Starting phenix.real_space_refine on Thu Sep 26 20:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_8117_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_8117.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_8117.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_8117_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5irx_8117/09_2024/5irx_8117_trim.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} 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: {'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 3} 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: 8.25, per 1000 atoms: 0.63 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: 2.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.24 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: 3.72 Time building geometry restraints manager: 3.49 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 751 or resid 801)) selection = (chain 'B' and (resid 335 through 751 or resid 801)) selection = (chain 'C' and (resid 335 through 751 or resid 801)) selection = (chain 'D' and (resid 335 through 751 or resid 801)) } ncs_group { reference = (chain 'E' and (resid 1 through 75 or resid 101)) selection = (chain 'F' and (resid 1 through 75 or resid 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: 1.910 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.880 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- 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 : 0.014 0.194 13486 Z= 0.952 Angle : 1.437 19.195 18340 Z= 0.660 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 : 9.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.003 TRP E 53 HIS 0.004 0.001 HIS C 358 PHE 0.034 0.003 PHE D 448 TYR 0.022 0.003 TYR C 653 ARG 0.010 0.002 ARG D 355 *********************** 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 fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.405 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: 0.8383 (mtpt) REVERT: B 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8343 (mtpt) REVERT: C 639 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8254 (mtpt) REVERT: D 445 MET cc_start: 0.7699 (mmm) cc_final: 0.7418 (mmp) REVERT: D 639 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8239 (mtpt) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 1.3175 time to fit residues: 409.2285 Evaluate side-chains 189 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.0970 chunk 99 optimal weight: 0.7980 chunk 154 optimal weight: 40.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13486 Z= 0.157 Angle : 0.608 7.812 18340 Z= 0.311 Chirality : 0.039 0.187 2038 Planarity : 0.005 0.059 2224 Dihedral : 19.145 174.405 2612 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.69 % Allowed : 14.49 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.17), residues: 1714 helix: -1.62 (0.13), residues: 1036 sheet: -4.88 (0.37), residues: 92 loop : -3.89 (0.20), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 740 HIS 0.002 0.001 HIS B 410 PHE 0.014 0.001 PHE D 448 TYR 0.016 0.001 TYR E 22 ARG 0.003 0.000 ARG B 579 *********************** 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 306 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 568 MET cc_start: 0.7970 (ptp) cc_final: 0.7683 (ptp) REVERT: D 418 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7734 (pp) REVERT: D 568 MET cc_start: 0.7967 (ptp) cc_final: 0.7644 (ptp) outliers start: 28 outliers final: 18 residues processed: 286 average time/residue: 0.9278 time to fit residues: 296.0855 Evaluate side-chains 236 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 628 ASN Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain C residue 358 HIS 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 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 85 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 167 optimal weight: 0.0040 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 overall best weight: 2.1396 ------------------------------------------------------------------------------- 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 494 GLN D 628 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13486 Z= 0.273 Angle : 0.640 9.214 18340 Z= 0.319 Chirality : 0.042 0.180 2038 Planarity : 0.004 0.057 2224 Dihedral : 16.791 164.094 2612 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.80 % Allowed : 16.31 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.19), residues: 1714 helix: -0.20 (0.16), residues: 992 sheet: -4.87 (0.36), residues: 92 loop : -3.76 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 549 HIS 0.001 0.000 HIS A 364 PHE 0.013 0.001 PHE B 448 TYR 0.014 0.001 TYR D 653 ARG 0.003 0.000 ARG B 579 *********************** 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 281 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 GLU cc_start: 0.7411 (tp30) cc_final: 0.7197 (mm-30) REVERT: B 697 TRP cc_start: 0.7368 (OUTLIER) cc_final: 0.7087 (t60) REVERT: D 697 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.7114 (t60) outliers start: 50 outliers final: 20 residues processed: 252 average time/residue: 1.0235 time to fit residues: 285.3873 Evaluate side-chains 240 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 218 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET 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 B residue 358 