 0.309: 40 0.309 - 0.386: 4 Chirality restraints: 2733 Sorted by residual: chirality pdb=" CB VAL A 601 " pdb=" CA VAL A 601 " pdb=" CG1 VAL A 601 " pdb=" CG2 VAL A 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA CYS A 589 " pdb=" N CYS A 589 " pdb=" C CYS A 589 " pdb=" CB CYS A 589 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PRO D 717 " pdb=" N PRO D 717 " pdb=" C PRO D 717 " pdb=" CB PRO D 717 " both_signs ideal model delta sigma weight residual False 2.72 3.04 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2730 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BPHE B 574 " -0.031 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C BPHE B 574 " 0.111 2.00e-02 2.50e+03 pdb=" O BPHE B 574 " -0.041 2.00e-02 2.50e+03 pdb=" N ASN B 575 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 420 " -0.528 9.50e-02 1.11e+02 2.37e-01 3.42e+01 pdb=" NE ARG A 420 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 420 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 420 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 420 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 420 " -0.515 9.50e-02 1.11e+02 2.31e-01 3.27e+01 pdb=" NE ARG D 420 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG D 420 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 420 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 420 " -0.020 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4044 2.77 - 3.30: 17664 3.30 - 3.83: 27036 3.83 - 4.37: 33920 4.37 - 4.90: 54855 Nonbonded interactions: 137519 Sorted by model distance: nonbonded pdb=" N VAL B 395 " pdb=" O LYS B 439 " model vdw 2.233 2.520 nonbonded pdb=" O LYS G 129 " pdb=" OG1 THR G 130 " model vdw 2.236 2.440 nonbonded pdb=" O SER G 104 " pdb=" N ILE G 106 " model vdw 2.257 2.520 nonbonded pdb=" N VAL D 395 " pdb=" O LYS D 439 " model vdw 2.259 2.520 nonbonded pdb=" O ASP D 427 " pdb=" OE1 GLU D 431 " model vdw 2.290 3.040 ... (remaining 137514 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 393 through 505 or (resid 506 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 573 or resid 575 o \ r (resid 576 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 77 through 626 or resid 636 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 393 through 505 or (resid 506 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 549 or (resid 550 \ and (name N or name CA or name C or name O or name CB )) or resid 551 or (resid \ 569 and (name N or name CA or name C or name O or name CB )) or resid 570 throug \ h 573 or resid 575 or (resid 576 and (name N or name CA or name C or name O or n \ ame CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name \ C or name O or name CB )) or resid 595 through 636 or (resid 637 through 638 and \ (name N or name CA or name C or name O or name CB )) or resid 639 through 823)) \ selection = (chain 'C' and (resid 393 through 505 or (resid 506 and (name N or name CA or na \ me C or name O or name CB )) or resid 511 through 549 or (resid 550 and (name N \ or name CA or name C or name O or name CB )) or resid 551 through 573 or resid 5 \ 75 through 593 or (resid 594 and (name N or name CA or name C or name O or name \ CB )) or resid 595 through 626 or resid 636 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 818 or (resi \ d 819 through 823 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 549 or (resid 550 and (name N or name CA or na \ me C or name O or name CB )) or resid 551 or (resid 569 and (name N or name CA o \ r name C or name O or name CB )) or resid 570 through 573 or resid 575 or (resid \ 576 and (name N or name CA or name C or name O or name CB )) or resid 577 throu \ gh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) or \ resid 595 through 626 or resid 636 through 773 or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 16 \ 2 or resid 173 through 210)) } 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=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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.550 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 50.290 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5696 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 : 0.013 0.116 17358 Z= 0.846 Angle : 1.650 12.309 23571 Z= 1.247 Chirality : 0.114 0.386 2733 Planarity : 0.015 0.237 2896 Dihedral : 14.120 88.325 5739 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.39 % Favored : 95.25 % Rotamer: Outliers : 1.02 % Allowed : 6.92 % Favored : 92.06 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 23.08 % 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: -1.65 (0.15), residues: 2218 helix: -0.34 (0.12), residues: 1299 sheet: -1.86 (0.36), residues: 165 loop : -2.11 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 605 HIS 0.008 0.002 HIS G 60 PHE 0.027 0.005 PHE B 517 TYR 0.021 0.004 TYR B 440 ARG 0.011 0.002 ARG F 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 519 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.9257 (mmt) cc_final: 0.8976 (mmm) REVERT: B 545 ARG cc_start: 0.8626 (mtm180) cc_final: 0.8077 (mtm-85) REVERT: C 485 ARG cc_start: -0.0034 (mtt180) cc_final: -0.2947 (mtt90) REVERT: C 496 MET cc_start: -0.2567 (ptm) cc_final: -0.4362 (ttp) REVERT: C 813 GLU cc_start: 0.8917 (tt0) cc_final: 0.8516 (tp30) REVERT: C 817 LYS cc_start: 0.9137 (mmtp) cc_final: 0.8925 (mmtt) REVERT: D 611 ILE cc_start: 0.8199 (mm) cc_final: 0.7804 (mm) REVERT: D 803 LEU cc_start: 0.8917 (mt) cc_final: 0.8648 (mt) REVERT: E 24 MET cc_start: 0.8386 (tpt) cc_final: 0.8126 (tpp) REVERT: E 133 ASN cc_start: 0.8699 (t0) cc_final: 0.8393 (t0) REVERT: E 140 ILE cc_start: 0.9399 (mm) cc_final: 0.8860 (pt) REVERT: E 176 TYR cc_start: 0.7878 (m-80) cc_final: 0.7357 (m-80) REVERT: F 13 THR cc_start: 0.8527 (m) cc_final: 0.8327 (m) REVERT: F 84 PRO cc_start: 0.8231 (Cg_endo) cc_final: 0.7887 (Cg_exo) REVERT: F 174 TYR cc_start: 0.7789 (p90) cc_final: 0.7221 (p90) REVERT: F 187 PHE cc_start: 0.7627 (t80) cc_final: 0.7218 (t80) REVERT: F 192 MET cc_start: 0.7909 (mtt) cc_final: 0.7650 (mmt) REVERT: G 76 LEU cc_start: 0.8981 (mm) cc_final: 0.8465 (mt) REVERT: G 105 SER cc_start: 0.8840 (m) cc_final: 0.8626 (p) REVERT: G 108 PRO cc_start: 0.8587 (Cg_exo) cc_final: 0.8387 (Cg_endo) REVERT: G 160 ASN cc_start: 0.8212 (m-40) cc_final: 0.7976 (m-40) REVERT: H 6 ARG cc_start: 0.7606 (tmt170) cc_final: 0.7366 (ttp80) REVERT: H 105 SER cc_start: 0.7623 (m) cc_final: 0.7235 (m) REVERT: H 125 SER cc_start: 0.9324 (t) cc_final: 0.9106 (p) REVERT: H 137 SER cc_start: 0.9180 (m) cc_final: 0.8914 (p) outliers start: 17 outliers final: 4 residues processed: 531 average time/residue: 0.3203 time to fit residues: 245.7237 Evaluate side-chains 295 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 291 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 504 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS C 461 ASN D 461 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 199 HIS G 79 GLN ** H 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17358 Z= 0.206 Angle : 0.631 10.652 23571 Z= 0.334 Chirality : 0.043 0.171 2733 Planarity : 0.004 0.050 2896 Dihedral : 4.591 54.378 2436 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.43 % Allowed : 15.51 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 0.75 (0.18), residues: 2218 helix: 