Starting phenix.real_space_refine on Sat Sep 12 03:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5irz_8118/09_2026/5irz_8118.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 72 5.16 5 C 8260 2.51 5 N 1952 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12504 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 3, 'ARG:plan': 4, 'TRP:plan': 2, 'TYR:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 197 Chain: "E" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 3, 'ARG:plan': 4, 'TRP:plan': 2, 'TYR:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 197 Chain: "B" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 3, 'ARG:plan': 4, 'TRP:plan': 2, 'TYR:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 197 Chain: "C" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2951 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 77} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 3, 'ARG:plan': 4, 'TRP:plan': 2, 'TYR:plan': 2, 'ASP:plan': 11, 'ASN:plan1': 4, 'PHE:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 197 Chain: "D" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 175 Unusual residues: {'6ES': 1, '6O8': 1, '6OE': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.37, per 1000 atoms: 0.19 Number of scatterers: 12504 At special positions: 0 Unit cell: (120.344, 120.344, 98.4636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 24 15.00 O 2196 8.00 N 1952 7.00 C 8260 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 - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 447.4 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 4 sheets defined 65.8% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 4.032A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 4.243A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 497 removed outlier: 3.628A pdb=" N PHE D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 510 removed outlier: 3.664A pdb=" N SER D 510 " --> pdb=" O LEU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.592A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.949A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 548 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR D 550 " --> pdb=" O ALA D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.585A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 576 removed outlier: 3.593A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 597 removed outlier: 4.160A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 628 removed outlier: 3.625A pdb=" N ASN D 628 " --> pdb=" O GLY D 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 602 through 628' Processing helix chain 'D' and resid 629 through 643 removed outlier: 3.777A pdb=" N THR D 633 " --> pdb=" O SER D 629 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.545A pdb=" N LEU D 663 " --> pdb=" O PHE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 689 removed outlier: 3.813A pdb=" N ALA D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 710 removed outlier: 3.603A pdb=" N THR D 708 " --> pdb=" O THR D 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 344 Processing helix chain 'E' and resid 345 through 353 Processing helix chain 'E' and resid 394 through 401 Processing helix chain 'E' and resid 411 through 414 Processing helix chain 'E' and resid 415 through 429 removed outlier: 4.031A pdb=" N ARG E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 454 removed outlier: 4.242A pdb=" N ILE E 433 " --> pdb=" O PHE E 429 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 497 removed outlier: 3.629A pdb=" N PHE E 496 " --> pdb=" O GLY E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 removed outlier: 3.664A pdb=" N SER E 510 " --> pdb=" O LEU E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 532 removed outlier: 3.592A pdb=" N ILE E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 551 removed outlier: 3.950A pdb=" N SER E 540 " --> pdb=" O GLU E 536 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 548 " --> pdb=" O SER E 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP E 549 " --> pdb=" O LEU E 545 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR E 550 " --> pdb=" O ALA E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.585A pdb=" N ARG E 557 " --> pdb=" O TYR E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 576 removed outlier: 3.593A pdb=" N TYR E 565 " --> pdb=" O GLN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 597 removed outlier: 4.160A pdb=" N PHE E 582 " --> pdb=" O CYS E 578 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 628 removed outlier: 3.625A pdb=" N ASN E 628 " --> pdb=" O GLY E 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 602 through 628' Processing helix chain 'E' and resid 629 through 643 removed outlier: 3.778A pdb=" N THR E 633 " --> pdb=" O SER E 629 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE E 640 " --> pdb=" O GLU E 636 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR E 641 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 671 removed outlier: 3.546A pdb=" N LEU E 663 " --> pdb=" O PHE E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 689 removed outlier: 3.814A pdb=" N ALA E 680 " --> pdb=" O ASN E 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN E 687 " --> pdb=" O GLY E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 691 through 710 removed outlier: 3.602A pdb=" N THR E 708 " --> pdb=" O THR E 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 710 " --> pdb=" O LEU E 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 4.032A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 4.242A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 497 removed outlier: 3.628A pdb=" N PHE B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.663A pdb=" N SER B 510 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.592A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.949A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 548 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 