Starting phenix.real_space_refine on Fri Mar 15 14:22:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5is0_8119/03_2024/5is0_8119_trim_updated.pdb" } resolution = 3.43 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 S 76 5.16 5 Cl 4 4.86 5 C 7804 2.51 5 N 1932 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 420": "NH1" <-> "NH2" Residue "E ARG 474": "NH1" <-> "NH2" Residue "E ARG 491": "NH1" <-> "NH2" Residue "E ARG 500": "NH1" <-> "NH2" Residue "E ARG 557": "NH1" <-> "NH2" Residue "E TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11808 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "D" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "E" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2927 Classifications: {'peptide': 394} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 82} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 383} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 438 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 212 Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'6ET': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.30, per 1000 atoms: 0.53 Number of scatterers: 11808 At special positions: 0 Unit cell: (120.344, 120.344, 98.4636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 76 16.00 O 1992 8.00 N 1932 7.00 C 7804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.47 Conformation dependent library (CDL) restraints added in 2.3 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.634A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.936A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 470 through 499 removed outlier: 3.686A pdb=" N ARG C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 509 No H-bonds generated for 'chain 'C' and resid 506 through 509' Processing helix chain 'C' and resid 514 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 3.516A pdb=" N MET C 541 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 543 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 550 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C 555 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 576 removed outlier: 3.636A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.545A pdb=" N THR C 593 " --> pdb=" O PHE C 589 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 628 No H-bonds generated for 'chain 'C' and resid 603 through 628' Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.753A pdb=" N GLU C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 711 removed outlier: 3.946A pdb=" N ILE C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 687 " --> pdb=" O GLY C 683 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU C 709 " --> pdb=" O ILE C 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 3.634A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.936A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 470 through 499 removed outlier: 3.686A pdb=" N ARG B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 498 " --> pdb=" O GLN B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 No H-bonds generated for 'chain 'B' and resid 506 through 509' Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.516A pdb=" N MET B 541 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 543 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 550 " --> pdb=" O MET B 547 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 555 " --> pdb=" O MET B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 576 removed outlier: 3.636A pdb=" N ILE B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.545A pdb=" N THR B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 628 No H-bonds generated for 'chain 'B' and resid 603 through 628' Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.753A pdb=" N GLU B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 711 removed outlier: 3.946A pdb=" N ILE B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 687 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.634A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.936A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 470 through 499 removed outlier: 3.686A pdb=" N ARG D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN D 498 " --> pdb=" O GLN D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 509 No H-bonds generated for 'chain 'D' and resid 506 through 509' Processing helix chain 'D' and resid 514 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.516A pdb=" N MET D 541 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 543 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA D 546 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET D 547 " --> pdb=" O SER D 544 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP D 549 " --> pdb=" O ALA D 546 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 550 " --> pdb=" O MET D 547 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D 555 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 576 removed outlier: 3.637A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 598 removed outlier: 3.545A pdb=" N THR D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 628 No H-bonds generated for 'chain 'D' and resid 603 through 628' Processing helix chain 'D' and resid 630 through 642 removed outlier: 3.753A pdb=" N GLU D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 711 removed outlier: 3.946A pdb=" N ILE D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 687 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 709 " --> pdb=" O ILE D 705 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.634A pdb=" N GLN E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 400 Processing helix chain 'E' and resid 412 through 414 No H-bonds generated for 'chain 'E' and resid 412 through 414' Processing helix