Starting phenix.real_space_refine on Thu Sep 18 04:39:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5irx_8117/09_2025/5irx_8117.map" } resolution = 2.95 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 16 5.49 5 S 90 5.16 5 C 8710 2.51 5 N 2098 2.21 5 O 2248 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13162 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 13, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 13, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 195 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 13, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 195 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2893 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 108} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 365 Unresolved non-hydrogen angles: 466 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 5, 'HIS:plan': 1, 'ASP:plan': 13, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 493 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 102 Unusual residues: {'6EU': 1, '6O8': 1, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 151 Unusual residues: {'6EU': 1, '6O8': 1, '6O9': 1, '6OE': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'6O9': 1, '6OE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'6O9': 2, '6OE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.16, per 1000 atoms: 0.24 Number of scatterers: 13162 At special positions: 0 Unit cell: (120.344, 120.344, 110.62, 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 90 16.00 P 16 15.00 O 2248 8.00 N 2098 7.00 C 8710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 593.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3228 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 60.3% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 418 through 429 removed outlier: 3.769A pdb=" N GLN A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.911A pdb=" N ILE A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.559A pdb=" N PHE A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 532 removed outlier: 3.741A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.947A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 555 Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.565A pdb=" N VAL A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 581 Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.775A pdb=" N PHE A 587 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.530A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 4.080A pdb=" N LEU A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 692 removed outlier: 3.581A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 713 removed outlier: 4.427A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 701 " --> pdb=" O TRP A 697 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 418 through 429 removed outlier: 3.768A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.911A pdb=" N ILE B 433 " --> pdb=" O PHE B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.560A pdb=" N PHE B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 532 removed outlier: 3.741A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.948A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 555 Processing helix chain 'B' and resid 563 through 575 removed outlier: 3.565A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 573 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 581 Processing helix chain 'B' and resid 583 through 599 removed outlier: 3.776A pdb=" N PHE B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 removed outlier: 3.530A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 4.080A pdb=" N LEU B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 692 removed outlier: 3.580A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 713 removed outlier: 4.427A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 699 " --> pdb=" O ASN B 695 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 701 " --> pdb=" O TRP B 697 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 720 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 418 through 429 removed outlier: 3.768A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 removed outlier: 3.911A pdb=" N ILE C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.560A pdb=" N PHE C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 532 removed outlier: 3.741A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.947A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 555 Processing helix chain 'C' and resid 563 through 575 removed outlier: 3.565A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 570 " --> pdb=" O ALA C 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 573 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 581 Processing helix chain 'C' and resid 583 through 599 removed outlier: 3.775A pdb=" N PHE C 587 " --> pdb=" O VAL C 583 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 removed outlier: 3.529A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 4.080A pdb=" N LEU C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 692 removed outlier: 3.581A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 713 removed outlier: 4.427A pdb=" N LYS C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU C 699 " --> pdb=" O ASN C 695 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN C 700 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 701 " --> pdb=" O TRP C 697 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 