550 " --> pdb=" O ALA B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.585A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.593A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 597 removed outlier: 4.161A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 628 removed outlier: 3.625A pdb=" N ASN B 628 " --> pdb=" O GLY B 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 602 through 628' Processing helix chain 'B' and resid 629 through 643 removed outlier: 3.777A pdb=" N THR B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.545A pdb=" N LEU B 663 " --> pdb=" O PHE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 689 removed outlier: 3.813A pdb=" N ALA B 680 " --> pdb=" O ASN B 676 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 710 removed outlier: 3.603A pdb=" N THR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 4.033A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 4.242A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 497 removed outlier: 3.629A pdb=" N PHE C 496 " --> pdb=" O GLY C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 removed outlier: 3.664A pdb=" N SER C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.591A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.950A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY C 548 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 550 " --> pdb=" O ALA C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.585A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 removed outlier: 3.593A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 597 removed outlier: 4.160A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 628 removed outlier: 3.626A pdb=" N ASN C 628 " --> pdb=" O GLY C 602 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 628' Processing helix chain 'C' and resid 629 through 643 removed outlier: 3.778A pdb=" N THR C 633 " --> pdb=" O SER C 629 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.545A pdb=" N LEU C 663 " --> pdb=" O PHE C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 689 removed outlier: 3.813A pdb=" N ALA C 680 " --> pdb=" O ASN C 676 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 710 removed outlier: 3.602A pdb=" N THR C 708 " --> pdb=" O THR C 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 710 " --> pdb=" O LEU C 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 368 through 369 removed outlier: 3.623A pdb=" N SER D 380 " --> pdb=" O ASP D 745 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 368 through 369 removed outlier: 3.623A pdb=" N SER E 380 " --> pdb=" O ASP E 745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 369 removed outlier: 3.622A pdb=" N SER B 380 " --> pdb=" O ASP B 745 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 369 removed outlier: 3.624A pdb=" N SER C 380 " --> pdb=" O ASP C 745 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1959 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: 1.70 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1792 1.29 - 1.42: 3648 1.42 - 1.55: 7144 1.55 - 1.68: 48 1.68 - 1.81: 124 Bond restraints: 12756 Sorted by residual: bond pdb=" C17 6O8 D 801 " pdb=" N18 6O8 D 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 B 801 " pdb=" N18 6O8 B 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 C 801 " pdb=" N18 6O8 C 801 " ideal model delta sigma weight residual 1.506 1.422 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C17 6O8 E 801 " pdb=" N18 6O8 E 801 " ideal model delta sigma weight residual 1.506 1.423 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C19 6O8 C 801 " pdb=" N18 6O8 C 801 " ideal model delta sigma weight residual 1.490 1.411 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 12751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 16711 3.33 - 6.67: 381 6.67 - 10.00: 117 10.00 - 13.33: 15 13.33 - 16.67: 16 Bond angle restraints: 17240 Sorted by residual: angle pdb=" O04 6OE B 803 " pdb=" P05 6OE B 803 " pdb=" O08 6OE B 803 " ideal model delta sigma weight residual 93.39 110.06 -16.67 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O04 6OE C 803 " pdb=" P05 6OE C 803 " pdb=" O08 6OE C 803 " ideal model delta sigma weight residual 93.39 110.03 -16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O04 6OE D 805 " pdb=" P05 6OE D 805 " pdb=" O08 6OE D 805 " ideal model delta sigma weight residual 93.39 110.00 -16.61 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O04 6OE E 804 " pdb=" P05 6OE E 804 " pdb=" O08 6OE E 804 " ideal model delta sigma weight residual 93.39 110.00 -16.61 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O04 6OE B 805 " pdb=" P05 6OE B 805 " pdb=" O08 6OE B 805 " ideal model delta sigma weight residual 93.39 109.39 -16.00 3.00e+00 1.11e-01 2.84e+01 ... (remaining 17235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.60: 7339 32.60 - 65.20: 197 65.20 - 97.80: 76 97.80 - 130.40: 40 130.40 - 163.00: 20 Dihedral angle restraints: 7672 sinusoidal: 3060 harmonic: 4612 Sorted by residual: dihedral pdb=" CA GLY C 375 " pdb=" C GLY C 375 " pdb=" N PRO C 376 " pdb=" CA PRO C 376 " ideal model delta harmonic sigma weight residual -180.00 -139.32 -40.68 0 5.00e+00 4.00e-02 6.62e+01 dihedral pdb=" CA GLY E 375 " pdb=" C GLY E 375 " pdb=" N PRO E 376 " pdb=" CA PRO E 376 " ideal model delta harmonic sigma weight residual -180.00 -139.34 -40.66 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA GLY D 375 " pdb=" C GLY D 375 " pdb=" N PRO D 376 " pdb=" CA PRO D 376 " ideal model delta harmonic sigma weight residual -180.00 -139.36 -40.64 0 5.00e+00 4.00e-02 6.61e+01 ... (remaining 7669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1264 0.054 - 0.107: 589 0.107 - 0.161: 63 0.161 - 0.214: 24 0.214 - 0.268: 12 Chirality restraints: 1952 Sorted by residual: chirality pdb=" CB ILE D 689 " pdb=" CA ILE D 689 " pdb=" CG1 ILE D 689 " pdb=" CG2 ILE D 689 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE C 689 " pdb=" CA ILE C 689 " pdb=" CG1 ILE C 689 " pdb=" CG2 ILE C 