Starting phenix.real_space_refine on Thu Feb 15 11:49:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qq6_4619/02_2024/6qq6_4619_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 P 3 5.49 5 S 46 5.16 5 C 8019 2.51 5 N 1991 2.21 5 O 2056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 559": "OE1" <-> "OE2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A ASP 724": "OD1" <-> "OD2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ASP 396": "OD1" <-> "OD2" Residue "B ASP 410": "OD1" <-> "OD2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B ARG 471": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B ARG 575": "NH1" <-> "NH2" Residue "B ASP 724": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12123 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6041 Chain: "B" Number of atoms: 5872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 743, 5862 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 707} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 6041 Chain: "A" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 130 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LOP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'LMT': 2, 'LOP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.50 residue: pdb=" N AHIS B 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.50 Time building chain proxies: 12.19, per 1000 atoms: 1.01 Number of scatterers: 12123 At special positions: 0 Unit cell: (118.65, 74.55, 103.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 46 16.00 P 3 15.00 O 2056 8.00 N 1991 7.00 C 8019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 4.0 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 0 sheets defined 58.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 3.559A pdb=" N PHE A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 83 through 104 removed outlier: 3.883A pdb=" N LEU A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.155A pdb=" N ALA A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 removed outlier: 3.988A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.977A pdb=" N HIS A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.722A pdb=" N LEU A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 removed outlier: 4.663A pdb=" N LEU A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.880A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) Proline residue: A 352 - end of helix Processing helix chain 'A' and resid 364 through 389 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 413 through 437 removed outlier: 3.924A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.658A pdb=" N ALA A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 527 through 530 No H-bonds generated for 'chain 'A' and resid 527 through 530' Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.841A pdb=" N PHE A 536 " --> pdb=" O PRO A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 removed outlier: 3.535A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.590A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 578 " --> pdb=" O TRP A 574 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 579' Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.925A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TRP A 588 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Proline residue: A 589 - end of helix removed outlier: 4.078A pdb=" N PHE A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 596 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP A 599 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 626 through 634 Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.584A pdb=" N LEU A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.582A pdb=" N ILE A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.740A pdb=" N ARG A 703 " --> pdb=" O MET A 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 699 through 703' Processing helix chain 'A' and resid 705 through 708 No H-bonds generated for 'chain 'A' and resid 705 through 708' Processing helix chain 'A' and resid 713 through 741 removed outlier: 3.574A pdb=" N ARG A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 722 " --> pdb=" O TRP A 718 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 removed outlier: 3.551A pdb=" N PHE B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU B 28 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 83 through 104 removed outlier: 3.826A pdb=" N LEU B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.164A pdb=" N ALA B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.967A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 