chain 'E' and resid 416 through 428 removed outlier: 3.937A pdb=" N ARG E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN E 423 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 453 Processing helix chain 'E' and resid 470 through 499 removed outlier: 3.686A pdb=" N ARG E 474 " --> pdb=" O GLY E 470 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN E 498 " --> pdb=" O GLN E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 509 No H-bonds generated for 'chain 'E' and resid 506 through 509' Processing helix chain 'E' and resid 514 through 531 Processing helix chain 'E' and resid 535 through 556 removed outlier: 3.516A pdb=" N MET E 541 " --> pdb=" O VAL E 538 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E 543 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA E 546 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET E 547 " --> pdb=" O SER E 544 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP E 549 " --> pdb=" O ALA E 546 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR E 550 " --> pdb=" O MET E 547 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR E 555 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 576 removed outlier: 3.637A pdb=" N ILE E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 565 " --> pdb=" O GLN E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 598 removed outlier: 3.544A pdb=" N THR E 593 " --> pdb=" O PHE E 589 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU E 598 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 628 No H-bonds generated for 'chain 'E' and resid 603 through 628' Processing helix chain 'E' and resid 630 through 642 removed outlier: 3.753A pdb=" N GLU E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE E 640 " --> pdb=" O GLU E 636 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR E 641 " --> pdb=" O LEU E 637 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 642 " --> pdb=" O PHE E 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 670 Processing helix chain 'E' and resid 674 through 711 removed outlier: 3.947A pdb=" N ILE E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN E 687 " --> pdb=" O GLY E 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS E 688 " --> pdb=" O GLU E 684 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN E 691 " --> pdb=" O ASN E 687 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU E 692 " --> pdb=" O LYS E 688 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS E 694 " --> pdb=" O ALA E 690 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU E 709 " --> pdb=" O ILE E 705 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1704 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: 3.15 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3514 1.34 - 1.46: 2975 1.46 - 1.57: 5455 1.57 - 1.69: 4 1.69 - 1.81: 128 Bond restraints: 12076 Sorted by residual: bond pdb=" C14 6ET B 801 " pdb=" S15 6ET B 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C14 6ET C 801 " pdb=" S15 6ET C 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET D 801 " pdb=" S15 6ET D 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET E 801 " pdb=" S15 6ET E 801 " ideal model delta sigma weight residual 1.689 1.588 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C14 6ET B 801 " pdb=" N08 6ET B 801 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 12071 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.57: 156 104.57 - 111.89: 5447 111.89 - 119.21: 4163 119.21 - 126.52: 6549 126.52 - 133.84: 89 Bond angle restraints: 16404 Sorted by residual: angle pdb=" N GLU B 513 " pdb=" CA GLU B 513 " pdb=" C GLU B 513 " ideal model delta sigma weight residual 114.56 104.09 10.47 1.27e+00 6.20e-01 6.79e+01 angle pdb=" N GLU C 513 " pdb=" CA GLU C 513 " pdb=" C GLU C 513 " ideal model delta sigma weight residual 114.56 104.10 10.46 1.27e+00 6.20e-01 6.78e+01 angle pdb=" N GLU E 513 " pdb=" CA GLU E 513 " pdb=" C GLU E 513 " ideal model delta sigma weight residual 114.56 104.14 10.42 1.27e+00 6.20e-01 6.73e+01 angle pdb=" N GLU D 513 " pdb=" CA GLU D 513 " pdb=" C GLU D 513 " ideal model delta sigma weight residual 114.56 104.17 10.39 1.27e+00 6.20e-01 6.69e+01 angle pdb=" C07 6ET B 801 " pdb=" N08 6ET B 801 " pdb=" C09 6ET B 801 " ideal model delta sigma weight residual 115.16 130.54 -15.38 3.00e+00 1.11e-01 2.63e+01 ... (remaining 16399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 6828 24.69 - 49.38: 132 49.38 - 74.07: 8 74.07 - 98.76: 4 98.76 - 123.45: 16 Dihedral angle restraints: 6988 sinusoidal: 2376 harmonic: 4612 Sorted by residual: dihedral pdb=" CA GLY C 375 " pdb=" C GLY C 375 " pdb=" N PRO C 376 " pdb=" CA PRO C 376 " ideal model delta harmonic sigma weight residual -180.00 -141.79 -38.21 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY E 375 " pdb=" C GLY E 375 " pdb=" N PRO E 376 " pdb=" CA PRO E 376 " ideal model delta harmonic sigma weight residual -180.00 -141.80 -38.20 0 5.00e+00 4.00e-02 5.84e+01 dihedral pdb=" CA GLY B 375 " pdb=" C GLY B 375 " pdb=" N PRO B 376 " pdb=" CA PRO B 376 " ideal model delta harmonic sigma weight residual -180.00 -141.83 -38.17 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 6985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1058 0.051 - 0.103: 667 0.103 - 0.154: 139 0.154 - 0.206: 19 0.206 - 0.257: 13 Chirality restraints: 1896 Sorted by residual: chirality pdb=" CB VAL B 595 " pdb=" CA VAL B 595 " pdb=" CG1 VAL B 595 " pdb=" CG2 VAL B 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB VAL D 595 " pdb=" CA VAL D 595 " pdb=" CG1 VAL D 595 " pdb=" CG2 VAL D 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB VAL E 595 " pdb=" CA VAL E 595 " pdb=" CG1 VAL E 595 " pdb=" CG2 VAL E 595 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1893 