689 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE B 689 " pdb=" CA ILE B 689 " pdb=" CG1 ILE B 689 " pdb=" CG2 ILE B 689 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1949 not shown) Planarity restraints: 2068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 375 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY E 375 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY E 375 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO E 376 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 375 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C GLY B 375 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY B 375 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 376 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 375 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C GLY D 375 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY D 375 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO D 376 " -0.012 2.00e-02 2.50e+03 ... (remaining 2065 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 121 2.59 - 3.16: 10183 3.16 - 3.74: 18435 3.74 - 4.32: 25987 4.32 - 4.90: 42233 Nonbonded interactions: 96959 Sorted by model distance: nonbonded pdb=" O ASP E 509 " pdb=" O22 6ES E 802 " model vdw 2.008 3.040 nonbonded pdb=" O ASP D 509 " pdb=" O22 6ES D 802 " model vdw 2.012 3.040 nonbonded pdb=" O ASP B 509 " pdb=" O22 6ES B 802 " model vdw 2.024 3.040 nonbonded pdb=" O ASP C 509 " pdb=" O22 6ES C 802 " model vdw 2.044 3.040 nonbonded pdb=" OE2 GLU C 570 " pdb=" O25 6ES C 802 " model vdw 2.175 3.040 ... (remaining 96954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 0.446 12768 Z= 0.935 Angle : 1.371 16.665 17240 Z= 0.591 Chirality : 0.059 0.268 1952 Planarity : 0.005 0.048 2068 Dihedral : 21.464 163.004 4728 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.78 (0.14), residues: 1568 helix: -3.99 (0.08), residues: 960 sheet: -2.77 (0.66), residues: 56 loop : -3.24 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 579 TYR 0.017 0.002 TYR E 511 PHE 0.027 0.003 PHE C 448 TRP 0.018 0.002 TRP B 697 HIS 0.001 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00980 / 0.45 (12756) covalent geometry : angle 1.37111 / 0.59 (17240) hydrogen bonds : bond 0.29812 / 20.70 ( 665) hydrogen bonds : angle 10.42105 / 7.37 ( 1959) Misc. bond : bond 0.26686 / 17.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.362 Fit side-chains REVERT: D 644 MET cc_start: 0.8298 (mmm) cc_final: 0.8087 (mmm) REVERT: D 700 GLN cc_start: 0.8087 (mt0) cc_final: 0.7846 (mt0) REVERT: E 636 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7037 (mm-30) REVERT: E 700 GLN cc_start: 0.8094 (mt0) cc_final: 0.7877 (mt0) REVERT: B 644 MET cc_start: 0.8264 (mmm) cc_final: 0.8009 (mmm) REVERT: B 700 GLN cc_start: 0.8102 (mt0) cc_final: 0.7873 (mt0) REVERT: C 592 SER cc_start: 0.8349 (p) cc_final: 0.8024 (p) REVERT: C 700 GLN cc_start: 0.8124 (mt0) cc_final: 0.7915 (mt0) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.1069 time to fit residues: 56.4438 Evaluate side-chains 229 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 410 HIS D 551 ASN D 561 GLN D 628 ASN E 410 HIS E 551 ASN E 628 ASN B 410 HIS B 551 ASN B 628 ASN C 410 HIS C 628 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091570 restraints weight = 22829.247| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.56 r_work: 0.2982 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12768 Z= 0.134 Angle : 0.626 8.110 17240 Z= 0.327 Chirality : 0.041 0.171 1952 Planarity : 0.004 0.032 2068 Dihedral : 22.279 130.043 2428 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.65 % Allowed : 11.40 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.19), residues: 1568 helix: -1.20 (0.14), residues: 1012 sheet: -2.38 (0.63), residues: 56 loop : -2.87 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 743 TYR 0.018 0.002 TYR D 511 PHE 0.022 0.001 PHE C 582 TRP 0.021 0.002 TRP D 697 HIS 0.001 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (12756) covalent geometry : angle 0.62615 / 0.33 (17240) hydrogen bonds : bond 0.04500 / 3.05 ( 665) hydrogen bonds : angle 4.85027 / 3.40 ( 1959) Misc. bond : bond 0.00380 / 0.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 292 time to evaluate : 0.294 Fit side-chains REVERT: D 508 VAL cc_start: 0.9224 (t) cc_final: 0.8936 (m) REVERT: D 540 SER cc_start: 0.9386 (m) cc_final: 0.8934 (p) REVERT: D 568 MET cc_start: 0.9042 (mtt) cc_final: 0.8811 (mtm) REVERT: D 584 TYR cc_start: 0.8980 (t80) cc_final: 0.8477 (t80) REVERT: D 636 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8527 (mm-30) REVERT: D 646 ASP cc_start: 0.8454 (t0) cc_final: 0.8214 (t0) REVERT: D 652 ASN cc_start: 0.8870 (p0) cc_final: 0.8321 (p0) REVERT: D 741 CYS cc_start: 0.6743 (p) cc_final: 0.6109 (p) REVERT: E 508 VAL cc_start: 0.9205 (t) cc_final: 0.8929 (m) REVERT: E 561 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8715 (mp10) REVERT: E 568 MET cc_start: 0.9032 (mtt) cc_final: 0.8804 (mtm) REVERT: E 584 TYR cc_start: 0.9005 (t80) cc_final: 0.8508 (t80) REVERT: E 646 ASP cc_start: 0.8479 (t0) cc_final: 0.8274 (t0) REVERT: E 652 ASN cc_start: 0.8882 (p0) cc_final: 0.8370 (p0) REVERT: E 741 CYS cc_start: 0.6997 (p) cc_final: 0.6133 (p) REVERT: B 508 VAL cc_start: 0.9214 (t) cc_final: 0.8920 (m) REVERT: B 540 SER cc_start: 0.9381 (m) cc_final: 0.8907 (p) REVERT: B 561 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8668 (mp10) REVERT: B 568 MET cc_start: 0.9050 (mtt) cc_final: 0.8824 (mtm) REVERT: B 584 TYR cc_start: 0.8961 (t80) cc_final: 0.8464 (t80) REVERT: B 636 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8528 (mm-30) REVERT: B 644 MET cc_start: 0.9171 (mmm) cc_final: 0.8797 (mmp) REVERT: B 646 ASP cc_start: 0.8384 (t0) cc_final: 0.8008 (t0) REVERT: B 652 ASN cc_start: 0.8888 (p0) cc_final: 0.8344 (p0) REVERT: B 741 CYS cc_start: 0.6796 (p) cc_final: 0.6236 (p) REVERT: C 508 VAL cc_start: 0.9218 (t) cc_final: 0.9005 (m) REVERT: C 540 SER cc_start: 0.9360 (m) cc_final: 0.8886 (p) REVERT: C 568 MET cc_start: 0.9042 (mtt) cc_final: 0.8832 (mtm) REVERT: C 584 TYR cc_start: 0.8924 (t80) cc_final: 0.8470 (t80) REVERT: C 636 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8406 (mm-30) REVERT: C 646 ASP cc_start: 0.8514 (t0) cc_final: 0.8251 (t0) REVERT: C 652 ASN cc_start: 0.8897 (p0) cc_final: 0.8375 (p0) REVERT: C 741 CYS cc_start: 0.6961 (p) cc_final: 0.6142 (p) outliers start: 18 outliers final: 8 residues processed: 299 average time/residue: 0.0869 time to fit residues: 39.4813 Evaluate side-chains 239 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 231 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain C residue 433 ILE Chi-restraints excluded: chain C residue 634 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 145 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 561 GLN D 628 ASN E 628 ASN B 628 ASN C 561 GLN C 628 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.088924 restraints weight = 23058.683| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.60 r_work: 0.2952 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12768 Z= 0.137 Angle : 0.594 12.190 17240 Z= 0.295 Chirality : 0.041 0.177 1952 Planarity : 0.003 0.026 2068 Dihedral : 19.692 95.383 2428 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.93 % Allowed : 13.88 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.21), residues: 1568 helix: 0.17 (0.16), residues: 996 sheet: -2.45 (0.59), residues: 56 loop : -2.71 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 743 TYR 0.015 0.001 TYR C 511 PHE 0.012 0.001 PHE C 582 TRP 0.009 0.001 TRP E 697 HIS 0.001 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12756) covalent geometry : angle 0.59381 / 0.30 (17240) hydrogen bonds : bond 0.03697 / 2.50 ( 665) hydrogen bonds : angle 4.21449 / 2.94 ( 1959) Misc. bond : bond 0.00372 / 0.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.368 Fit side-chains REVERT: D 442 CYS cc_start: 0.9334 (t) cc_final: 0.8660 (t) REVERT: D 540 SER cc_start: 0.9415 (m) cc_final: 0.8943 (p) REVERT: D 584 TYR cc_start: 0.9040 (t80) cc_final: 0.8554 (t80) REVERT: D 636 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8575 (mm-30) REVERT: D 646 ASP cc_start: 0.8519 (t0) cc_final: 0.8252 (t0) REVERT: D 652 ASN cc_start: 0.8710 (p0) cc_final: 0.8220 (p0) REVERT: E 442 CYS cc_start: 0.9330 (t) cc_final: 0.8938 (m) REVERT: E 540 SER cc_start: 0.9404 (m) cc_final: 0.8927 (p) REVERT: E 584 TYR cc_start: 0.9054 (t80) cc_final: 0.8590 (t80) REVERT: E 636 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8385 (mm-30) REVERT: E 646 ASP cc_start: 0.8581 (t0) cc_final: 0.8268 (t0) REVERT: E 652 ASN cc_start: 0.8787 (p0) cc_final: 0.8288 (p0) REVERT: B 540 SER cc_start: 0.9410 (m) cc_final: 0.8909 (p) REVERT: B 584 TYR cc_start: 0.9017 (t80) cc_final: 0.8498 (t80) REVERT: B 636 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 646 ASP cc_start: 0.8532 (t0) cc_final: 0.8266 (t0) REVERT: B 652 ASN cc_start: 0.8728 (p0) cc_final: 0.8234 (p0) REVERT: C 540 SER cc_start: 0.9388 (m) cc_final: 0.8894 (p) REVERT: C 551 ASN cc_start: 0.9141 (m-40) cc_final: 0.8901 (m-40) REVERT: C 584 TYR cc_start: 0.8985 (t80) cc_final: 0.8588 (t80) REVERT: C 646 ASP cc_start: 0.8589 (t0) cc_final: 0.8337 (t0) REVERT: C 652 ASN cc_start: 0.8755 (p0) cc_final: 0.8280 (p0) outliers start: 21 outliers final: 9 residues processed: 247 average time/residue: 0.0802 time to fit residues: 31.2564 Evaluate side-chains 222 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 642 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN E 628 ASN B 628 ASN B 691 GLN C 628 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.088256 restraints weight = 22655.622| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.58 r_work: 0.2930 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12768 Z= 0.134 Angle : 0.557 9.550 17240 Z= 0.279 Chirality : 0.041 0.168 1952 Planarity : 0.003 0.031 2068 Dihedral : 17.884 89.006 2428 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.40 % Allowed : 14.25 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1568 helix: 0.96 (0.16), residues: 996 sheet: -2.52 (0.57), residues: 56 loop : -2.59 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 557 TYR 0.012 0.001 TYR B 511 PHE 0.012 0.001 PHE E 516 TRP 0.009 0.001 TRP E 697 HIS 0.000 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12756) covalent geometry : angle 0.55669 / 0.28 (17240) hydrogen bonds : bond 0.03132 / 2.11 ( 665) hydrogen bonds : angle 3.91951 / 2.72 ( 1959) Misc. bond : bond 0.00253 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.399 Fit side-chains REVERT: D 429 PHE cc_start: 0.8440 (t80) cc_final: 0.8071 (t80) REVERT: D 442 CYS cc_start: 0.9355 (t) cc_final: 0.8682 (t) REVERT: D 445 MET cc_start: 0.9055 (mmm) cc_final: 0.8844 (mmm) REVERT: D 540 SER cc_start: 0.9400 (m) cc_final: 0.8919 (p) REVERT: D 584 TYR cc_start: 0.9091 (t80) cc_final: 0.8737 (t80) REVERT: D 636 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8626 (mm-30) REVERT: D 646 ASP cc_start: 0.8601 (t0) cc_final: 0.8359 (t0) REVERT: D 652 ASN cc_start: 0.8739 (p0) cc_final: 0.8228 (p0) REVERT: E 429 PHE cc_start: 0.8422 (t80) cc_final: 0.7997 (t80) REVERT: E 442 CYS cc_start: 0.9344 (t) cc_final: 0.8677 (t) REVERT: E 445 MET cc_start: 0.9075 (mmm) cc_final: 0.8875 (mmm) REVERT: E 540 SER cc_start: 0.9380 (m) cc_final: 0.8897 (p) REVERT: E 636 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8438 (mm-30) REVERT: E 646 ASP cc_start: 0.8657 (t0) cc_final: 0.8378 (t0) REVERT: E 652 ASN cc_start: 0.8815 (p0) cc_final: 0.8322 (p0) REVERT: B 429 PHE cc_start: 0.8421 (t80) cc_final: 0.8053 (t80) REVERT: B 442 CYS cc_start: 0.9295 (t) cc_final: 0.8785 (t) REVERT: B 445 MET cc_start: 0.9037 (mmm) cc_final: 0.8825 (mmm) REVERT: B 540 SER cc_start: 0.9396 (m) cc_final: 0.8903 (p) REVERT: B 584 TYR cc_start: 0.9077 (t80) cc_final: 0.8736 (t80) REVERT: B 636 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 646 ASP cc_start: 0.8611 (t0) cc_final: 0.8309 (t0) REVERT: B 652 ASN cc_start: 0.8769 (p0) cc_final: 0.8275 (p0) REVERT: C 429 PHE cc_start: 0.8429 (t80) cc_final: 0.8006 (t80) REVERT: C 442 CYS cc_start: 0.9366 (t) cc_final: 0.8688 (t) REVERT: C 504 LYS cc_start: 0.8942 (tptp) cc_final: 0.8620 (tptm) REVERT: C 540 SER cc_start: 0.9361 (m) cc_final: 0.8852 (p) REVERT: C 551 ASN cc_start: 0.9166 (m-40) cc_final: 0.8885 (m-40) REVERT: C 561 GLN cc_start: 0.8942 (mm110) cc_final: 0.8679 (mp10) REVERT: C 568 MET cc_start: 0.9063 (mtt) cc_final: 0.8814 (mtp) REVERT: C 584 TYR cc_start: 0.9091 (t80) cc_final: 0.8794 (t80) REVERT: C 646 ASP cc_start: 0.8671 (t0) cc_final: 0.8369 (t0) REVERT: C 652 ASN cc_start: 0.8777 (p0) cc_final: 0.8300 (p0) outliers start: 37 outliers final: 21 residues processed: 266 average time/residue: 0.0810 time to fit residues: 33.8085 Evaluate side-chains 240 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 88 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 90 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 551 ASN D 628 ASN E 551 ASN B 551 ASN C 419 ASN ** C 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.088619 restraints weight = 22822.526| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.61 r_work: 0.2936 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12768 Z= 0.130 Angle : 0.534 7.630 17240 Z= 0.272 Chirality : 0.040 0.157 1952 Planarity : 0.003 0.027 2068 Dihedral : 17.219 94.762 2428 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.67 % Allowed : 17.46 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1568 helix: 1.29 (0.16), residues: 1000 sheet: -2.59 (0.54), residues: 56 loop : -2.45 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 557 TYR 0.012 0.001 TYR E 671 PHE 0.010 0.001 PHE D 591 TRP 0.008 0.001 TRP E 697 HIS 0.000 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (12756) covalent geometry : angle 0.53412 / 0.27 (17240) hydrogen bonds : bond 0.02954 / 1.99 ( 665) hydrogen bonds : angle 3.82099 / 2.64 ( 1959) Misc. bond : bond 0.00249 / 0.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.385 Fit side-chains REVERT: D 429 PHE cc_start: 0.8388 (t80) cc_final: 0.8051 (t80) REVERT: D 442 CYS cc_start: 0.9298 (t) cc_final: 0.8679 (t) REVERT: D 540 SER cc_start: 0.9393 (m) cc_final: 0.8887 (p) REVERT: D 551 ASN cc_start: 0.9214 (m-40) cc_final: 0.8818 (m110) REVERT: D 568 MET cc_start: 0.9025 (mtt) cc_final: 0.8806 (mtp) REVERT: D 636 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8556 (mm-30) REVERT: D 646 ASP cc_start: 0.8688 (t0) cc_final: 0.8402 (t0) REVERT: D 652 ASN cc_start: 0.8764 (p0) cc_final: 0.8252 (p0) REVERT: E 429 PHE cc_start: 0.8395 (t80) cc_final: 0.8051 (t80) REVERT: E 442 CYS cc_start: 0.9299 (t) cc_final: 0.8671 (t) REVERT: E 540 SER cc_start: 0.9343 (m) cc_final: 0.8844 (p) REVERT: E 551 ASN cc_start: 0.9202 (m-40) cc_final: 0.8797 (m110) REVERT: E 568 MET cc_start: 0.9041 (mtt) cc_final: 0.8815 (mtp) REVERT: E 636 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8412 (mm-30) REVERT: E 646 ASP cc_start: 0.8684 (t0) cc_final: 0.8429 (t0) REVERT: E 652 ASN cc_start: 0.8837 (p0) cc_final: 0.8345 (p0) REVERT: B 429 PHE cc_start: 0.8440 (t80) cc_final: 0.8036 (t80) REVERT: B 442 CYS cc_start: 0.9287 (t) cc_final: 0.8789 (t) REVERT: B 540 SER cc_start: 0.9403 (m) cc_final: 0.8919 (p) REVERT: B 551 ASN cc_start: 0.9208 (m-40) cc_final: 0.8957 (m110) REVERT: B 568 MET cc_start: 0.9047 (mtt) cc_final: 0.8811 (mtp) REVERT: B 584 TYR cc_start: 0.9109 (t80) cc_final: 0.8831 (t80) REVERT: B 636 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8542 (mm-30) REVERT: B 646 ASP cc_start: 0.8664 (t0) cc_final: 0.8348 (t0) REVERT: B 652 ASN cc_start: 0.8806 (p0) cc_final: 0.8313 (p0) REVERT: C 429 PHE cc_start: 0.8458 (t80) cc_final: 0.8070 (t80) REVERT: C 442 CYS cc_start: 0.9350 (t) cc_final: 0.8683 (t) REVERT: C 540 SER cc_start: 0.9373 (m) cc_final: 0.8880 (p) REVERT: C 551 ASN cc_start: 0.9177 (m-40) cc_final: 0.8866 (m110) REVERT: C 561 GLN cc_start: 0.9006 (mm110) cc_final: 0.8711 (mp10) REVERT: C 568 MET cc_start: 0.9042 (mtt) cc_final: 0.8796 (mtp) REVERT: C 584 TYR cc_start: 0.9103 (t80) cc_final: 0.8817 (t80) REVERT: C 636 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8471 (mm-30) REVERT: C 646 ASP cc_start: 0.8689 (t0) cc_final: 0.8384 (t0) REVERT: C 652 ASN cc_start: 0.8826 (p0) cc_final: 0.8350 (p0) outliers start: 29 outliers final: 20 residues processed: 257 average time/residue: 0.0840 time to fit residues: 33.8709 Evaluate side-chains 254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 510 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 4.9990 chunk 37 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088893 restraints weight = 22586.542| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.56 r_work: 0.2940 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12768 Z= 0.122 Angle : 0.523 9.193 17240 Z= 0.267 Chirality : 0.040 0.144 1952 Planarity : 0.002 0.028 2068 Dihedral : 16.386 103.172 2428 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.76 % Allowed : 18.29 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1568 helix: 1.75 (0.17), residues: 972 sheet: -2.51 (0.55), residues: 56 loop : -2.16 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 428 TYR 0.011 0.001 TYR E 472 PHE 0.011 0.001 PHE D 591 TRP 0.008 0.001 TRP E 697 HIS 0.000 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12756) covalent geometry : angle 0.52297 / 0.27 (17240) hydrogen bonds : bond 0.02769 / 1.86 ( 665) hydrogen bonds : angle 3.74017 / 2.58 ( 1959) Misc. bond : bond 0.00232 / 0.15 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 0.329 Fit side-chains REVERT: D 429 PHE cc_start: 0.8392 (t80) cc_final: 0.8078 (t80) REVERT: D 442 CYS cc_start: 0.9299 (t) cc_final: 0.8694 (t) REVERT: D 540 SER cc_start: 0.9338 (m) cc_final: 0.8855 (p) REVERT: D 551 ASN cc_start: 0.9238 (m-40) cc_final: 0.8829 (m110) REVERT: D 561 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8715 (mm-40) REVERT: D 562 MET cc_start: 0.9053 (mmm) cc_final: 