156 " --> pdb=" O THR B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.976A pdb=" N HIS B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.733A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 303 removed outlier: 4.712A pdb=" N LEU B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLY B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 324 through 354 removed outlier: 3.881A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) Proline residue: B 352 - end of helix Processing helix chain 'B' and resid 364 through 389 Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 413 through 437 removed outlier: 3.928A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 494 through 497 No H-bonds generated for 'chain 'B' and resid 494 through 497' Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 518 through 521 No H-bonds generated for 'chain 'B' and resid 518 through 521' Processing helix chain 'B' and resid 527 through 530 No H-bonds generated for 'chain 'B' and resid 527 through 530' Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.889A pdb=" N PHE B 536 " --> pdb=" O PRO B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 557 removed outlier: 3.879A pdb=" N SER B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 4.057A pdb=" N LEU B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR B 578 " --> pdb=" O TRP B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 578' Processing helix chain 'B' and resid 581 through 601 removed outlier: 3.932A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 587 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP B 588 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.017A pdb=" N PHE B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 596 " --> pdb=" O PHE B 593 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 599 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 609 No H-bonds generated for 'chain 'B' and resid 606 through 609' Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 626 through 634 Processing helix chain 'B' and resid 641 through 650 removed outlier: 3.589A pdb=" N LEU B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 649 " --> pdb=" O PHE B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 671 through 680 removed outlier: 3.588A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.758A pdb=" N ARG B 703 " --> pdb=" O MET B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 703' Processing helix chain 'B' and resid 705 through 708 No H-bonds generated for 'chain 'B' and resid 705 through 708' Processing helix chain 'B' and resid 713 through 741 removed outlier: 3.627A pdb=" N ARG B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N PHE B 722 " --> pdb=" O TRP B 718 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1443 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: 3.31 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3747 1.35 - 1.53: 7671 1.53 - 1.70: 992 1.70 - 1.88: 88 1.88 - 2.05: 16 Bond restraints: 12514 Sorted by residual: bond pdb=" C1B LMT B 807 " pdb=" O5B LMT B 807 " ideal model delta sigma weight residual 1.393 1.508 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C1B LMT B 808 " pdb=" O5B LMT B 808 " ideal model delta sigma weight residual 1.393 1.506 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C1' LMT B 807 " pdb=" O5' LMT B 807 " ideal model delta sigma weight residual 1.408 1.499 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1' LMT B 808 " pdb=" O5' LMT B 808 " ideal model delta sigma weight residual 1.408 1.493 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C24 LOP B 806 " pdb=" O6 LOP B 806 " ideal model delta sigma weight residual 1.325 1.401 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 12509 not shown) Histogram of bond angle deviations from ideal: 89.01 - 107.17: 497 107.17 - 125.32: 16076 125.32 - 143.47: 528 143.47 - 161.62: 0 161.62 - 179.78: 8 Bond angle restraints: 17109 Sorted by residual: angle pdb=" N ILE B 712 " pdb=" CA ILE B 712 " pdb=" C ILE B 712 " ideal model delta sigma weight residual 112.96 106.66 6.30 1.00e+00 1.00e+00 3.97e+01 angle pdb=" N ILE A 712 " pdb=" CA ILE A 712 " pdb=" C ILE A 712 " ideal model delta sigma weight residual 112.96 106.69 6.27 1.00e+00 1.00e+00 3.93e+01 angle pdb=" N GLU A 572 " pdb=" CA GLU A 572 " pdb=" C GLU A 572 " ideal model delta sigma weight residual 111.14 104.83 6.31 1.08e+00 8.57e-01 3.41e+01 angle pdb=" CA PHE A 536 " pdb=" C PHE A 536 " pdb=" N HIS A 537 " ideal model delta sigma weight residual 118.59 127.92 -9.33 1.63e+00 3.76e-01 3.28e+01 