1.87 (0.14), residues: 1313 sheet: -1.41 (0.34), residues: 190 loop : -1.61 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 767 HIS 0.007 0.001 HIS F 60 PHE 0.025 0.002 PHE G 180 TYR 0.013 0.001 TYR A 405 ARG 0.008 0.001 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 334 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 TRP cc_start: 0.1607 (m100) cc_final: 0.0949 (m100) REVERT: C 485 ARG cc_start: 0.0906 (mtt180) cc_final: -0.2422 (mtt90) REVERT: C 496 MET cc_start: -0.2546 (ptm) cc_final: -0.4484 (ttp) REVERT: C 813 GLU cc_start: 0.8888 (tt0) cc_final: 0.8479 (tp30) REVERT: D 519 ASP cc_start: 0.8309 (m-30) cc_final: 0.7999 (t70) REVERT: E 24 MET cc_start: 0.8476 (tpt) cc_final: 0.8220 (tpp) REVERT: E 59 THR cc_start: 0.7189 (p) cc_final: 0.6922 (p) REVERT: E 147 LEU cc_start: 0.9440 (mm) cc_final: 0.9179 (mt) REVERT: E 174 TYR cc_start: 0.7404 (p90) cc_final: 0.6921 (p90) REVERT: G 41 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7277 (mtmm) REVERT: G 76 LEU cc_start: 0.9047 (mm) cc_final: 0.8828 (tp) REVERT: H 6 ARG cc_start: 0.8071 (tmt170) cc_final: 0.7586 (ttp80) REVERT: H 10 MET cc_start: 0.8397 (tmm) cc_final: 0.8075 (tmm) REVERT: H 32 TYR cc_start: 0.7888 (m-80) cc_final: 0.7395 (m-80) REVERT: H 95 GLU cc_start: 0.9106 (tt0) cc_final: 0.8647 (tm-30) outliers start: 57 outliers final: 32 residues processed: 366 average time/residue: 0.3028 time to fit residues: 163.9410 Evaluate side-chains 296 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 787 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 789 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 720 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 121 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 139 optimal weight: 40.0000 chunk 56 optimal weight: 0.1980 chunk 204 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS H 160 ASN H 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 17358 Z= 0.367 Angle : 0.687 8.502 23571 Z= 0.364 Chirality : 0.045 0.234 2733 Planarity : 0.004 0.039 2896 Dihedral : 4.323 40.015 2429 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.63 % Allowed : 15.81 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2218 helix: 2.06 (0.14), residues: 1332 sheet: -1.58 (0.38), residues: 158 loop : -1.30 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 766 HIS 0.046 0.003 HIS E 199 PHE 0.021 0.002 PHE E 127 TYR 0.023 0.002 TYR D 549 ARG 0.009 0.001 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 256 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 803 LEU cc_start: 0.9445 (mt) cc_final: 0.9216 (mp) REVERT: C 485 ARG cc_start: 0.0639 (mtt180) cc_final: -0.1882 (mtt90) REVERT: C 496 MET cc_start: -0.2370 (ptm) cc_final: -0.3849 (ttp) REVERT: C 669 LYS cc_start: 0.5176 (tptt) cc_final: 0.4975 (tptt) REVERT: C 671 TRP cc_start: -0.0468 (t-100) cc_final: -0.0860 (t-100) REVERT: C 813 GLU cc_start: 0.9208 (tt0) cc_final: 0.8850 (tp30) REVERT: D 519 ASP cc_start: 0.9371 (m-30) cc_final: 0.8905 (t70) REVERT: D 543 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9218 (t) REVERT: E 205 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7828 (t-90) REVERT: F 37 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6293 (ptt-90) REVERT: F 70 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: G 6 ARG cc_start: 0.7830 (tpt90) cc_final: 0.7526 (tpt90) REVERT: G 10 MET cc_start: 0.7747 (ptt) cc_final: 0.7320 (ptt) REVERT: G 41 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7767 (ptpp) REVERT: G 76 LEU cc_start: 0.9225 (mm) cc_final: 0.8922 (tp) REVERT: H 6 ARG cc_start: 0.8419 (tmt170) cc_final: 0.8078 (ttp80) REVERT: H 10 MET cc_start: 0.8548 (tmm) cc_final: 0.8277 (tmm) REVERT: H 95 GLU cc_start: 0.9294 (tt0) cc_final: 0.8880 (tm-30) REVERT: H 200 MET cc_start: 0.9305 (ttm) cc_final: 0.9091 (ttm) outliers start: 77 outliers final: 43 residues processed: 311 average time/residue: 0.3203 time to fit residues: 146.0144 Evaluate side-chains 265 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 97 PHE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 133 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 106 optimal weight: 30.0000 chunk 22 optimal weight: 30.0000 chunk 97 optimal weight: 0.5980 chunk 137 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN E 199 HIS ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN H 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17358 Z= 0.175 Angle : 0.553 7.996 23571 Z= 0.290 Chirality : 0.041 0.179 2733 Planarity : 0.003 0.033 2896 Dihedral : 3.936 37.994 2427 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.71 % Allowed : 19.06 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.60 (0.18), residues: 2218 helix: 2.52 (0.14), residues: 1323 sheet: -1.20 (0.39), residues: 159 loop : -1.21 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 178 HIS 0.007 0.001 HIS E 199 PHE 0.020 0.001 PHE F 73 TYR 0.011 0.001 TYR E 174 ARG 0.006 0.001 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9201 (p0) cc_final: 0.8998 (p0) REVERT: C 485 ARG cc_start: 0.0673 (mtt180) cc_final: -0.2495 (mtt90) REVERT: C 496 MET cc_start: -0.2419 (ptm) cc_final: -0.3811 (ttp) REVERT: C 670 MET cc_start: 0.1452 (mtp) cc_final: 0.1108 (ptp) REVERT: C 671 TRP cc_start: -0.0546 (t-100) cc_final: -0.0819 (t-100) REVERT: C 813 GLU cc_start: 0.9187 (tt0) cc_final: 0.8845 (tp30) REVERT: D 519 ASP cc_start: 0.9269 (m-30) cc_final: 0.8868 (t70) REVERT: E 160 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8938 (m-40) REVERT: E 191 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8666 (mm-30) REVERT: F 37 ARG cc_start: 0.6931 (ttm170) cc_final: 0.6021 (ptt-90) REVERT: F 70 GLU cc_start: 0.8506 (mp0) cc_final: 0.7590 (pp20) REVERT: F 84 PRO cc_start: 0.7017 (Cg_exo) cc_final: 0.6495 (Cg_endo) REVERT: F 128 TYR cc_start: 0.8343 (t80) cc_final: 0.7882 (t80) REVERT: G 6 ARG cc_start: 0.7946 (tpt90) cc_final: 0.7648 (tpt90) REVERT: G 10 MET cc_start: 0.7703 (ptt) cc_final: 0.7220 (ptt) REVERT: G 41 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7622 (ptpp) REVERT: G 76 LEU cc_start: 0.9276 (mm) cc_final: 0.9018 (tp) REVERT: H 6 ARG cc_start: 0.8416 (tmt170) cc_final: 0.8113 (ttp80) REVERT: H 92 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7115 (p0) REVERT: H 95 GLU cc_start: 0.9307 (tt0) cc_final: 0.8816 (tm-30) REVERT: H 109 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9141 (pt) outliers start: 45 outliers final: 26 residues processed: 290 average time/residue: 0.3220 time to fit residues: 136.5232 Evaluate side-chains 258 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 109 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 185 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 54 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN E 199 HIS F 207 GLN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17358 Z= 0.170 Angle : 0.548 9.044 23571 Z= 0.283 Chirality : 0.040 0.159 2733 Planarity : 0.003 0.037 2896 Dihedral : 3.754 17.772 2425 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.37 % Allowed : 18.88 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.70 (0.19), residues: 2218 helix: 2.56 (0.14), residues: 1329 sheet: -1.10 (0.40), residues: 158 loop : -1.13 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 178 HIS 0.013 0.001 HIS E 199 PHE 0.020 0.001 