712 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 720 Processing helix chain 'D' and resid 336 through 342 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 418 through 429 removed outlier: 3.769A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 removed outlier: 3.911A pdb=" N ILE D 433 " --> pdb=" O PHE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 499 removed outlier: 3.560A pdb=" N PHE D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 532 removed outlier: 3.741A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.948A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 555 Processing helix chain 'D' and resid 563 through 575 removed outlier: 3.565A pdb=" N VAL D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 570 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 573 " --> pdb=" O ILE D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 581 Processing helix chain 'D' and resid 583 through 599 removed outlier: 3.776A pdb=" N PHE D 587 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 removed outlier: 3.529A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 4.080A pdb=" N LEU D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 692 removed outlier: 3.580A pdb=" N ILE D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 713 removed outlier: 4.427A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN D 700 " --> pdb=" O ILE D 696 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 701 " --> pdb=" O TRP D 697 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 712 " --> pdb=" O THR D 708 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 720 Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 374 removed outlier: 4.844A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 724 through 725 Processing sheet with id=AA3, first strand: chain 'B' and resid 369 through 374 removed outlier: 4.843A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 724 through 725 Processing sheet with id=AA5, first strand: chain 'C' and resid 369 through 374 removed outlier: 4.844A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 724 through 725 Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 374 removed outlier: 4.843A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 724 through 725 693 hydrogen bonds defined for protein. 2043 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: 2.08 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1902 1.30 - 1.44: 4159 1.44 - 1.58: 7249 1.58 - 1.71: 32 1.71 - 1.85: 144 Bond restraints: 13486 Sorted by residual: bond pdb=" CAV 6EU D 805 " pdb=" CBB 6EU D 805 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" CAV 6EU C 803 " pdb=" CBB 6EU C 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU B 803 " pdb=" CBB 6EU B 803 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAV 6EU A 804 " pdb=" CBB 6EU A 804 " ideal model delta sigma weight residual 1.330 1.524 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" CAR 6EU B 803 " pdb=" CAZ 6EU B 803 " ideal model delta sigma weight residual 1.538 1.373 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 13481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 17853 3.84 - 7.68: 380 7.68 - 11.52: 83 11.52 - 15.36: 16 15.36 - 19.19: 8 Bond angle restraints: 18340 Sorted by residual: angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CA PRO F 24 " ideal model delta sigma weight residual 127.00 146.19 -19.19 2.40e+00 1.74e-01 6.40e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " ideal model delta sigma weight residual 127.00 146.15 -19.15 2.40e+00 1.74e-01 6.37e+01 angle pdb=" C CYS F 23 " pdb=" N PRO F 24 " pdb=" CD PRO F 24 " ideal model delta sigma weight residual 120.60 105.11 15.49 2.20e+00 2.07e-01 4.96e+01 angle pdb=" C CYS E 23 " pdb=" N PRO E 24 " pdb=" CD PRO E 24 " ideal model delta sigma weight residual 120.60 105.15 15.45 2.20e+00 2.07e-01 4.93e+01 angle pdb=" O04 6O9 E 101 " pdb=" P05 6O9 E 101 " pdb=" O08 6O9 E 101 " ideal model delta sigma weight residual 93.00 108.99 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 18335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.85: 7865 34.85 - 69.70: 134 69.70 - 104.54: 37 104.54 - 139.39: 29 139.39 - 174.24: 23 Dihedral angle restraints: 8088 sinusoidal: 3036 harmonic: 5052 Sorted by residual: dihedral pdb=" CA GLU A 416 " pdb=" C GLU A 416 " pdb=" N PRO A 417 " pdb=" CA PRO A 417 " ideal model delta harmonic sigma weight residual 180.00 133.67 46.33 0 5.00e+00 4.00e-02 8.59e+01 dihedral pdb=" CA GLU C 416 " pdb=" C GLU C 416 " pdb=" N PRO C 417 " pdb=" CA PRO C 417 " ideal model delta harmonic sigma weight residual 180.00 133.70 46.30 0 5.00e+00 4.00e-02 8.58e+01 dihedral pdb=" CA GLU B 416 " pdb=" C GLU B 416 " pdb=" N PRO B 417 " pdb=" CA PRO B 417 " ideal model delta harmonic sigma weight residual 180.00 133.72 46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 8085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1639 0.079 - 0.157: 343 0.157 - 0.236: 38 0.236 - 0.314: 10 0.314 - 0.393: 8 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CAR 6EU A 804 " pdb=" CAO 6EU A 804 " pdb=" CAU 6EU A 804 " pdb=" CAZ 6EU A 804 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU C 803 " pdb=" CAO 6EU C 803 " pdb=" CAU 6EU C 803 " pdb=" CAZ 6EU C 803 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" CAR 6EU D 805 " pdb=" CAO 6EU D 805 " pdb=" CAU 6EU D 805 " pdb=" CAZ 6EU D 805 " both_signs ideal model delta sigma weight residual False 2.83 2.44 0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 