angle pdb=" N ARG B 579 " pdb=" CA ARG B 579 " pdb=" C ARG B 579 " ideal model delta sigma weight residual 111.36 117.57 -6.21 1.09e+00 8.42e-01 3.25e+01 ... (remaining 17104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 6525 22.36 - 44.71: 442 44.71 - 67.07: 81 67.07 - 89.43: 16 89.43 - 111.79: 14 Dihedral angle restraints: 7078 sinusoidal: 2846 harmonic: 4232 Sorted by residual: dihedral pdb=" CA ASN A 214 " pdb=" C ASN A 214 " pdb=" N TRP A 215 " pdb=" CA TRP A 215 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ASN B 214 " pdb=" C ASN B 214 " pdb=" N TRP B 215 " pdb=" CA TRP B 215 " ideal model delta harmonic sigma weight residual -180.00 -154.51 -25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA TYR B 652 " pdb=" C TYR B 652 " pdb=" N ILE B 653 " pdb=" CA ILE B 653 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1510 0.066 - 0.133: 256 0.133 - 0.199: 31 0.199 - 0.266: 5 0.266 - 0.332: 5 Chirality restraints: 1807 Sorted by residual: chirality pdb=" CA ILE B 392 " pdb=" N ILE B 392 " pdb=" C ILE B 392 " pdb=" CB ILE B 392 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE A 620 " pdb=" CA ILE A 620 " pdb=" CG1 ILE A 620 " pdb=" CG2 ILE A 620 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 1804 not shown) Planarity restraints: 2113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 179 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C THR A 179 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 179 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU A 180 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO B 589 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 588 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO A 589 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " -0.032 5.00e-02 4.00e+02 ... (remaining 2110 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 89 2.52 - 3.11: 8190 3.11 - 3.71: 19944 3.71 - 4.30: 29018 4.30 - 4.90: 48267 Nonbonded interactions: 105508 Sorted by model distance: nonbonded pdb=" O ASP A 162 " pdb=" OD1 ASP A 162 " model vdw 1.924 3.040 nonbonded pdb=" NE2 HIS B 538 " pdb="FE FE B 803 " model vdw 1.988 2.340 nonbonded pdb=" NE2 HIS A 538 " pdb="FE FE A 803 " model vdw 1.989 2.340 nonbonded pdb=" NE2 HIS B 631 " pdb="FE HEM B 801 " model vdw 1.996 3.080 nonbonded pdb=" NE2 HIS A 631 " pdb="FE HEM A 801 " model vdw 1.996 3.080 ... (remaining 105503 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 1 through 223 or resid 225 through 743 or resid 801 throug \ h 804 or (resid 805 and (name C1 or name C10 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C24 or name C25 or name C26 or name C27 or name C28 or n \ ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name \ O5 or name O6 or name O7 or name O8 or name P1 )))) selection = (chain 'B' and (resid 1 through 223 or resid 225 through 743 or resid 801 throug \ h 804 or (resid 805 and (name C1 or name C10 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name \ C2 or name C20 or name C24 or name C25 or name C26 or name C27 or name C28 or n \ ame C29 or name C3 or name C30 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 or name \ O5 or name O6 or name O7 or name O8 or name P1 )))) } 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: 0.350 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: 2.340 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 41.850 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 48.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.007 0.115 12514 Z= 0.415 Angle : 1.076 11.372 17109 Z= 0.544 Chirality : 0.055 0.332 1807 Planarity : 0.007 0.059 2113 Dihedral : 16.787 111.787 4390 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.15), residues: 1488 helix: -3.17 (0.11), residues: 988 sheet: None (None), residues: 0 loop : -3.43 (0.21), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 215 HIS 0.007 0.002 HIS B 537 PHE 0.022 0.002 PHE A 635 TYR 0.019 0.002 TYR A 468 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3616 (ptp) cc_final: 0.2964 (ttp) REVERT: A 718 TRP cc_start: 0.6828 (t60) cc_final: 0.6101 (t60) REVERT: B 1 MET cc_start: 0.3557 (ptp) cc_final: 0.3099 (ptp) REVERT: B 355 ASN cc_start: 0.8773 (t0) cc_final: 0.8303 (t0) REVERT: B 430 MET cc_start: 0.8193 (mmm) cc_final: 0.7888 (tpt) REVERT: B 718 TRP cc_start: 0.6139 (t60) cc_final: 0.5721 (t60) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2542 time to fit residues: 78.5639 Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 130 ASN A 224 HIS A A 305 HIS A 355 ASN A 398 ASN B 68 GLN B 130 ASN B 214 ASN B 355 ASN B 398 