PHE E 73 TYR 0.011 0.001 TYR E 174 ARG 0.008 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 LYS cc_start: 0.5072 (OUTLIER) cc_final: 0.4147 (mmtt) REVERT: C 485 ARG cc_start: 0.0701 (mtt180) cc_final: -0.2495 (mtt90) REVERT: C 496 MET cc_start: -0.2059 (ptm) cc_final: -0.4164 (ttp) REVERT: C 586 ARG cc_start: 0.9550 (mmm-85) cc_final: 0.9294 (ttm110) REVERT: C 670 MET cc_start: 0.1238 (mtp) cc_final: 0.1013 (ptp) REVERT: C 813 GLU cc_start: 0.9193 (tt0) cc_final: 0.8849 (tp30) REVERT: D 519 ASP cc_start: 0.9271 (m-30) cc_final: 0.8853 (t70) REVERT: D 669 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5476 (ptmt) REVERT: E 191 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8643 (mm-30) REVERT: F 70 GLU cc_start: 0.8581 (mp0) cc_final: 0.7359 (pp20) REVERT: F 128 TYR cc_start: 0.8283 (t80) cc_final: 0.7855 (t80) REVERT: F 207 GLN cc_start: 0.9251 (pt0) cc_final: 0.8942 (pp30) REVERT: G 6 ARG cc_start: 0.7762 (tpt90) cc_final: 0.7549 (tpt90) REVERT: G 10 MET cc_start: 0.7716 (ptt) cc_final: 0.7297 (ptt) REVERT: G 41 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7566 (ptpp) REVERT: G 76 LEU cc_start: 0.9256 (mm) cc_final: 0.9022 (tp) REVERT: G 127 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: H 6 ARG cc_start: 0.8441 (tmt170) cc_final: 0.8146 (ttp80) REVERT: H 92 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7002 (p0) REVERT: H 95 GLU cc_start: 0.9328 (tt0) cc_final: 0.8822 (tm-30) REVERT: H 109 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9062 (pt) outliers start: 56 outliers final: 35 residues processed: 275 average time/residue: 0.3271 time to fit residues: 131.8965 Evaluate side-chains 262 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 221 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 60 HIS Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 30.0000 chunk 195 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 ASN ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17358 Z= 0.265 Angle : 0.590 9.182 23571 Z= 0.307 Chirality : 0.041 0.166 2733 Planarity : 0.004 0.047 2896 Dihedral : 3.813 17.171 2425 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.51 % Allowed : 19.84 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.73 (0.19), residues: 2218 helix: 2.54 (0.14), residues: 1323 sheet: -0.93 (0.43), residues: 149 loop : -1.03 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 766 HIS 0.026 0.002 HIS E 199 PHE 0.016 0.001 PHE F 73 TYR 0.013 0.001 TYR A 440 ARG 0.006 0.001 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 224 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 485 ARG cc_start: 0.0377 (mtt180) cc_final: -0.2041 (mtt90) REVERT: C 586 ARG cc_start: 0.9559 (mmm-85) cc_final: 0.9328 (ttm110) REVERT: C 813 GLU cc_start: 0.9207 (tt0) cc_final: 0.8897 (tp30) REVERT: D 519 ASP cc_start: 0.9319 (m-30) cc_final: 0.8905 (t70) REVERT: D 669 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5431 (ptmt) REVERT: F 128 TYR cc_start: 0.8240 (t80) cc_final: 0.7762 (t80) REVERT: G 127 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: H 6 ARG cc_start: 0.8570 (tmt170) cc_final: 0.8270 (tmm160) REVERT: H 58 MET cc_start: 0.9059 (tpt) cc_final: 0.8734 (tpt) REVERT: H 92 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7354 (p0) REVERT: H 95 GLU cc_start: 0.9260 (tt0) cc_final: 0.8839 (tm-30) REVERT: H 109 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9116 (pt) outliers start: 75 outliers final: 48 residues processed: 278 average time/residue: 0.3094 time to fit residues: 128.1156 Evaluate side-chains 270 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 135 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17358 