2035 not shown) Planarity restraints: 2224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 455 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO B 456 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 455 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO D 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 456 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 455 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO C 456 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 456 " -0.035 5.00e-02 4.00e+02 ... (remaining 2221 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 32 2.38 - 3.01: 6641 3.01 - 3.64: 19051 3.64 - 4.27: 28832 4.27 - 4.90: 47564 Nonbonded interactions: 102120 Sorted by model distance: nonbonded pdb=" O GLU F 26 " pdb=" O07 6OE F 103 " model vdw 1.744 3.040 nonbonded pdb=" O GLU E 26 " pdb=" O07 6OE E 102 " model vdw 1.819 3.040 nonbonded pdb=" OD1 ASN B 437 " pdb=" O06 6O8 B 801 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN A 437 " pdb=" O06 6O8 A 801 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN C 437 " pdb=" O06 6O8 C 801 " model vdw 2.162 3.040 ... (remaining 102115 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 335 through 801) selection = (chain 'B' and resid 335 through 801) selection = (chain 'C' and resid 335 through 801) selection = (chain 'D' and resid 335 through 801) } ncs_group { reference = (chain 'E' and resid 1 through 101) selection = (chain 'F' and resid 1 through 101) } 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.510 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 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 : 0.015 0.258 13502 Z= 0.781 Angle : 1.439 19.195 18364 Z= 0.661 Chirality : 0.067 0.393 2038 Planarity : 0.006 0.063 2224 Dihedral : 19.899 174.240 4824 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.68 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -6.45 (0.12), residues: 1714 helix: -4.13 (0.08), residues: 988 sheet: -4.38 (0.62), residues: 52 loop : -4.31 (0.17), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 355 TYR 0.022 0.003 TYR C 653 PHE 0.034 0.003 PHE D 448 TRP 0.017 0.003 TRP E 53 HIS 0.004 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.01436 (13486) covalent geometry : angle 1.43653 (18340) SS BOND : bond 0.00597 ( 12) SS BOND : angle 2.60380 ( 24) hydrogen bonds : bond 0.28600 ( 693) hydrogen bonds : angle 10.11214 ( 2043) Misc. bond : bond 0.23902 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7579 (mmm) cc_final: 0.7331 (mmp) REVERT: A 639 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8384 (mtpt) REVERT: B 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8344 (mtpt) REVERT: C 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8255 (mtpt) REVERT: D 445 MET cc_start: 0.7699 (mmm) cc_final: 0.7417 (mmp) REVERT: D 639 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8238 (mtpt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.6302 time to fit residues: 194.5723 Evaluate side-chains 189 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 628 ASN A 691 GLN B 628 ASN B 691 GLN C 628 ASN C 691 GLN D 437 ASN D 494 GLN D 628 ASN D 691 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097440 restraints weight = 21265.745| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.59 r_work: 0.3100 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13502 Z= 0.147 Angle : 0.638 8.106 18364 Z= 0.325 Chirality : 0.040 0.188 2038 Planarity : 0.005 0.060 2224 Dihedral : 19.236 174.796 2612 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.88 % Allowed : 14.68 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -3.99 (0.16), residues: 1714 helix: -1.68 (0.13), residues: 1016 sheet: -4.89 (0.37), residues: 92 loop : -3.85 (0.19), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 575 TYR 0.015 0.001 TYR E 22 PHE 0.016 0.001 PHE D 448 TRP 0.009 0.001 TRP D 740 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd covalent geometry : bond 0.00332 (13486) covalent geometry : angle 0.63654 (18340) SS BOND : bond 0.00343 ( 12) SS BOND : angle 1.33372 ( 24) hydrogen bonds : bond 0.03879 ( 693) hydrogen bonds : angle 4.51698 ( 2043) Misc. bond : bond 0.00055 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.427 Fit side-chains REVERT: A 418 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 483 SER cc_start: 0.9164 (t) cc_final: 0.8895 (p) REVERT: A 581 MET cc_start: 0.8573 (ppp) cc_final: 0.8005 (tpt) REVERT: A 601 ASP cc_start: 0.7684 (m-30) cc_final: 0.7368 (m-30) REVERT: B 365 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8803 (pp) REVERT: B 418 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7590 (pp) REVERT: B 483 SER cc_start: 0.9160 (t) cc_final: 0.8915 (p) REVERT: B 697 TRP cc_start: 0.8962 (OUTLIER) cc_final: 0.8525 (t60) REVERT: C 418 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7642 (pp) REVERT: C 483 SER cc_start: 0.9186 (t) cc_final: 0.8903 (p) REVERT: C 601 ASP cc_start: 0.7723 (m-30) cc_final: 0.7442 (m-30) REVERT: C 631 TYR cc_start: 0.8790 (t80) cc_final: 0.8566 (t80) REVERT: D 365 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8796 (pp) REVERT: D 418 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7650 (pp) REVERT: D 601 ASP cc_start: 0.7734 (m-30) cc_final: 0.7437 (m-30) REVERT: E 7 GLU cc_start: 0.8585 (mt-10) cc_final: 0.7789 (mt-10) REVERT: E 25 MET cc_start: 0.7814 (ttm) cc_final: 0.7532 (ttm) REVERT: F 7 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7775 (mt-10) outliers start: 30 outliers final: 16 residues processed: 272 average time/residue: 0.4367 time to fit residues: 131.7275 Evaluate side-chains 236 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 697 TRP Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 628 ASN Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 90 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 153 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 628 ASN A 687 ASN B 437 ASN B 494 GLN B 628 ASN C 354 GLN C 437 ASN C 494 GLN C 628 ASN C 687 ASN D 354 GLN D 494 GLN D 628 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095038 restraints weight = 21445.442| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.58 r_work: 0.3043 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13502 Z= 0.204 Angle : 0.652 8.473 18364 Z= 0.325 Chirality : 0.042 0.182 2038 Planarity : 0.004 0.057 2224 Dihedral : 16.896 162.256 2612 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.61 % Allowed : 15.26 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -2.62 (0.19), residues: 1714 helix: -0.26 (0.16), residues: 992 sheet: -4.90 (0.35), residues: 92 loop : -3.71 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.014 0.001 TYR D 653 PHE 0.015 0.001 PHE D 448 TRP 0.008 0.001 TRP D 740 HIS 0.003 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00473 (13486) covalent geometry : angle 0.65093 (18340) SS BOND : bond 0.00370 ( 12) SS BOND : angle 1.12873 ( 24) hydrogen bonds : bond 0.03705 ( 693) hydrogen bonds : angle 4.03885 ( 2043) Misc. bond : bond 0.00071 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.462 Fit side-chains REVERT: A 483 SER cc_start: 0.9157 (t) cc_final: 0.8876 (p) REVERT: A 581 MET cc_start: 0.8594 (ppp) cc_final: 0.8064 (tpt) REVERT: A 601 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7417 (m-30) REVERT: A 636 GLU cc_start: 0.8901 (tp30) cc_final: 0.8603 (mm-30) REVERT: A 710 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8983 (mtmt) REVERT: B 359 GLU cc_start: 0.6751 (mp0) cc_final: 0.6366 (mp0) REVERT: B 365 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 483 SER cc_start: 0.9165 (t) cc_final: 0.8904 (p) REVERT: B 677 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9008 (ttm) REVERT: B 697 TRP cc_start: 0.8930 (OUTLIER) cc_final: 0.8364 (t60) REVERT: B 710 LYS cc_start: 0.9330 (mmmm) cc_final: 0.8951 (mtmt) REVERT: C 346 ILE cc_start: 0.8609 (mp) cc_final: 0.8385 (mm) REVERT: C 483 SER cc_start: 0.9165 (t) cc_final: 0.8711 (p) REVERT: C 601 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 697 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8377 (t60) REVERT: C 710 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8988 (mtmt) REVERT: D 346 ILE cc_start: 0.8612 (mp) cc_final: 0.8392 (mm) REVERT: D 365 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8804 (pp) REVERT: D 581 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8049 (tpt) REVERT: D 601 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: D 636 GLU cc_start: 0.8884 (tp30) cc_final: 0.8584 (mm-30) REVERT: D 697 TRP cc_start: 0.8933 (OUTLIER) cc_final: 0.8347 (t60) REVERT: D 710 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8979 (mtmt) REVERT: E 7 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8066 (mt-10) REVERT: E 49 GLU cc_start: 0.8696 (mt-10) cc_final: 0.7962 (mt-10) REVERT: F 7 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 49 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8530 (mt-10) outliers start: 48 outliers final: 19 residues processed: 248 average time/residue: 0.5102 time to fit residues: 138.7883 Evaluate side-chains 239 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 697 TRP Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 581 MET Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 697 TRP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 159 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 628 ASN B 354 GLN B 494 GLN B 628 ASN C 354 GLN C 494 GLN C 628 ASN D 354 GLN D 494 GLN D 628 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.097788 restraints weight = 21301.686| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.57 r_work: 0.3104 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13502 Z= 0.118 Angle : 0.568 7.831 18364 Z= 0.282 Chirality : 0.039 0.173 2038 Planarity : 0.004 0.056 2224 Dihedral : 15.063 135.195 2612 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.09 % Allowed : 19.00 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -1.72 (0.20), residues: 1714 helix: 0.51 (0.17), residues: 1020 sheet: -4.23 (0.48), residues: 64 loop : -3.74 (0.20), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 575 TYR 0.015 0.001 TYR E 22 PHE 0.011 0.001 PHE B 448 TRP 0.005 0.001 TRP D 740 HIS 0.001 0.000 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00267 (13486) covalent geometry : angle 0.56737 (18340) SS BOND : bond 0.00274 ( 12) SS BOND : angle 0.86641 ( 24) hydrogen bonds : bond 0.03016 ( 693) hydrogen bonds : angle 3.67873 ( 2043) Misc. bond : bond 0.00043 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.509 Fit side-chains REVERT: A 359 GLU cc_start: 0.7439 (mp0) cc_final: 0.7219 (mp0) REVERT: A 483 SER cc_start: 0.9066 (t) cc_final: 0.8704 (p) REVERT: A 601 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: A 636 GLU cc_start: 0.8857 (tp30) cc_final: 0.8579 (mm-30) REVERT: A 710 LYS cc_start: 0.9304 (mmmm) cc_final: 0.8998 (mtmt) REVERT: B 365 LEU cc_start: 0.9357 (tp) cc_final: 0.8873 (pp) REVERT: B 