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 375 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" C GLY D 375 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY D 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO D 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 375 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C GLY E 375 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY E 375 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO E 376 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 375 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C GLY B 375 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B 375 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO B 376 " 0.015 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 4 2.01 - 2.73: 1457 2.73 - 3.45: 16842 3.45 - 4.18: 27571 4.18 - 4.90: 48225 Nonbonded interactions: 94099 Sorted by model distance: nonbonded pdb=" OG SER B 512 " pdb=" O13 6ET B 801 " model vdw 1.283 2.440 nonbonded pdb=" OG SER C 512 " pdb=" O13 6ET C 801 " model vdw 1.302 2.440 nonbonded pdb=" OG SER E 512 " pdb=" O13 6ET E 801 " model vdw 1.314 2.440 nonbonded pdb=" OG SER D 512 " pdb=" O13 6ET D 801 " model vdw 1.330 2.440 nonbonded pdb=" CB SER B 512 " pdb=" O13 6ET B 801 " model vdw 2.094 3.440 ... (remaining 94094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.250 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.300 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.120 12076 Z= 0.916 Angle : 1.237 15.382 16404 Z= 0.646 Chirality : 0.064 0.257 1896 Planarity : 0.006 0.043 2024 Dihedral : 12.935 123.449 4044 Min Nonbonded Distance : 1.283 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.08 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.27 (0.15), residues: 1568 helix: -3.51 (0.09), residues: 932 sheet: -3.99 (0.60), residues: 64 loop : -3.04 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP E 697 HIS 0.001 0.001 HIS C 410 PHE 0.035 0.004 PHE D 448 TYR 0.016 0.003 TYR D 653 ARG 0.012 0.002 ARG C 743 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 302 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 656 LYS cc_start: 0.8352 (tttt) cc_final: 0.8086 (tttm) REVERT: D 656 LYS cc_start: 0.8399 (tttt) cc_final: 0.8143 (tttm) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.2927 time to fit residues: 120.1254 Evaluate side-chains 167 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN B 700 GLN D 410 HIS D 423 GLN D 700 GLN E 410 HIS E 423 GLN E 700 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12076 Z= 0.199 Angle : 0.621 9.584 16404 Z= 0.324 Chirality : 0.041 0.157 1896 Planarity : 0.004 0.028 2024 Dihedral : 13.597 113.844 1788 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.59 % Allowed : 10.02 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.19), residues: 1568 helix: -0.97 (0.14), residues: 960 sheet: -3.05 (0.74), residues: 56 loop : -2.63 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 697 HIS 0.001 0.000 HIS D 410 PHE 0.016 0.001 PHE E 659 TYR 0.014 0.001 TYR B 565 ARG 0.006 0.001 ARG E 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 1.401 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 299 average time/residue: 0.1869 time to fit residues: 84.5009 Evaluate side-chains 212 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 564 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 691 GLN Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 691 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 0.1980 chunk 126 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 113 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS C 423 GLN C 700 GLN B 410 HIS B 423 GLN D 410 HIS D 423 GLN D 700 GLN E 410 HIS E 423 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12076 Z= 0.143 Angle : 0.539 6.514 16404 Z= 0.283 Chirality : 0.040 0.146 1896 Planarity : 0.003 0.022 2024 Dihedral : 12.931 110.729 1788 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.25 % Allowed : 12.36 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1568 helix: 0.32 (0.17), residues: 972 sheet: -3.12 (0.70), residues: 56 loop : -2.40 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 697 HIS 0.001 0.001 HIS D 410 PHE 0.014 0.001 PHE D 489 TYR 0.012 0.001 TYR B 511 ARG 0.004 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 276 average time/residue: 0.2097 time to fit residues: 84.6499 Evaluate side-chains 221 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 691 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN C 700 GLN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12076 Z= 0.298 Angle : 0.618 9.144 16404 Z= 0.318 Chirality : 0.043 0.156 1896 Planarity : 0.003 0.019 2024 Dihedral : 12.960 111.668 1788 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.43 % Allowed : 14.33 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1568 helix: 0.76 (0.17), residues: 988 sheet: -3.12 (0.67), residues: 56 loop : -2.23 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 697 HIS 0.001 0.000 HIS C 410 PHE 0.017 0.002 PHE C 448 TYR 0.012 0.001 TYR C 511 ARG 0.004 0.001 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 216 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 499 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.5707 (mtm180) outliers start: 26 outliers final: 22 residues processed: 233 average time/residue: 0.1947 time to fit residues: 68.3876 Evaluate side-chains 223 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 442 CYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 499 ARG Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 691 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12076 Z= 0.144 Angle : 0.541 8.351 16404 Z= 0.282 Chirality : 0.040 0.164 1896 Planarity : 0.002 0.017 2024 Dihedral : 12.696 110.766 1788 