Z= 0.253 Angle : 0.592 10.542 23571 Z= 0.306 Chirality : 0.041 0.234 2733 Planarity : 0.003 0.051 2896 Dihedral : 3.812 18.013 2425 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.21 % Allowed : 20.08 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.79 (0.19), residues: 2218 helix: 2.59 (0.14), residues: 1324 sheet: -0.99 (0.43), residues: 149 loop : -1.00 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 766 HIS 0.004 0.001 HIS H 205 PHE 0.028 0.001 PHE F 73 TYR 0.023 0.001 TYR C 711 ARG 0.006 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 233 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9313 (p0) cc_final: 0.9023 (p0) REVERT: C 485 ARG cc_start: 0.0418 (mtt180) cc_final: -0.2050 (mtt90) REVERT: C 496 MET cc_start: -0.4148 (ptm) cc_final: -0.4371 (tmm) REVERT: C 586 ARG cc_start: 0.9538 (mmm-85) cc_final: 0.9323 (ttm110) REVERT: C 813 GLU cc_start: 0.9227 (tt0) cc_final: 0.8947 (tp30) REVERT: D 519 ASP cc_start: 0.9327 (m-30) cc_final: 0.8892 (t70) REVERT: D 669 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5260 (ptmt) REVERT: D 704 LEU cc_start: 0.4375 (pt) cc_final: 0.4147 (pt) REVERT: E 160 ASN cc_start: 0.9254 (t0) cc_final: 0.8961 (m-40) REVERT: E 203 ASP cc_start: 0.9583 (t0) cc_final: 0.9299 (t70) REVERT: F 70 GLU cc_start: 0.8586 (mp0) cc_final: 0.7852 (pp20) REVERT: F 128 TYR cc_start: 0.8262 (t80) cc_final: 0.7745 (t80) REVERT: G 6 ARG cc_start: 0.7815 (tpt90) cc_final: 0.7410 (tpt90) REVERT: G 127 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: H 6 ARG cc_start: 0.8585 (tmt170) cc_final: 0.8261 (tmm160) REVERT: H 58 MET cc_start: 0.9097 (tpt) cc_final: 0.8691 (tpt) REVERT: H 109 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9015 (pt) REVERT: H 120 LEU cc_start: 0.9695 (tp) cc_final: 0.9490 (tp) outliers start: 70 outliers final: 50 residues processed: 281 average time/residue: 0.3191 time to fit residues: 133.0501 Evaluate side-chains 274 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 534 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 709 ASN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 197 optimal weight: 0.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17358 Z= 0.199 Angle : 0.591 11.348 23571 Z= 0.300 Chirality : 0.041 0.258 2733 Planarity : 0.003 0.044 2896 Dihedral : 3.770 18.045 2425 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.19 % Allowed : 20.99 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.85 (0.19), residues: 2218 helix: 2.61 (0.14), residues: 1329 sheet: -0.78 (0.45), residues: 141 loop : -0.99 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 766 HIS 0.004 0.001 HIS E 132 PHE 0.022 0.001 PHE F 73 TYR 0.012 0.001 TYR D 732 ARG 0.020 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 239 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.9335 (p0) cc_final: 0.9037 (p0) REVERT: A 722 LYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4332 (tppt) REVERT: C 485 ARG cc_start: -0.0143 (mtt180) cc_final: -0.1874 (mtt90) REVERT: C 496 MET cc_start: -0.3923 (ptm) cc_final: -0.4240 (tmm) REVERT: C 586 ARG cc_start: 0.9524 (mmm-85) cc_final: 0.9306 (ttm110) REVERT: C 813 GLU cc_start: 0.9225 (tt0) cc_final: 0.8959 (tp30) REVERT: D 519 ASP cc_start: 0.9317 (m-30) cc_final: 0.8872 (t70) REVERT: D 721 MET cc_start: 0.7212 (pmm) cc_final: 0.6839 (pmm) REVERT: E 160 ASN cc_start: 0.9229 (t0) cc_final: 0.8830 (m-40) REVERT: E 203 ASP cc_start: 0.9596 (t0) cc_final: 0.9361 (t70) REVERT: F 70 GLU cc_start: 0.8679 (mp0) cc_final: 0.7808 (pp20) REVERT: F 72 ASN cc_start: 0.8017 (p0) cc_final: 0.7759 (p0) REVERT: F 128 TYR cc_start: 0.8213 (t80) cc_final: 0.7660 (t80) REVERT: G 6 ARG cc_start: 0.7995 (tpt90) cc_final: 0.7331 (tpt90) REVERT: G 30 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9054 (p) REVERT: G 127 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: H 6 ARG cc_start: 0.8617 (tmt170) cc_final: 0.8283 (tmm160) REVERT: H 58 MET cc_start: 0.9114 (tpt) cc_final: 0.8750 (tpt) REVERT: H 95 GLU cc_start: 0.9301 (tt0) cc_final: 0.9054 (pp20) REVERT: H 109 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8895 (pt) outliers start: 53 outliers final: 41 residues processed: 276 average time/residue: 0.3219 time to fit residues: 130.8001 Evaluate side-chains 269 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 224 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.7920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 17358 Z= 0.376 Angle : 0.717 16.548 23571 Z= 0.366 Chirality : 0.043 0.318 2733 Planarity : 0.004 0.048 2896 Dihedral : 4.085 26.255 2425 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.85 % Allowed : 21.47 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.57 (0.18), residues: 2218 helix: 2.30 (0.14), residues: 1330 sheet: -0.90 (0.48), residues: 131 loop : -0.93 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 766 HIS 0.007 0.001 HIS H 199 PHE 0.023 0.002 PHE F 73 TYR 0.020 0.002 TYR C 711 ARG 0.012 0.001 ARG D 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 225 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.4614 (OUTLIER) cc_final: 0.4321 (pp) REVERT: A 722 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.4877 (ttmm) REVERT: C 485 ARG cc_start: -0.0101 (mtt180) cc_final: -0.2519 (mtt90) REVERT: C 496 MET cc_start: -0.4224 (ptm) cc_final: -0.4505 (tmm) REVERT: C 586 ARG cc_start: 0.9523 (mmm-85) cc_final: 0.9207 (ttm110) REVERT: C 813 GLU cc_start: 0.9284 (tt0) cc_final: 0.8958 (mm-30) REVERT: D 519 ASP cc_start: 0.9321 (m-30) cc_final: 0.8956 (t70) REVERT: D 721 MET cc_start: 0.7345 (pmm) cc_final: 0.6965 (pmm) REVERT: E 160 ASN cc_start: 0.9308 (t0) cc_final: 0.9044 (m-40) REVERT: E 203 ASP cc_start: 0.9596 (t0) cc_final: 0.9388 (t70) REVERT: F 69 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7407 (pp) REVERT: F 70 GLU cc_start: 0.8868 (mp0) cc_final: 0.8196 (pp20) REVERT: F 128 TYR cc_start: 0.8235 (t80) cc_final: 0.7576 (t80) REVERT: G 6 ARG cc_start: 0.7838 (tpt90) cc_final: 0.7183 (tpt90) REVERT: G 10 MET cc_start: 0.7680 (ptt) cc_final: 0.7352 (ptt) REVERT: G 30 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9046 (p) REVERT: G 127 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: H 6 ARG cc_start: 0.8576 (tmt170) cc_final: 0.8251 (tmm160) REVERT: H 109 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9052 (pt) REVERT: H 199 HIS cc_start: 0.9245 (OUTLIER) cc_final: 0.9009 (t-170) outliers start: 64 outliers final: 49 residues processed: 272 average time/residue: 0.3148 time to fit residues: 125.4396 Evaluate side-chains 267 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 211 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 811 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 651 ASP Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain D residue 755 GLU Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 60 HIS Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 101 optimal weight: 0.0670 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 206 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.8037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17358 Z= 0.167 Angle : 0.632 12.669 23571 Z= 0.316 Chirality : 0.041 0.257 2733 Planarity : 0.003 0.041 2896 Dihedral : 3.932 25.245 2425 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.29 % Allowed : 23.03 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % 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: 1.90 (0.19), residues: 2218 helix: 2.63 (0.15), residues: 1326 sheet: -0.79 (0.45), residues: 144 loop : -0.92 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 178 HIS 0.004 0.001 HIS E 199 PHE 0.023 0.001 PHE A 659 TYR 0.014 0.001 TYR D 732 ARG 0.011 0.001 ARG D 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4436 Ramachandran restraints generated. 