0.8835 (mmt) REVERT: D 568 MET cc_start: 0.9024 (mtt) cc_final: 0.8822 (mtp) REVERT: D 636 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 646 ASP cc_start: 0.8692 (t0) cc_final: 0.8393 (t0) REVERT: D 652 ASN cc_start: 0.8764 (p0) cc_final: 0.8251 (p0) REVERT: E 429 PHE cc_start: 0.8409 (t80) cc_final: 0.8095 (t80) REVERT: E 442 CYS cc_start: 0.9295 (t) cc_final: 0.8672 (t) REVERT: E 504 LYS cc_start: 0.9100 (tptt) cc_final: 0.8860 (tptm) REVERT: E 540 SER cc_start: 0.9332 (m) cc_final: 0.8846 (p) REVERT: E 551 ASN cc_start: 0.9214 (m-40) cc_final: 0.8798 (m110) REVERT: E 636 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 646 ASP cc_start: 0.8693 (t0) cc_final: 0.8420 (t0) REVERT: E 652 ASN cc_start: 0.8803 (p0) cc_final: 0.8319 (p0) REVERT: B 429 PHE cc_start: 0.8402 (t80) cc_final: 0.8047 (t80) REVERT: B 442 CYS cc_start: 0.9306 (t) cc_final: 0.8807 (t) REVERT: B 540 SER cc_start: 0.9329 (m) cc_final: 0.8849 (p) REVERT: B 551 ASN cc_start: 0.9230 (m-40) cc_final: 0.8820 (m110) REVERT: B 568 MET cc_start: 0.9046 (mtt) cc_final: 0.8836 (mtp) REVERT: B 584 TYR cc_start: 0.9124 (t80) cc_final: 0.8827 (t80) REVERT: B 636 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8532 (mm-30) REVERT: B 646 ASP cc_start: 0.8685 (t0) cc_final: 0.8363 (t0) REVERT: B 652 ASN cc_start: 0.8820 (p0) cc_final: 0.8327 (p0) REVERT: C 429 PHE cc_start: 0.8434 (t80) cc_final: 0.8064 (t80) REVERT: C 442 CYS cc_start: 0.9353 (t) cc_final: 0.8668 (t) REVERT: C 540 SER cc_start: 0.9329 (m) cc_final: 0.8852 (p) REVERT: C 551 ASN cc_start: 0.9180 (m-40) cc_final: 0.8867 (m110) REVERT: C 561 GLN cc_start: 0.8985 (mm110) cc_final: 0.8663 (mp10) REVERT: C 562 MET cc_start: 0.9049 (mmm) cc_final: 0.8831 (mmt) REVERT: C 584 TYR cc_start: 0.9114 (t80) cc_final: 0.8869 (t80) REVERT: C 636 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8305 (mm-30) REVERT: C 646 ASP cc_start: 0.8690 (t0) cc_final: 0.8402 (t0) REVERT: C 652 ASN cc_start: 0.8817 (p0) cc_final: 0.8334 (p0) outliers start: 30 outliers final: 22 residues processed: 248 average time/residue: 0.0863 time to fit residues: 33.2649 Evaluate side-chains 250 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 0.0770 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 0.0060 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN C 419 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.117460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.091016 restraints weight = 22435.654| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.59 r_work: 0.2974 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12768 Z= 0.093 Angle : 0.501 8.832 17240 Z= 0.255 Chirality : 0.039 0.125 1952 Planarity : 0.002 0.024 2068 Dihedral : 15.764 109.116 2428 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.03 % Allowed : 19.03 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1568 helix: 2.06 (0.17), residues: 960 sheet: -2.33 (0.54), residues: 56 loop : -2.19 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 499 TYR 0.012 0.001 TYR D 472 PHE 0.009 0.001 PHE D 516 TRP 0.008 0.001 TRP D 697 HIS 0.000 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (12756) covalent geometry : angle 0.50149 / 0.25 (17240) hydrogen bonds : bond 0.02516 / 1.69 ( 665) hydrogen bonds : angle 3.63647 / 2.49 ( 1959) Misc. bond : bond 0.00194 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 252 time to evaluate : 0.459 Fit side-chains REVERT: D 429 PHE cc_start: 0.8414 (t80) cc_final: 0.8120 (t80) REVERT: D 442 CYS cc_start: 0.9351 (t) cc_final: 0.8716 (t) REVERT: D 540 SER cc_start: 0.9313 (m) cc_final: 0.8805 (p) REVERT: D 551 ASN cc_start: 0.9185 (m-40) cc_final: 0.8766 (m110) REVERT: D 561 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8759 (mm110) REVERT: D 562 MET cc_start: 0.8995 (mmm) cc_final: 0.8787 (mmt) REVERT: D 584 TYR cc_start: 0.9094 (t80) cc_final: 0.8758 (t80) REVERT: D 636 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8518 (mm-30) REVERT: D 644 MET cc_start: 0.9231 (mmm) cc_final: 0.9019 (mmm) REVERT: D 646 ASP cc_start: 0.8686 (t0) cc_final: 0.8376 (t0) REVERT: D 652 ASN cc_start: 0.8699 (p0) cc_final: 0.8193 (p0) REVERT: E 429 PHE cc_start: 0.8395 (t80) cc_final: 0.8091 (t80) REVERT: E 442 CYS cc_start: 0.9303 (t) cc_final: 0.8676 (t) REVERT: E 504 LYS cc_start: 0.9047 (tptt) cc_final: 0.8807 (tptm) REVERT: E 540 SER cc_start: 0.9320 (m) cc_final: 0.8837 (p) REVERT: E 551 ASN cc_start: 0.9210 (m-40) cc_final: 0.8816 (m110) REVERT: E 584 TYR cc_start: 0.9071 (t80) cc_final: 0.8546 (t80) REVERT: E 644 MET cc_start: 0.8836 (mmp) cc_final: 0.8556 (mmp) REVERT: E 646 ASP cc_start: 0.8644 (t0) cc_final: 0.8312 (t0) REVERT: E 652 ASN cc_start: 0.8751 (p0) cc_final: 0.8271 (p0) REVERT: B 429 PHE cc_start: 0.8393 (t80) cc_final: 0.8048 (t80) REVERT: B 442 CYS cc_start: 0.9339 (t) cc_final: 0.8823 (t) REVERT: B 540 SER cc_start: 0.9334 (m) cc_final: 0.8849 (p) REVERT: B 551 ASN cc_start: 0.9173 (m-40) cc_final: 0.8754 (m110) REVERT: B 584 TYR cc_start: 0.9085 (t80) cc_final: 0.8762 (t80) REVERT: B 636 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8502 (mm-30) REVERT: B 646 ASP cc_start: 0.8653 (t0) cc_final: 0.8362 (t0) REVERT: B 652 ASN cc_start: 0.8748 (p0) cc_final: 0.8254 (p0) REVERT: C 429 PHE cc_start: 0.8424 (t80) cc_final: 0.8059 (t80) REVERT: C 442 CYS cc_start: 0.9359 (t) cc_final: 0.9031 (m) REVERT: C 540 SER cc_start: 0.9291 (m) cc_final: 0.8806 (p) REVERT: C 551 ASN cc_start: 0.9145 (m-40) cc_final: 0.8847 (m110) REVERT: C 561 GLN cc_start: 0.8977 (mm110) cc_final: 0.8641 (mp10) REVERT: C 584 TYR cc_start: 0.9070 (t80) cc_final: 0.8793 (t80) REVERT: C 636 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8244 (mm-30) REVERT: C 646 ASP cc_start: 0.8704 (t0) cc_final: 0.8395 (t0) REVERT: C 652 ASN cc_start: 0.8771 (p0) cc_final: 0.8287 (p0) outliers start: 33 outliers final: 23 residues processed: 262 average time/residue: 0.0876 time to fit residues: 35.6530 Evaluate side-chains 259 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 