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.72 % Allowed : 15.36 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1568 helix: 0.86 (0.17), residues: 996 sheet: -2.80 (0.70), residues: 56 loop : -2.27 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.001 0.000 HIS C 410 PHE 0.012 0.001 PHE D 496 TYR 0.013 0.001 TYR E 511 ARG 0.003 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 246 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 267 average time/residue: 0.2044 time to fit residues: 81.3713 Evaluate side-chains 237 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 691 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12076 Z= 0.191 Angle : 0.600 11.898 16404 Z= 0.297 Chirality : 0.040 0.172 1896 Planarity : 0.002 0.015 2024 Dihedral : 12.543 109.731 1788 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.09 % Allowed : 15.64 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.23), residues: 1568 helix: 0.98 (0.17), residues: 996 sheet: -2.72 (0.70), residues: 56 loop : -2.24 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 697 HIS 0.000 0.000 HIS E 410 PHE 0.014 0.001 PHE D 496 TYR 0.013 0.001 TYR E 401 ARG 0.003 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 235 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 27 residues processed: 256 average time/residue: 0.1879 time to fit residues: 73.4097 Evaluate side-chains 247 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 220 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12076 Z= 0.192 Angle : 0.586 10.756 16404 Z= 0.295 Chirality : 0.040 0.176 1896 Planarity : 0.002 0.021 2024 Dihedral : 12.452 109.100 1788 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.37 % Allowed : 15.45 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1568 helix: 1.00 (0.17), residues: 1000 sheet: -2.68 (0.70), residues: 56 loop : -2.27 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 697 HIS 0.001 0.000 HIS B 410 PHE 0.009 0.001 PHE C 448 TYR 0.013 0.001 TYR E 511 ARG 0.003 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 31 residues processed: 259 average time/residue: 0.1843 time to fit residues: 73.4931 Evaluate side-chains 254 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 223 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 670 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 0.4980 chunk 144 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12076 Z= 0.154 Angle : 0.579 9.439 16404 Z= 0.296 Chirality : 0.039 0.183 1896 Planarity : 0.002 0.024 2024 Dihedral : 12.135 106.098 1788 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.00 % Allowed : 17.04 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.23), residues: 1568 helix: 1.00 (0.17), residues: 996 sheet: -2.57 (0.72), residues: 56 loop : -2.34 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 697 HIS 0.001 0.000 HIS E 410 PHE 0.010 0.001 PHE D 496 TYR 0.014 0.001 TYR C 511 ARG 0.006 0.000 ARG B 579 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 241 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 642 ILE cc_start: 0.8653 (mt) cc_final: 0.8434 (mt) outliers start: 32 outliers final: 24 residues processed: 262 average time/residue: 0.2052 time to fit residues: 83.2377 Evaluate side-chains 250 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12076 Z= 0.168 Angle : 0.627 13.825 16404 Z= 0.316 Chirality : 0.040 0.189 1896 Planarity : 0.003 0.028 2024 Dihedral : 12.109 105.578 1788 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.53 % Allowed : 18.63 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1568 helix: 0.99 (0.17), residues: 996 sheet: -2.62 (0.71), residues: 56 loop : -2.38 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 697 HIS 0.002 0.000 HIS E 410 PHE 0.010 0.001 PHE C 496 TYR 0.016 0.001 TYR D 351 ARG 0.002 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 257 average time/residue: 0.1906 time to fit residues: 74.0457 Evaluate side-chains 245 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 0.0570 chunk 95 optimal weight: 0.1980 chunk 75 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12076 Z= 0.168 Angle : 0.642 14.015 16404 Z= 0.319 Chirality : 0.040 0.194 1896 Planarity : 0.002 0.032 2024 Dihedral : 11.878 103.431 1788 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.15 % Allowed : 19.94 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1568 helix: 0.96 (0.17), residues: 1000 sheet: -2.52 (0.72), residues: 56 loop : -2.30 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 697 HIS 0.001 0.000 HIS D 410 PHE 0.012 0.001 PHE D 496 TYR 0.019 0.001 TYR D 511 ARG 0.002 0.000 ARG C 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 20 residues processed: 257 average time/residue: 0.2013 time to fit residues: 78.0170 Evaluate side-chains 244 residues out of total 1420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 574 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 0.0030 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088570 restraints weight = 27867.419| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.83 r_work: 0.3048 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12076 Z= 0.158 Angle : 0.649 13.626 16404 Z= 0.316 Chirality : 0.040 0.177 1896 Planarity : 0.003 0.029 2024 Dihedral : 11.628 101.330 1788 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.97 % Allowed : 20.41 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1568 helix: 1.02 (0.17), residues: 1004 sheet: -2.51 (0.71), residues: 56 loop : -2.23 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 697 HIS 0.001 0.000 HIS D 410 PHE 0.007 0.001 PHE C 659 TYR 0.020 0.001 TYR B 511 ARG 0.004 0.000 ARG D 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2490.07 seconds wall clock time: 45 minutes 35.69 seconds (2735.69 seconds total)