483 SER cc_start: 0.9104 (t) cc_final: 0.8751 (p) REVERT: B 581 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7989 (tpt) REVERT: B 601 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7505 (m-30) REVERT: B 710 LYS cc_start: 0.9309 (mmmm) cc_final: 0.8997 (mtmt) REVERT: C 346 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 359 GLU cc_start: 0.7429 (mp0) cc_final: 0.7026 (mp0) REVERT: C 483 SER cc_start: 0.9042 (t) cc_final: 0.8789 (p) REVERT: C 601 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: C 636 GLU cc_start: 0.8851 (tp30) cc_final: 0.8583 (mm-30) REVERT: C 710 LYS cc_start: 0.9305 (mmmm) cc_final: 0.9012 (mtmt) REVERT: D 365 LEU cc_start: 0.9338 (tp) cc_final: 0.8878 (pp) REVERT: D 581 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: D 601 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: D 710 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8975 (mtmt) REVERT: E 7 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7961 (mt-10) REVERT: E 49 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8460 (mt-10) REVERT: F 4 LYS cc_start: 0.8743 (mppt) cc_final: 0.8457 (mmpt) REVERT: F 7 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8126 (mt-10) REVERT: F 25 MET cc_start: 0.7927 (ttp) cc_final: 0.7249 (tpp) outliers start: 53 outliers final: 18 residues processed: 267 average time/residue: 0.4972 time to fit residues: 145.6457 Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 122 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 533 GLN B 354 GLN B 494 GLN B 533 GLN C 354 GLN C 494 GLN D 354 GLN D 494 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099457 restraints weight = 21509.973| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.60 r_work: 0.3125 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13502 Z= 0.100 Angle : 0.540 6.956 18364 Z= 0.271 Chirality : 0.039 0.206 2038 Planarity : 0.003 0.053 2224 Dihedral : 14.054 123.799 2612 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.41 % Allowed : 21.40 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -1.38 (0.20), residues: 1714 helix: 0.82 (0.16), residues: 1060 sheet: -4.11 (0.48), residues: 64 loop : -3.97 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.008 0.001 TYR B 653 PHE 0.010 0.001 PHE A 655 TRP 0.007 0.001 TRP D 549 HIS 0.001 0.000 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00221 (13486) covalent geometry : angle 0.53879 (18340) SS BOND : bond 0.00402 ( 12) SS BOND : angle 1.10634 ( 24) hydrogen bonds : bond 0.02782 ( 693) hydrogen bonds : angle 3.51591 ( 2043) Misc. bond : bond 0.00030 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.424 Fit side-chains REVERT: A 483 SER cc_start: 0.9001 (t) cc_final: 0.8773 (p) REVERT: A 601 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: A 636 GLU cc_start: 0.8842 (tp30) cc_final: 0.8536 (mm-30) REVERT: B 359 GLU cc_start: 0.7479 (mp0) cc_final: 0.7270 (mp0) REVERT: B 365 LEU cc_start: 0.9350 (tp) cc_final: 0.8911 (pp) REVERT: B 483 SER cc_start: 0.9016 (t) cc_final: 0.8800 (p) REVERT: B 677 MET cc_start: 0.9126 (ttt) cc_final: 0.8845 (ttm) REVERT: C 483 SER cc_start: 0.9006 (t) cc_final: 0.8765 (p) REVERT: C 547 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8540 (ttp) REVERT: C 601 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: C 636 GLU cc_start: 0.8834 (tp30) cc_final: 0.8585 (mm-30) REVERT: D 365 LEU cc_start: 0.9338 (tp) cc_final: 0.8946 (pp) REVERT: D 552 MET cc_start: 0.9066 (mtm) cc_final: 0.8780 (mtt) REVERT: D 601 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: D 636 GLU cc_start: 0.8824 (tp30) cc_final: 0.8567 (mm-30) REVERT: E 7 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 49 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8465 (mt-10) REVERT: F 4 LYS cc_start: 0.8829 (mppt) cc_final: 0.8544 (mmpt) REVERT: F 7 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8172 (mt-10) REVERT: F 25 MET cc_start: 0.7791 (ttp) cc_final: 0.7315 (tpp) REVERT: F 49 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8002 (pt0) outliers start: 46 outliers final: 13 residues processed: 267 average time/residue: 0.4715 time to fit residues: 139.4520 Evaluate side-chains 257 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 601 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 94 optimal weight: 8.9990 chunk 13 optimal weight: 30.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 494 GLN A 533 GLN B 354 GLN B 494 GLN C 354 GLN C 494 GLN D 354 GLN D 494 GLN D 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096355 restraints weight = 21144.983| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.56 r_work: 0.3075 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13502 Z= 0.153 Angle : 0.581 9.419 18364 Z= 0.293 Chirality : 0.041 0.212 2038 Planarity : 0.003 0.050 2224 Dihedral : 13.841 119.346 2612 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.93 % Allowed : 23.22 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -1.25 (0.20), residues: 1714 helix: 0.91 (0.16), residues: 1052 sheet: -4.08 (0.49), residues: 64 loop : -3.79 (0.20), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.014 0.001 TYR E 22 PHE 0.010 0.001 PHE D 448 TRP 0.013 0.001 TRP D 549 HIS 0.003 0.000 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00357 (13486) covalent geometry : angle 0.57978 (18340) SS BOND : bond 0.00207 ( 12) SS BOND : angle 1.32758 ( 24) hydrogen bonds : bond 0.03067 ( 693) hydrogen bonds : angle 3.54262 ( 2043) Misc. bond : bond 0.00010 