2218 Oldfield, 0 Emsley, 2218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.3478 (OUTLIER) cc_final: 0.3194 (pp) REVERT: A 722 LYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5106 (tppt) REVERT: C 485 ARG cc_start: -0.0318 (mtt180) cc_final: -0.2352 (mtt90) REVERT: C 496 MET cc_start: -0.3660 (ptm) cc_final: -0.4097 (tmm) REVERT: C 813 GLU cc_start: 0.9244 (tt0) cc_final: 0.8946 (mm-30) REVERT: D 519 ASP cc_start: 0.9300 (m-30) cc_final: 0.8864 (t70) REVERT: E 18 PHE cc_start: 0.9468 (t80) cc_final: 0.9261 (t80) REVERT: E 160 ASN cc_start: 0.9251 (t0) cc_final: 0.8951 (m-40) REVERT: E 191 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8950 (mm-30) REVERT: E 203 ASP cc_start: 0.9618 (t0) cc_final: 0.9396 (t70) REVERT: F 69 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7790 (pp) REVERT: F 70 GLU cc_start: 0.8777 (mp0) cc_final: 0.7866 (pp20) REVERT: F 120 LEU cc_start: 0.9124 (mt) cc_final: 0.8907 (tt) REVERT: F 128 TYR cc_start: 0.8237 (t80) cc_final: 0.7693 (t80) REVERT: G 6 ARG cc_start: 0.7806 (tpt90) cc_final: 0.7242 (tpt90) REVERT: G 10 MET cc_start: 0.7730 (ptt) cc_final: 0.7205 (ptt) REVERT: G 127 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: H 6 ARG cc_start: 0.8560 (tmt170) cc_final: 0.8189 (ttp80) REVERT: H 80 ILE cc_start: 0.8648 (mp) cc_final: 0.8341 (mp) REVERT: H 95 GLU cc_start: 0.9259 (tt0) cc_final: 0.8919 (pp20) REVERT: H 97 PHE cc_start: 0.9097 (t80) cc_final: 0.8882 (t80) REVERT: H 109 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8973 (pt) REVERT: H 192 MET cc_start: 0.8844 (mtm) cc_final: 0.8521 (mmt) outliers start: 38 outliers final: 27 residues processed: 261 average time/residue: 0.3220 time to fit residues: 123.7912 Evaluate side-chains 256 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 TRP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 613 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 580 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 674 MET Chi-restraints excluded: chain D residue 703 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 109 ILE Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.145311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090300 restraints weight = 93186.760| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 8.17 r_work: 0.2920 rms_B_bonded: 6.48 restraints_weight: 2.0000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.8332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17358 Z= 0.345 Angle : 0.685 13.022 23571 Z= 0.349 Chirality : 0.043 0.214 2733 Planarity : 0.004 0.043 2896 Dihedral : 4.043 25.847 2425 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.65 % Allowed : 23.27 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 23.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.19), residues: 2218 helix: 2.39 (0.15), residues: 1329 sheet: -0.68 (0.51), residues: 125 loop : -0.95 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 766 HIS 0.005 0.001 HIS H 205 PHE 0.019 0.002 PHE A 659 TYR 0.012 0.002 TYR F 176 ARG 0.010 0.001 ARG D 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4066.30 seconds wall clock time: 74 minutes 46.82 seconds (4486.82 seconds total)