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12514 Z= 0.208 Angle : 0.639 8.902 17109 Z= 0.310 Chirality : 0.041 0.337 1807 Planarity : 0.005 0.053 2113 Dihedral : 11.318 87.992 1874 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.12 % Allowed : 8.76 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.20), residues: 1488 helix: -1.38 (0.15), residues: 970 sheet: None (None), residues: 0 loop : -2.68 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 215 HIS 0.004 0.001 HIS A 331 PHE 0.014 0.001 PHE B 635 TYR 0.021 0.002 TYR B 108 ARG 0.009 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.198 Fit side-chains REVERT: A 1 MET cc_start: 0.3454 (ptp) cc_final: 0.2860 (ttp) REVERT: A 276 THR cc_start: 0.8236 (p) cc_final: 0.7767 (p) REVERT: A 280 ARG cc_start: 0.7225 (mtm110) cc_final: 0.6676 (mtm110) REVERT: A 494 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 677 LEU cc_start: 0.8327 (tp) cc_final: 0.8118 (tt) REVERT: A 718 TRP cc_start: 0.6884 (t60) cc_final: 0.6268 (t60) REVERT: B 1 MET cc_start: 0.3375 (ptp) cc_final: 0.2839 (ptp) REVERT: B 355 ASN cc_start: 0.8840 (t0) cc_final: 0.8334 (t0) REVERT: B 430 MET cc_start: 0.8587 (mmm) cc_final: 0.8216 (tpt) REVERT: B 494 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 718 TRP cc_start: 0.6205 (t60) cc_final: 0.5757 (t60) outliers start: 13 outliers final: 6 residues processed: 176 average time/residue: 0.2506 time to fit residues: 63.8113 Evaluate side-chains 158 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.0670 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 145 optimal weight: 0.0000 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 62 GLN B 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12514 Z= 0.164 Angle : 0.593 10.330 17109 Z= 0.285 Chirality : 0.038 0.255 1807 Planarity : 0.004 0.062 2113 Dihedral : 10.018 88.659 1874 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.77 % Allowed : 10.65 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1488 helix: -0.60 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 215 HIS 0.003 0.001 HIS B 692 PHE 0.013 0.001 PHE A 273 TYR 0.030 0.001 TYR B 406 ARG 0.006 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.223 Fit side-chains REVERT: A 1 MET cc_start: 0.3470 (ptp) cc_final: 0.2912 (ttp) REVERT: A 67 MET cc_start: 0.8672 (mtt) cc_final: 0.8408 (mtt) REVERT: A 494 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 677 LEU cc_start: 0.8416 (tp) cc_final: 0.8179 (tt) REVERT: A 718 TRP cc_start: 0.6909 (t60) cc_final: 0.6305 (t60) REVERT: B 1 MET cc_start: 0.3404 (ptp) cc_final: 0.2839 (ptp) REVERT: B 355 ASN cc_start: 0.8885 (t0) cc_final: 0.8503 (t0) REVERT: B 430 MET cc_start: 0.8547 (mmm) cc_final: 0.8186 (tpt) REVERT: B 494 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 718 TRP cc_start: 0.6230 (t60) cc_final: 0.5771 (t60) outliers start: 9 outliers final: 8 residues processed: 171 average time/residue: 0.2453 time to fit residues: 61.1594 Evaluate side-chains 159 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12514 Z= 0.180 Angle : 0.591 8.818 17109 Z= 0.283 Chirality : 0.039 0.270 1807 Planarity : 0.004 0.046 2113 Dihedral : 9.564 86.512 1874 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.20 % Allowed : 11.34 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1488 helix: -0.19 (0.17), residues: 964 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 215 HIS 0.003 0.001 HIS B 537 PHE 0.012 0.001 PHE B 194 TYR 0.025 0.001 TYR B 406 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.237 Fit side-chains REVERT: A 1 MET cc_start: 0.3504 (ptp) cc_final: 0.2753 (ttp) REVERT: A 231 MET cc_start: 0.6408 (tmm) cc_final: 0.6183 (tmm) REVERT: A 494 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 718 TRP cc_start: 0.6917 (t60) cc_final: 0.6314 (t60) REVERT: B 1 MET cc_start: 0.3490 (ptp) cc_final: 0.2909 (ptp) REVERT: B 355 ASN cc_start: 0.8884 (t0) cc_final: 0.8484 (t0) REVERT: B 430 MET cc_start: 0.8583 (mmm) cc_final: 0.8272 (tpt) REVERT: B 494 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 718 TRP cc_start: 0.6248 (t60) cc_final: 0.5800 (t60) outliers start: 14 outliers final: 10 residues processed: 166 average time/residue: 0.2440 time to fit residues: 59.1279 Evaluate side-chains 162 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12514 Z= 0.185 Angle : 0.595 9.385 17109 Z= 0.283 Chirality : 0.039 0.178 1807 Planarity : 0.004 0.044 2113 Dihedral : 9.029 84.682 1874 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.86 % Allowed : 12.63 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1488 helix: 0.11 (0.17), residues: 962 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 215 HIS 0.003 0.001 HIS A 537 PHE 0.012 0.001 PHE B 194 TYR 0.021 0.002 TYR B 652 ARG 0.010 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.153 Fit side-chains REVERT: A 1 MET cc_start: 0.3713 (ptp) cc_final: 0.2875 (ttp) REVERT: A 67 MET cc_start: 0.8750 (mtt) cc_final: 0.8502 (mtt) REVERT: A 231 MET cc_start: 0.6516 (tmm) cc_final: 0.6231 (tmm) REVERT: A 280 ARG cc_start: 0.7446 (mtm110) cc_final: 0.7007 (mtm110) REVERT: A 445 LYS cc_start: 0.6270 (ptmt) cc_final: 0.5101 (mmtm) REVERT: A 494 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7864 (tm-30) REVERT: A 718 TRP cc_start: 0.6863 (t60) cc_final: 0.6213 (t60) REVERT: B 1 MET cc_start: 0.3528 (ptp) cc_final: 0.2970 (ptp) REVERT: B 355 ASN cc_start: 0.8832 (t0) cc_final: 0.8472 (t0) REVERT: B 515 MET cc_start: 0.7526 (mmp) cc_final: 0.6849 (mtm) REVERT: B 718 TRP cc_start: 0.6381 (t60) cc_final: 0.5963 (t60) outliers start: 10 outliers final: 9 residues processed: 174 average time/residue: 0.2441 time to fit residues: 61.6581 Evaluate side-chains 169 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN B 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12514 Z= 0.307 Angle : 0.691 13.021 17109 Z= 0.323 Chirality : 0.043 0.174 1807 Planarity : 0.004 0.050 2113 Dihedral : 9.148 81.779 1874 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.29 % Allowed : 13.23 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1488 helix: -0.13 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 215 HIS 0.004 0.001 HIS A 486 PHE 0.018 0.001 PHE B 194 TYR 0.025 0.002 TYR B 406 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3548 (ptp) cc_final: 0.3061 (ptp) REVERT: A 445 LYS cc_start: 0.6188 (ptmt) cc_final: 0.4952 (mmtm) REVERT: A 494 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 718 TRP cc_start: 0.6808 (t60) cc_final: 0.6214 (t60) REVERT: B 1 MET cc_start: 0.3488 (ptp) cc_final: 0.2939 (ptp) REVERT: B 355 ASN cc_start: 0.8881 (t0) cc_final: 0.8496 (t0) REVERT: B 515 MET cc_start: 0.7580 (mmp) cc_final: 0.6793 (mtm) REVERT: B 680 PHE cc_start: 0.8754 (m-80) cc_final: 0.8517 (m-80) REVERT: B 718 TRP cc_start: 0.6410 (t60) cc_final: 0.6017 (t60) outliers start: 15 outliers final: 13 residues processed: 159 average time/residue: 0.2522 time to fit residues: 58.7459 Evaluate side-chains 156 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 120 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN B 116 GLN B 224 HIS A ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12514 Z= 0.277 Angle : 0.653 12.905 17109 Z= 0.308 Chirality : 0.042 0.172 1807 Planarity : 0.004 0.046 2113 Dihedral : 9.076 82.207 1874 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.12 % Allowed : 13.66 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1488 helix: -0.05 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 338 HIS 0.003 0.001 HIS A 537 PHE 0.017 0.001 PHE B 194 TYR 0.023 0.002 TYR B 108 ARG 0.011 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3470 (ptp) cc_final: 0.3000 (ptp) REVERT: A 67 MET cc_start: 0.8755 (mtt) cc_final: 0.8472 (mtt) REVERT: A 280 ARG cc_start: 0.7350 (mtm110) cc_final: 0.6819 (mtm110) REVERT: A 320 GLN cc_start: 0.8319 (pt0) cc_final: 0.7650 (mp10) REVERT: A 445 LYS cc_start: 0.6242 (ptmt) cc_final: 0.5023 (mmtm) REVERT: A 494 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 549 MET cc_start: 0.8792 (ttm) cc_final: 0.8563 (ttm) REVERT: A 718 TRP cc_start: 0.6788 (t60) cc_final: 0.6253 (t60) REVERT: B 1 MET cc_start: 0.3532 (ptp) cc_final: 0.2982 (ptp) REVERT: B 355 ASN cc_start: 0.8866 (t0) cc_final: 0.8479 (t0) REVERT: B 515 MET cc_start: 0.7515 (mmp) cc_final: 0.6711 (mtm) REVERT: B 718 TRP cc_start: 0.6463 (t60) cc_final: 0.6075 (t60) outliers start: 13 outliers final: 12 residues processed: 160 average time/residue: 0.2554 time to fit residues: 58.9448 Evaluate side-chains 157 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12514 Z= 0.169 Angle : 0.586 10.607 17109 Z= 0.279 Chirality : 0.039 0.180 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.737 84.207 1874 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.12 % Allowed : 13.32 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1488 helix: 0.35 (0.18), residues: 968 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 215 HIS 0.003 0.001 HIS A 537 PHE 0.013 0.001 PHE B 24 TYR 0.022 0.001 TYR B 108 ARG 0.010 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3449 (ptp) cc_final: 0.2965 (ptp) REVERT: A 67 MET cc_start: 0.8690 (mtt) cc_final: 0.8429 (mtt) REVERT: A 280 