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 230 time to evaluate : 0.425 Fit side-chains REVERT: A 483 SER cc_start: 0.9053 (t) cc_final: 0.8785 (p) REVERT: A 601 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: B 365 LEU cc_start: 0.9343 (tp) cc_final: 0.8895 (pp) REVERT: B 483 SER cc_start: 0.9063 (t) cc_final: 0.8808 (p) REVERT: B 682 MET cc_start: 0.9070 (mtm) cc_final: 0.8779 (mtp) REVERT: C 483 SER cc_start: 0.9021 (t) cc_final: 0.8760 (p) REVERT: C 585 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8898 (mp) REVERT: C 601 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: C 636 GLU cc_start: 0.8861 (tp30) cc_final: 0.8601 (mm-30) REVERT: D 359 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: D 365 LEU cc_start: 0.9331 (tp) cc_final: 0.8934 (pp) REVERT: D 601 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: D 636 GLU cc_start: 0.8834 (tp30) cc_final: 0.8576 (mm-30) REVERT: E 4 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8210 (mmmt) REVERT: E 7 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7898 (mt-10) REVERT: E 49 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8413 (mt-10) REVERT: F 4 LYS cc_start: 0.8813 (mppt) cc_final: 0.8529 (mmpt) REVERT: F 7 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8105 (mt-10) REVERT: F 25 MET cc_start: 0.7998 (ttp) cc_final: 0.7397 (tpp) outliers start: 41 outliers final: 19 residues processed: 250 average time/residue: 0.4719 time to fit residues: 130.0690 Evaluate side-chains 250 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain E residue 65 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 153 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 533 GLN B 354 GLN B 494 GLN C 494 GLN C 533 GLN D 354 GLN D 494 GLN D 533 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097179 restraints weight = 21277.471| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.57 r_work: 0.3089 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13502 Z= 0.125 Angle : 0.585 13.084 18364 Z= 0.295 Chirality : 0.041 0.322 2038 Planarity : 0.003 0.052 2224 Dihedral : 13.476 115.874 2612 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.84 % Allowed : 24.28 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -1.05 (0.20), residues: 1714 helix: 1.07 (0.16), residues: 1064 sheet: -4.07 (0.49), residues: 64 loop : -3.83 (0.20), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.010 0.001 TYR D 653 PHE 0.010 0.001 PHE B 655 TRP 0.009 0.001 TRP D 549 HIS 0.002 0.000 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00286 (13486) covalent geometry : angle 0.57213 (18340) SS BOND : bond 0.00488 ( 12) SS BOND : angle 3.37202 ( 24) hydrogen bonds : bond 0.02918 ( 693) hydrogen bonds : angle 3.48702 ( 2043) Misc. bond : bond 0.00009 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.329 Fit side-chains REVERT: A 483 SER cc_start: 0.9044 (t) cc_final: 0.8789 (p) REVERT: A 601 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: A 636 GLU cc_start: 0.8850 (tp30) cc_final: 0.8541 (mm-30) REVERT: B 365 LEU cc_start: 0.9338 (tp) cc_final: 0.8896 (pp) REVERT: B 483 SER cc_start: 0.9055 (t) cc_final: 0.8813 (p) REVERT: B 682 MET cc_start: 0.9048 (mtm) cc_final: 0.8804 (mtp) REVERT: C 483 SER cc_start: 0.9010 (t) cc_final: 0.8764 (p) REVERT: C 533 GLN cc_start: 0.9204 (mt0) cc_final: 0.8628 (mm110) REVERT: C 585 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8878 (mp) REVERT: C 601 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: C 636 GLU cc_start: 0.8852 (tp30) cc_final: 0.8602 (mm-30) REVERT: D 359 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: D 365 LEU cc_start: 0.9325 (tp) cc_final: 0.8934 (pp) REVERT: D 601 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: D 636 GLU cc_start: 0.8830 (tp30) cc_final: 0.8575 (mm-30) REVERT: E 4 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8110 (mmmt) REVERT: E 7 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7799 (mt-10) REVERT: E 49 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 4 LYS cc_start: 0.8841 (mppt) cc_final: 0.8563 (mmpt) REVERT: F 7 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8142 (mt-10) REVERT: F 49 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7973 (pt0) outliers start: 40 outliers final: 22 residues processed: 256 average time/residue: 0.4576 time to fit residues: 129.3266 Evaluate side-chains 256 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 533 GLN B 354 GLN B 494 GLN C 494 GLN D 494 GLN D 533 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.133906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.099408 restraints weight = 21104.747| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.57 r_work: 0.3119 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13502 Z= 0.104 Angle : 0.572 11.042 18364 Z= 0.288 Chirality : 0.040 0.274 2038 Planarity : 0.004 0.053 2224 Dihedral : 12.933 113.355 2612 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.36 % Allowed : 25.24 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -0.77 (0.21), residues: 1714 helix: 1.34 (0.16), residues: 1064 sheet: -4.05 (0.49), residues: 64 loop : -3.80 (0.20), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.015 0.001 TYR F 22 PHE 0.009 0.001 PHE C 655 TRP 0.006 0.001 TRP B 740 HIS 0.003 0.000 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00234 (13486) covalent geometry : angle 0.55738 (18340) SS BOND : bond 0.00386 ( 12) SS BOND : angle 3.60288 ( 24) hydrogen bonds : bond 0.02732 ( 693) hydrogen bonds : angle 3.41251 ( 