510 SER Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 544 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 152 optimal weight: 0.0170 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 100 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN D 691 GLN C 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.117755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.091176 restraints weight = 22354.971| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.59 r_work: 0.2977 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12768 Z= 0.100 Angle : 0.504 8.945 17240 Z= 0.255 Chirality : 0.039 0.117 1952 Planarity : 0.002 0.021 2068 Dihedral : 15.336 112.081 2428 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.85 % Allowed : 18.93 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1568 helix: 2.21 (0.16), residues: 960 sheet: -2.31 (0.54), residues: 56 loop : -2.15 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 579 TYR 0.012 0.001 TYR E 472 PHE 0.010 0.001 PHE E 591 TRP 0.007 0.001 TRP E 697 HIS 0.000 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12756) covalent geometry : angle 0.50354 / 0.25 (17240) hydrogen bonds : bond 0.02508 / 1.70 ( 665) hydrogen bonds : angle 3.62822 / 2.49 ( 1959) Misc. bond : bond 0.00196 / 0.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.347 Fit side-chains REVERT: D 429 PHE cc_start: 0.8412 (t80) cc_final: 0.8075 (t80) REVERT: D 442 CYS cc_start: 0.9372 (t) cc_final: 0.8689 (t) REVERT: D 540 SER cc_start: 0.9320 (m) cc_final: 0.8838 (p) REVERT: D 551 ASN cc_start: 0.9172 (m-40) cc_final: 0.8787 (m110) REVERT: D 561 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8749 (mm110) REVERT: D 584 TYR cc_start: 0.9120 (t80) cc_final: 0.8782 (t80) REVERT: D 636 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8530 (mm-30) REVERT: D 646 ASP cc_start: 0.8709 (t0) cc_final: 0.8377 (t0) REVERT: D 652 ASN cc_start: 0.8748 (p0) cc_final: 0.8240 (p0) REVERT: E 429 PHE cc_start: 0.8417 (t80) cc_final: 0.8064 (t80) REVERT: E 442 CYS cc_start: 0.9307 (t) cc_final: 0.8681 (t) REVERT: E 551 ASN cc_start: 0.9225 (m-40) cc_final: 0.8828 (m110) REVERT: E 646 ASP cc_start: 0.8700 (t0) cc_final: 0.8413 (t0) REVERT: E 652 ASN cc_start: 0.8783 (p0) cc_final: 0.8307 (p0) REVERT: B 429 PHE cc_start: 0.8408 (t80) cc_final: 0.8076 (t80) REVERT: B 442 CYS cc_start: 0.9356 (t) cc_final: 0.8798 (t) REVERT: B 540 SER cc_start: 0.9336 (m) cc_final: 0.8876 (p) REVERT: B 551 ASN cc_start: 0.9163 (m-40) cc_final: 0.8779 (m110) REVERT: B 584 TYR cc_start: 0.9113 (t80) cc_final: 0.8772 (t80) REVERT: B 636 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8509 (mm-30) REVERT: B 646 ASP cc_start: 0.8673 (t0) cc_final: 0.8350 (t0) REVERT: B 652 ASN cc_start: 0.8808 (p0) cc_final: 0.8306 (p0) REVERT: C 429 PHE cc_start: 0.8441 (t80) cc_final: 0.8091 (t80) REVERT: C 442 CYS cc_start: 0.9393 (t) cc_final: 0.9055 (m) REVERT: C 540 SER cc_start: 0.9297 (m) cc_final: 0.8806 (p) REVERT: C 551 ASN cc_start: 0.9090 (m-40) cc_final: 0.8767 (m110) REVERT: C 561 GLN cc_start: 0.9006 (mm110) cc_final: 0.8779 (mm-40) REVERT: C 568 MET cc_start: 0.9016 (mtt) cc_final: 0.8806 (mtp) REVERT: C 584 TYR cc_start: 0.9104 (t80) cc_final: 0.8810 (t80) REVERT: C 646 ASP cc_start: 0.8708 (t0) cc_final: 0.8388 (t0) REVERT: C 652 ASN cc_start: 0.8801 (p0) cc_final: 0.8319 (p0) outliers start: 31 outliers final: 19 residues processed: 245 average time/residue: 0.0869 time to fit residues: 33.0783 Evaluate side-chains 248 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 139 optimal weight: 0.1980 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN D 691 GLN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 ASN ** C 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.086621 restraints weight = 23054.209| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.60 r_work: 0.2898 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12768 Z= 0.187 Angle : 0.575 9.009 17240 Z= 0.290 Chirality : 0.043 0.146 1952 Planarity : 0.002 0.021 2068 Dihedral : 15.401 120.498 2428 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.85 % Allowed : 18.84 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1568 helix: 2.01 (0.16), residues: 980 sheet: -2.50 (0.52), residues: 56 loop : -2.30 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 499 TYR 0.014 0.002 TYR D 671 PHE 0.016 0.001 PHE E 591 TRP 0.007 0.001 TRP D 426 HIS 0.000 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (12756) covalent geometry : angle 0.57542 / 0.29 (17240) hydrogen bonds : bond 0.03050 / 2.06 ( 665) hydrogen bonds : angle 3.77934 / 2.61 ( 1959) Misc. bond : bond 0.00266 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.505 Fit side-chains REVERT: D 429 PHE cc_start: 0.8450 (t80) cc_final: 0.8129 (t80) REVERT: D 442 CYS cc_start: 0.9382 (t) cc_final: 0.8739 (t) REVERT: D 540 SER cc_start: 0.9322 (m) cc_final: 0.8840 (p) REVERT: D 561 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8785 (mm-40) REVERT: D 636 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8635 (mm-30) REVERT: D 646 ASP cc_start: 0.8735 (t0) cc_final: 0.8345 (t0) REVERT: D 652 ASN cc_start: 0.8864 (p0) cc_final: 0.8368 (p0) REVERT: E 429 PHE cc_start: 0.8469 (t80) cc_final: 0.8133 (t80) REVERT: E 442 CYS cc_start: 0.9252 (t) cc_final: 0.8662 (t) REVERT: E 504 LYS cc_start: 0.9066 (tptt) cc_final: 0.8724 (tppt) REVERT: E 540 SER cc_start: 0.9354 (m) cc_final: 0.8886 (p) REVERT: E 646 ASP cc_start: 0.8765 (t0) cc_final: 0.8411 (t0) REVERT: E 652 ASN cc_start: 0.8897 (p0) cc_final: 0.8364 (p0) REVERT: B 429 PHE cc_start: 0.8460 (t80) cc_final: 0.8150 (t80) REVERT: B 442 CYS cc_start: 0.9306 (t) cc_final: 0.8834 (t) REVERT: B 540 SER cc_start: 0.9321 (m) cc_final: 0.8837 (p) REVERT: B 562 MET cc_start: 0.9149 (mmm) cc_final: 0.8934 (mmt) REVERT: B 636 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8619 (mm-30) REVERT: B 644 MET cc_start: 0.9208 (mmm) cc_final: 0.8862 (mmm) REVERT: B 646 ASP cc_start: 0.8671 (t0) cc_final: 0.8324 (t0) REVERT: B 652 ASN cc_start: 0.8892 (p0) cc_final: 0.8416 (p0) REVERT: C 429 PHE cc_start: 0.8479 (t80) cc_final: 0.8131 (t80) REVERT: C 442 CYS cc_start: 0.9388 (t) cc_final: 0.8739 (t) REVERT: C 540 SER cc_start: 0.9348 (m) cc_final: 0.8893 (p) REVERT: C 551 ASN cc_start: 0.9177 (m-40) cc_final: 0.8849 (m110) REVERT: C 561 GLN cc_start: 0.9063 (mm110) cc_final: 0.8806 (mm-40) REVERT: C 646 ASP cc_start: 0.8713 (t0) cc_final: 0.8394 (t0) REVERT: C 652 ASN cc_start: 0.8846 (p0) cc_final: 0.8381 (p0) outliers start: 31 outliers final: 25 residues processed: 240 average time/residue: 0.0885 time to fit residues: 32.8134 Evaluate side-chains 247 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 677 MET Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 628 ASN ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 GLN ** 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 = 0.3531 r_free = 0.3531 target = 0.115970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.089000 restraints weight = 22621.297| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.59 r_work: 0.2941 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12768 Z= 0.124 Angle : 0.526 8.981 17240 Z= 0.265 Chirality : 0.040 0.136 1952 Planarity : 0.002 0.019 2068 Dihedral : 15.013 123.046 2428 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.76 % Allowed : 19.49 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1568 helix: 2.09 (0.16), residues: 980 sheet: -2.30 (0.53), residues: 56 loop : -2.24 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 428 TYR 0.015 0.001 TYR D 472 PHE 0.012 0.001 PHE E 591 TRP 0.007 0.001 TRP E 697 HIS 0.000 0.000 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (12756) covalent geometry : angle 0.52615 / 0.27 (17240) hydrogen bonds : bond 0.02739 / 1.85 ( 665) hydrogen bonds : angle 3.70919 / 2.56 ( 1959) Misc. bond : bond 0.00212 / 0.14 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.492 Fit side-chains REVERT: D 429 PHE cc_start: 0.8444 (t80) cc_final: 0.8107 (t80) REVERT: D 442 CYS cc_start: 0.9386 (t) cc_final: 0.8717 (t) REVERT: D 540 SER cc_start: 0.9354 (m) cc_final: 0.8888 (p) REVERT: D 547 MET cc_start: 0.8824 (tpp) cc_final: 0.8199 (tpp) REVERT: D 551 ASN cc_start: 0.9178 (m-40) cc_final: 0.8790 (m-40) REVERT: D 561 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8790 (mm-40) REVERT: D 636 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8581 (mm-30) REVERT: D 646 ASP cc_start: 0.8705 (t0) cc_final: 0.8293 (t0) REVERT: D 652 ASN cc_start: 0.8822 (p0) cc_final: 0.8338 (p0) REVERT: E 429 PHE cc_start: 0.8453 (t80) cc_final: 0.8111 (t80) REVERT: E 442 CYS cc_start: 0.9296 (t) cc_final: 0.8739 (t) REVERT: E 540 SER cc_start: 0.9353 (m) cc_final: 0.8889 (p) REVERT: E 562 MET cc_start: 0.8635 (mmt) cc_final: 0.8433 (mmm) REVERT: E 646 ASP cc_start: 0.8713 (t0) cc_final: 0.8308 (t0) REVERT: E 652 ASN cc_start: 0.8856 (p0) cc_final: 0.8320 (p0) REVERT: B 429 PHE cc_start: 0.8465 (t80) cc_final: 0.8153 (t80) REVERT: B 442 CYS cc_start: 0.9338 (t) cc_final: 0.8842 (t) REVERT: B 540 SER cc_start: 0.9319 (m) cc_final: 0.8803 (p) REVERT: B 547 MET cc_start: 0.8809 (tpp) cc_final: 0.8207 (tpp) REVERT: B 551 ASN cc_start: 0.9173 (m-40) cc_final: 0.8772 (m110) REVERT: B 636 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 644 MET cc_start: 0.9167 (mmm) cc_final: 0.8812 (mmm) REVERT: B 646 ASP cc_start: 0.8633 (t0) cc_final: 0.8255 (t0) REVERT: B 652 ASN cc_start: 0.8853 (p0) cc_final: 0.8372 (p0) REVERT: C 429 PHE cc_start: 0.8469 (t80) cc_final: 0.8123 (t80) REVERT: C 442 CYS cc_start: 0.9366 (t) cc_final: 0.8712 (t) REVERT: C 540 SER cc_start: 0.9338 (m) cc_final: 0.8866 (p) REVERT: C 551 ASN cc_start: 0.9144 (m-40) cc_final: 0.8838 (m110) REVERT: C 561 GLN cc_start: 0.9040 (mm110) cc_final: 0.8800 (mm-40) REVERT: C 584 TYR cc_start: 0.9125 (t80) cc_final: 0.8829 (t80) REVERT: C 646 ASP cc_start: 0.8709 (t0) cc_final: 0.8326 (t0) REVERT: C 652 ASN cc_start: 0.8824 (p0) cc_final: 0.8292 (p0) outliers start: 30 outliers final: 23 residues processed: 241 average time/residue: 0.0978 time to fit residues: 36.3910 Evaluate side-chains 254 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 741 CYS Chi-restraints excluded: chain E residue 396 LEU Chi-restraints excluded: chain E residue 494 GLN Chi-restraints excluded: chain E residue 541 MET Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 672 ILE Chi-restraints excluded: chain E residue 677 MET Chi-restraints excluded: chain E residue 741 CYS Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 544 SER Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 741 CYS Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 541 MET Chi-restraints excluded: chain C residue 544 SER Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 741 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.0470 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.118837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.092273 restraints weight = 22483.317| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.59 r_work: 0.2992 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12768 Z= 0.095 Angle : 0.495 8.780 17240 Z= 0.251 Chirality : 0.039 0.133 1952 Planarity : 0.002 0.018 2068 Dihedral : 14.435 124.756 2428 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.30 % Allowed : 19.94 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.22), residues: 1568 helix: 2.20 (0.17), residues: 980 sheet: -2.64 (0.54), residues: 64 loop : -2.13 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 499 TYR 0.016 0.001 TYR C 351 PHE 0.011 0.001 PHE E 591 TRP 0.007 0.001 TRP D 426 HIS 0.000 0.000 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (12756) covalent geometry : angle 0.49516 / 0.25 (17240) hydrogen bonds : bond 0.02546 / 1.71 ( 665) hydrogen bonds : angle 3.58780 / 2.48 ( 1959) Misc. bond : bond 0.00188 / 0.13 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2274.38 seconds wall clock time: 39 minutes 49.84 seconds (2389.84 seconds total)