ARG cc_start: 0.7359 (mtm110) cc_final: 0.6826 (mtm110) REVERT: A 320 GLN cc_start: 0.8270 (pt0) cc_final: 0.7599 (mp10) REVERT: A 445 LYS cc_start: 0.6151 (ptmt) cc_final: 0.4966 (mmtm) REVERT: A 494 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 718 TRP cc_start: 0.6772 (t60) cc_final: 0.6277 (t60) REVERT: B 1 MET cc_start: 0.3471 (ptp) cc_final: 0.2935 (ptp) REVERT: B 355 ASN cc_start: 0.8822 (t0) cc_final: 0.8446 (t0) REVERT: B 515 MET cc_start: 0.7484 (mmp) cc_final: 0.6672 (mtm) REVERT: B 718 TRP cc_start: 0.6480 (t60) cc_final: 0.6109 (t60) outliers start: 13 outliers final: 9 residues processed: 167 average time/residue: 0.2670 time to fit residues: 63.3107 Evaluate side-chains 163 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 355 ASN ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12514 Z= 0.233 Angle : 0.614 10.499 17109 Z= 0.291 Chirality : 0.041 0.176 1807 Planarity : 0.004 0.043 2113 Dihedral : 8.752 83.004 1874 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.03 % Allowed : 13.49 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1488 helix: 0.28 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -1.57 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 215 HIS 0.003 0.001 HIS A 537 PHE 0.014 0.001 PHE B 194 TYR 0.021 0.002 TYR B 108 ARG 0.008 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3464 (ptp) cc_final: 0.2982 (ptp) REVERT: A 320 GLN cc_start: 0.8328 (pt0) cc_final: 0.7656 (mp10) REVERT: A 445 LYS cc_start: 0.6183 (ptmt) cc_final: 0.5061 (mmtm) REVERT: A 494 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 718 TRP cc_start: 0.6805 (t60) cc_final: 0.6363 (t60) REVERT: B 1 MET cc_start: 0.3587 (ptp) cc_final: 0.3034 (ptp) REVERT: B 355 ASN cc_start: 0.8847 (t0) cc_final: 0.8475 (t0) REVERT: B 445 LYS cc_start: 0.6524 (ptmt) cc_final: 0.5497 (mmtm) REVERT: B 515 MET cc_start: 0.7521 (mmp) cc_final: 0.6705 (mtm) REVERT: B 718 TRP cc_start: 0.6493 (t60) cc_final: 0.6125 (t60) outliers start: 12 outliers final: 11 residues processed: 164 average time/residue: 0.2557 time to fit residues: 59.9933 Evaluate side-chains 162 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.0020 chunk 97 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN ** B 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12514 Z= 0.174 Angle : 0.586 10.448 17109 Z= 0.279 Chirality : 0.039 0.176 1807 Planarity : 0.004 0.042 2113 Dihedral : 8.570 83.797 1874 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.77 % Allowed : 14.00 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1488 helix: 0.49 (0.18), residues: 966 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 338 HIS 0.003 0.001 HIS A 537 PHE 0.012 0.001 PHE B 194 TYR 0.021 0.001 TYR B 108 ARG 0.012 0.000 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3431 (ptp) cc_final: 0.2950 (ptp) REVERT: A 280 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6908 (mtm110) REVERT: A 320 GLN cc_start: 0.8295 (pt0) cc_final: 0.7618 (mp10) REVERT: A 445 LYS cc_start: 0.6147 (ptmt) cc_final: 0.5018 (mmtm) REVERT: A 494 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 718 TRP cc_start: 0.6846 (t60) cc_final: 0.6423 (t60) REVERT: B 1 MET cc_start: 0.3594 (ptp) cc_final: 0.3068 (ptp) REVERT: B 31 ARG cc_start: 0.8032 (ptp90) cc_final: 0.7826 (ptp90) REVERT: B 355 ASN cc_start: 0.8795 (t0) cc_final: 0.8435 (t0) REVERT: B 515 MET cc_start: 0.7520 (mmp) cc_final: 0.6720 (mtm) REVERT: B 718 TRP cc_start: 0.6486 (t60) cc_final: 0.6125 (t60) outliers start: 9 outliers final: 8 residues processed: 166 average time/residue: 0.2549 time to fit residues: 60.5538 Evaluate side-chains 164 residues out of total 1164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0170 chunk 108 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 305 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.096697 restraints weight = 35055.004| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.01 r_work: 0.2822 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12514 Z= 0.168 Angle : 0.577 10.273 17109 Z= 0.274 Chirality : 0.039 0.175 1807 Planarity : 0.003 0.043 2113 Dihedral : 8.435 84.738 1874 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.69 % Allowed : 14.18 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1488 helix: 0.57 (0.18), residues: 974 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 338 HIS 0.002 0.001 HIS A 537 PHE 0.011 0.001 PHE B 24 TYR 0.020 0.001 TYR B 108 ARG 0.010 0.000 ARG A 280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.62 seconds wall clock time: 46 minutes 50.26 seconds (2810.26 seconds total)