2043) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 0.394 Fit side-chains REVERT: A 483 SER cc_start: 0.8993 (t) cc_final: 0.8762 (p) REVERT: A 601 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: A 631 TYR cc_start: 0.8763 (t80) cc_final: 0.8541 (t80) REVERT: A 636 GLU cc_start: 0.8855 (tp30) cc_final: 0.8564 (mm-30) REVERT: B 365 LEU cc_start: 0.9344 (tp) cc_final: 0.8949 (pp) REVERT: B 483 SER cc_start: 0.9008 (t) cc_final: 0.8795 (p) REVERT: B 631 TYR cc_start: 0.8770 (t80) cc_final: 0.8265 (t80) REVERT: B 682 MET cc_start: 0.9030 (mtm) cc_final: 0.8769 (mtp) REVERT: C 483 SER cc_start: 0.8992 (t) cc_final: 0.8759 (p) REVERT: C 513 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8713 (mm-30) REVERT: C 533 GLN cc_start: 0.9176 (mt0) cc_final: 0.8636 (mm110) REVERT: C 585 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9023 (mt) REVERT: C 600 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 601 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: C 631 TYR cc_start: 0.8799 (t80) cc_final: 0.8343 (t80) REVERT: C 636 GLU cc_start: 0.8841 (tp30) cc_final: 0.8596 (mm-30) REVERT: C 720 PHE cc_start: 0.7496 (m-80) cc_final: 0.7295 (t80) REVERT: D 359 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: D 365 LEU cc_start: 0.9319 (tp) cc_final: 0.8948 (pp) REVERT: D 533 GLN cc_start: 0.9193 (mt0) cc_final: 0.8644 (mm110) REVERT: D 600 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7626 (mm-30) REVERT: D 601 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: D 636 GLU cc_start: 0.8841 (tp30) cc_final: 0.8574 (mm-30) REVERT: E 4 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8253 (mmmt) REVERT: E 7 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7799 (mt-10) REVERT: E 49 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8401 (mt-10) REVERT: E 56 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8101 (ttpp) REVERT: F 4 LYS cc_start: 0.8837 (mppt) cc_final: 0.8564 (mmpt) REVERT: F 7 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7957 (mt-10) REVERT: F 14 LYS cc_start: 0.8314 (ptmm) cc_final: 0.8066 (pttm) REVERT: F 49 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8038 (pt0) outliers start: 35 outliers final: 16 residues processed: 258 average time/residue: 0.4699 time to fit residues: 134.3271 Evaluate side-chains 253 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 56 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 354 GLN B 494 GLN C 494 GLN D 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099260 restraints weight = 21275.062| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.58 r_work: 0.3109 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13502 Z= 0.110 Angle : 0.582 10.370 18364 Z= 0.290 Chirality : 0.040 0.287 2038 Planarity : 0.003 0.050 2224 Dihedral : 12.754 112.563 2612 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.07 % Allowed : 26.39 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -0.64 (0.21), residues: 1714 helix: 1.44 (0.16), residues: 1064 sheet: -3.98 (0.49), residues: 64 loop : -3.76 (0.20), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.010 0.001 TYR D 631 PHE 0.011 0.001 PHE A 655 TRP 0.007 0.001 TRP A 740 HIS 0.001 0.000 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00250 (13486) covalent geometry : angle 0.57098 (18340) SS BOND : bond 0.00245 ( 12) SS BOND : angle 3.11310 ( 24) hydrogen bonds : bond 0.02801 ( 693) hydrogen bonds : angle 3.40811 ( 2043) Misc. bond : bond 0.00006 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.443 Fit side-chains REVERT: A 483 SER cc_start: 0.8996 (t) cc_final: 0.8764 (p) REVERT: A 585 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 600 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 601 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: A 636 GLU cc_start: 0.8883 (tp30) cc_final: 0.8602 (mm-30) REVERT: B 365 LEU cc_start: 0.9337 (tp) cc_final: 0.8947 (pp) REVERT: B 483 SER cc_start: 0.8999 (t) cc_final: 0.8782 (p) REVERT: B 585 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 682 MET cc_start: 0.9069 (mtm) cc_final: 0.8763 (mtp) REVERT: C 483 SER cc_start: 0.8979 (t) cc_final: 0.8743 (p) REVERT: C 513 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8695 (mm-30) REVERT: C 533 GLN cc_start: 0.9178 (mt0) cc_final: 0.8640 (mm110) REVERT: C 585 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9030 (mt) REVERT: C 600 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 601 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: C 631 TYR cc_start: 0.8814 (t80) cc_final: 0.8338 (t80) REVERT: C 636 GLU cc_start: 0.8841 (tp30) cc_final: 0.8597 (mm-30) REVERT: C 720 PHE cc_start: 0.7537 (m-80) cc_final: 0.7268 (t80) REVERT: D 359 GLU cc_start: 0.7757 (mp0) cc_final: 0.7426 (mp0) REVERT: D 365 LEU cc_start: 0.9344 (tp) cc_final: 0.8944 (pp) REVERT: D 533 GLN cc_start: 0.9189 (mt0) cc_final: 0.8640 (mm110) REVERT: D 585 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8722 (mp) REVERT: D 600 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 601 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: E 7 GLU cc_start: 0.8575 (mt-10) cc_final: 0.7839 (mt-10) REVERT: E 49 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8383 (mt-10) REVERT: E 56 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8101 (ttpp) REVERT: F 4 LYS cc_start: 0.8821 (mppt) cc_final: 0.8546 (mmpt) REVERT: F 7 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8059 (mt-10) REVERT: F 14 LYS cc_start: 0.8395 (ptmm) cc_final: 0.8119 (pttm) REVERT: F 49 