HIS Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 685 THR 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 660 ILE 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 660 ILE 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 152 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 494 GLN B 628 ASN C 354 GLN C 494 GLN C 533 GLN C 628 ASN D 354 GLN D 494 GLN D 533 GLN D 628 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13486 Z= 0.173 Angle : 0.574 8.052 18340 Z= 0.287 Chirality : 0.040 0.174 2038 Planarity : 0.004 0.055 2224 Dihedral : 15.300 146.839 2612 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.70 % Allowed : 19.87 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1714 helix: 0.49 (0.17), residues: 1020 sheet: -4.21 (0.48), residues: 64 loop : -3.84 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 549 HIS 0.001 0.000 HIS A 410 PHE 0.011 0.001 PHE B 448 TYR 0.014 0.001 TYR E 22 ARG 0.001 0.000 ARG B 420 *********************** 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 292 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 243 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 65 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6688 (tp) outliers start: 49 outliers final: 23 residues processed: 263 average time/residue: 1.0678 time to fit residues: 309.7818 Evaluate side-chains 253 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.381 ------------------------------------------------------------------------------- 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 535 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 685 THR 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 601 ASP Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 358 HIS 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 660 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 B 628 ASN C 354 GLN C 494 GLN D 354 GLN D 494 GLN D 533 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13486 Z= 0.219 Angle : 0.578 7.418 18340 Z= 0.291 Chirality : 0.041 0.173 2038 Planarity : 0.004 0.053 2224 Dihedral : 14.439 118.657 2612 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.18 % Allowed : 20.54 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.20), residues: 1714 helix: 0.76 (0.16), residues: 1036 sheet: -4.23 (0.46), residues: 64 loop : -3.89 (0.20), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 549 HIS 0.001 0.000 HIS C 410 PHE 0.011 0.001 PHE C 448 TYR 0.013 0.001 TYR B 653 ARG 0.002 0.000 ARG D 355 *********************** 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 289 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 1.348 Fit side-chains REVERT: B 412 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6082 (mmt) outliers start: 54 outliers final: 26 residues processed: 259 average time/residue: 1.0110 time to fit residues: 290.1570 Evaluate side-chains 249 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 358 HIS Chi-restraints excluded: chain B residue 412 MET 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 B residue 685 THR 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 542 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 660 ILE 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 628 ASN Chi-restraints excluded: chain D residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 76 optimal weight: 0.0980 chunk 13 optimal weight: 30.0000 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 494 GLN D 533 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 13486 Z= 0.163 Angle : 0.571 12.580 18340 Z= 0.290 Chirality : 0.040 0.246 2038 Planarity : 0.004 0.053 2224 Dihedral : 13.855 123.645 2612 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.84 % Allowed : 22.55 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1714 helix: 0.97 (0.16), residues: 1060 sheet: -4.22 (0.46), residues: 64 loop : -3.91 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 740 HIS 0.003 0.000 HIS E 30 PHE 0.011 0.001 PHE A 655 TYR 0.020 0.001 TYR E 22 ARG 0.002 0.000 ARG B 420 *********************** 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 281 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 1.394 Fit side-chains outliers start: 40 outliers final: 13 residues processed: 252 average time/residue: 1.0131 time to fit residues: 282.9755 Evaluate side-chains 242 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 229 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 660 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 354 GLN C 494 GLN D 354 GLN D 494 GLN D 533 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13486 Z= 0.179 Angle : 0.597 10.744 18340 Z= 0.301 Chirality : 0.041 0.337 2038 Planarity : 0.004 0.053 2224 Dihedral : 13.473 123.893 2612 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 3.65 % Allowed : 23.90 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.20), residues: 1714 helix: 1.18 (0.16), residues: 1060 sheet: -4.08 (0.50), residues: 64 loop : -3.82 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 11 HIS 0.004 0.001 HIS F 30 PHE 0.009 0.001 PHE C 582 TYR 0.011 0.001 TYR E 34 ARG 0.001 0.000 ARG B 420 *********************** 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 268 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 230 time to evaluate : 1.443 Fit side-chains outliers start: 38 outliers final: 18 residues processed: 244 average time/residue: 1.0260 time to fit residues: 277.0429 Evaluate side-chains 244 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 226 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 552 MET 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 C residue 443 LEU Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 660 ILE 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 552 MET Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13486 Z= 0.202 Angle : 0.610 10.314 18340 Z= 0.307 Chirality : 0.041 0.274 2038 Planarity : 0.004 0.051 2224 Dihedral : 13.294 123.605 2612 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.78 % Allowed : 24.