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8047 (pt0) outliers start: 32 outliers final: 16 residues processed: 246 average time/residue: 0.5153 time to fit residues: 139.7903 Evaluate side-chains 249 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 0.0170 chunk 121 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 354 GLN B 494 GLN C 494 GLN D 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096995 restraints weight = 21220.117| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.57 r_work: 0.3077 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13502 Z= 0.154 Angle : 0.617 9.782 18364 Z= 0.306 Chirality : 0.042 0.296 2038 Planarity : 0.004 0.050 2224 Dihedral : 12.713 109.929 2612 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.07 % Allowed : 26.10 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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 aren not related in a simple way. whole: -0.65 (0.21), residues: 1714 helix: 1.40 (0.16), residues: 1072 sheet: -3.95 (0.51), residues: 64 loop : -3.75 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.013 0.001 TYR A 631 PHE 0.010 0.001 PHE B 720 TRP 0.011 0.001 TRP D 549 HIS 0.001 0.000 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00358 (13486) covalent geometry : angle 0.60764 (18340) SS BOND : bond 0.00309 ( 12) SS BOND : angle 2.97045 ( 24) hydrogen bonds : bond 0.03063 ( 693) hydrogen bonds : angle 3.49088 ( 2043) Misc. bond : bond 0.00002 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.485 Fit side-chains REVERT: A 483 SER cc_start: 0.9053 (t) cc_final: 0.8790 (p) REVERT: A 513 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8729 (mm-30) REVERT: A 585 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 600 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7672 (mm-30) REVERT: A 601 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: A 636 GLU cc_start: 0.8892 (tp30) cc_final: 0.8603 (mm-30) REVERT: B 365 LEU cc_start: 0.9332 (tp) cc_final: 0.8928 (pp) REVERT: B 483 SER cc_start: 0.9050 (t) cc_final: 0.8798 (p) REVERT: B 513 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8753 (mm-30) REVERT: B 585 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 631 TYR cc_start: 0.8797 (t80) cc_final: 0.8317 (t80) REVERT: B 682 MET cc_start: 0.9066 (mtm) cc_final: 0.8776 (mtp) REVERT: C 483 SER cc_start: 0.9050 (t) cc_final: 0.8784 (p) REVERT: C 513 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8705 (mm-30) REVERT: C 533 GLN cc_start: 0.9190 (mt0) cc_final: 0.8645 (mm110) REVERT: C 585 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8897 (mp) REVERT: C 600 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7656 (mm-30) REVERT: C 601 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: C 631 TYR cc_start: 0.8877 (t80) cc_final: 0.8439 (t80) REVERT: C 636 GLU cc_start: 0.8861 (tp30) cc_final: 0.8598 (mm-30) REVERT: C 720 PHE cc_start: 0.7503 (m-80) cc_final: 0.7241 (t80) REVERT: D 359 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: D 365 LEU cc_start: 0.9342 (tp) cc_final: 0.8930 (pp) REVERT: D 513 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8726 (mm-30) REVERT: D 533 GLN cc_start: 0.9184 (mt0) cc_final: 0.8624 (mm110) REVERT: D 585 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 601 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7618 (m-30) REVERT: D 636 GLU cc_start: 0.8889 (tp30) cc_final: 0.8583 (mm-30) REVERT: E 7 GLU cc_start: 0.8621 (mt-10) cc_final: 0.7925 (mt-10) REVERT: E 49 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8372 (mt-10) REVERT: F 4 LYS cc_start: 0.8831 (mppt) cc_final: 0.8549 (mmpt) REVERT: F 7 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8061 (mt-10) REVERT: F 14 LYS cc_start: 0.8321 (ptmm) cc_final: 0.8050 (pttm) REVERT: F 25 MET cc_start: 0.8148 (tpp) cc_final: 0.7303 (tpp) REVERT: F 49 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8041 (pt0) outliers start: 32 outliers final: 20 residues processed: 242 average time/residue: 0.5309 time to fit residues: 141.1868 Evaluate side-chains 254 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 535 LYS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 720 PHE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 0.0570 chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN B 354 GLN C 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099186 restraints weight = 21087.867| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.58 r_work: 0.3111 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13502 Z= 0.106 Angle : 0.592 10.119 18364 Z= 0.293 Chirality : 0.040 0.263 2038 Planarity : 0.003 0.051 2224 Dihedral : 12.450 109.135 2612 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.88 % Allowed : 26.39 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 aren not related in a simple way. whole: -0.45 (0.21), residues: 1714 helix: 1.56 (0.16), residues: 1072 sheet: -3.86 (0.52), residues: 64 loop : -3.70 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 575 TYR 0.013 0.001 TYR A 631 PHE 0.012 0.001 PHE A 655 TRP 0.008 0.001 TRP A 740 HIS 0.001 0.000 HIS F 30 Details of bonding type rmsd covalent geometry : bond 0.00238 (13486) covalent geometry : angle 0.58495 (18340) SS BOND : bond 0.00239 ( 12) SS BOND : angle 2.62741 ( 24) hydrogen bonds : bond 0.02831 ( 693) hydrogen bonds : angle 3.44367 ( 2043) Misc. bond : bond 0.00012 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4006.16 seconds wall clock time: 69 minutes 2.65 seconds (4142.65 seconds total)