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1714 helix: 1.24 (0.16), residues: 1060 sheet: -3.93 (0.52), residues: 64 loop : -3.79 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 740 HIS 0.002 0.000 HIS F 30 PHE 0.011 0.001 PHE A 582 TYR 0.021 0.001 TYR E 22 ARG 0.001 0.000 ARG D 355 *********************** 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 253 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.465 Fit side-chains REVERT: B 523 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6826 (ttp) outliers start: 29 outliers final: 22 residues processed: 234 average time/residue: 1.0977 time to fit residues: 287.4759 Evaluate side-chains 244 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 221 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 552 MET 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 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 720 PHE 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 542 VAL Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 720 PHE 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 552 MET Chi-restraints excluded: chain D residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN B 494 GLN C 494 GLN D 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 13486 Z= 0.503 Angle : 0.772 12.447 18340 Z= 0.386 Chirality : 0.048 0.441 2038 Planarity : 0.004 0.046 2224 Dihedral : 14.095 117.470 2612 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.55 % Allowed : 24.38 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1714 helix: 0.73 (0.16), residues: 1060 sheet: -4.03 (0.50), residues: 64 loop : -3.77 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 11 HIS 0.002 0.001 HIS D 358 PHE 0.017 0.002 PHE C 720 TYR 0.014 0.002 TYR C 627 ARG 0.004 0.001 ARG B 355 *********************** 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 220 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 183 time to evaluate : 1.457 Fit side-chains REVERT: B 523 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6967 (ttp) outliers start: 37 outliers final: 18 residues processed: 202 average time/residue: 1.2317 time to fit residues: 271.9173 Evaluate side-chains 201 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 630 LEU 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 552 MET Chi-restraints excluded: chain B residue 720 PHE Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 523 MET Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 720 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13486 Z= 0.209 Angle : 0.644 9.210 18340 Z= 0.327 Chirality : 0.042 0.338 2038 Planarity : 0.004 0.053 2224 Dihedral : 13.570 123.216 2612 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.73 % Allowed : 26.49 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1714 helix: 1.17 (0.16), residues: 1060 sheet: -4.11 (0.48), residues: 64 loop : -3.67 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 11 HIS 0.002 0.000 HIS E 30 PHE 0.022 0.001 PHE D 720 TYR 0.018 0.001 TYR E 22 ARG 0.001 0.000 ARG B 355 ********************** 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 229 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 1.410 Fit side-chains REVERT: B 523 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.6909 (ttp) outliers start: 18 outliers final: 12 residues processed: 219 average time/residue: 1.1067 time to fit residues: 267.0523 Evaluate side-chains 219 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 720 PHE Chi-restraints excluded: chain B residue 335 THR Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain C residue 358 HIS Chi-restraints excluded: chain C residue 523 MET Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 720 PHE Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 523 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 17 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.131975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096948 restraints weight = 21238.342| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.57 r_work: 0.3073 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13486 Z= 0.214 Angle : 0.644 9.107 18340 Z= 0.327 Chirality : 0.042 0.333 2038 Planarity : 0.003 0.052 2224 Dihedral : 13.379 123.713 2612 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.73 % Allowed : 27.06 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1714 helix: 1.28 (0.16), residues: 1060 sheet: -4.07 (0.48), residues: 64 loop : -3.64 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 11 HIS 0.001 0.000 HIS E 30 PHE 0.018 0.001 PHE D 720 TYR 0.010 0.001 TYR D 631 ARG 0.001 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4864.20 seconds wall clock time: 86 minutes 28.69 seconds (5188.69 seconds total)