Starting phenix.real_space_refine on Fri Jul 19 11:22:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/07_2024/8jh5_36254.cif" } resolution = 3.7 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= 0.003 sd= 0.079 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5070 2.51 5 N 1266 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7734 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'NPS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'NPS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.61 Number of scatterers: 7734 At special positions: 0 Unit cell: (106.7, 121, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1342 8.00 N 1266 7.00 C 5070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.5 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 48.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.149A pdb=" N PHE A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 11 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.532A pdb=" N TYR A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 49 removed outlier: 4.120A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 43 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.597A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 removed outlier: 4.010A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.505A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.764A pdb=" N VAL A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.557A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.565A pdb=" N THR A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 474 " --> pdb=" O TRP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.929A pdb=" N PHE A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.589A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.556A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.657A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.690A pdb=" N VAL A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 575 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.636A pdb=" N ALA A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 4.022A pdb=" N LEU A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 621 removed outlier: 4.348A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.148A pdb=" N PHE B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 30 removed outlier: 3.533A pdb=" N TYR B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.120A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.597A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 4.009A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.505A pdb=" N LEU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.764A pdb=" N VAL B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.558A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 474 removed outlier: 3.566A pdb=" N THR B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 474 " --> pdb=" O TRP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.929A pdb=" N PHE B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.589A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.556A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.657A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.689A pdb=" N VAL B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.636A pdb=" N ALA B 588 " --> pdb=" O PRO B 584 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 590 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 4.022A pdb=" N LEU B 598 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 621 removed outlier: 4.348A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.563A pdb=" N GLN C 7 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 56 removed outlier: 6.623A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA C 54 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 38 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 41 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 99 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.563A pdb=" N GLN D 7 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 16 Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 56 removed outlier: 6.623A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 41 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 99 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.534A pdb=" N TRP D 107 " --> pdb=" O ALA B 194 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 3.03 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: 1178 1.30 - 1.43: 2126 1.43 - 1.55: 4515 1.55 - 1.68: 3 1.68 - 1.81: 100 Bond restraints: 7922 Sorted by residual: bond pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA PHE A 585 " pdb=" C PHE A 585 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.37e-02 5.33e+03 3.55e+01 bond pdb=" CA PHE B 585 " pdb=" C PHE B 585 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.37e-02 5.33e+03 3.46e+01 bond pdb=" C PHE B 585 " pdb=" O PHE B 585 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.28e-02 6.10e+03 2.82e+01 ... (remaining 7917 not shown) Histogram of bond angle deviations from ideal: 99.37 - 107.29: 316 107.29 - 115.20: 4715 115.20 - 123.11: 5285 123.11 - 131.03: 410 131.03 - 138.94: 46 Bond angle restraints: 10772 Sorted by residual: angle pdb=" O NPS A 701 " pdb=" C15 NPS A 701 " pdb=" OXT NPS A 701 " ideal model delta sigma weight residual 126.82 103.80 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" O NPS B 701 " pdb=" C15 NPS B 701 " pdb=" OXT NPS B 701 " ideal model delta sigma weight residual 126.82 103.82 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O NPS B 701 " pdb=" C15 NPS B 701 " pdb=" C14 NPS B 701 " ideal model delta sigma weight residual 116.41 138.94 -22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O NPS A 701 " pdb=" C15 NPS A 701 " pdb=" C14 NPS A 701 " ideal model delta sigma weight residual 116.41 138.92 -22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" N PHE A 585 " pdb=" CA PHE A 585 " pdb=" C PHE A 585 " ideal model delta sigma weight residual 112.45 104.66 7.79 1.39e+00 5.18e-01 3.14e+01 ... (remaining 10767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 4440 14.88 - 29.76: 147 29.76 - 44.64: 71 44.64 - 59.51: 6 59.51 - 74.39: 2 Dihedral angle restraints: 4666 sinusoidal: 1806 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ILE D 35 " pdb=" C ILE D 35 " pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta harmonic sigma weight residual -180.00 -141.45 -38.55 0 5.00e+00 4.00e-02 5.95e+01 dihedral pdb=" CA ILE C 35 " pdb=" C ILE C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta harmonic sigma weight residual -180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" C ASN B 112 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" CB ASN B 112 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 4663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 614 0.035 - 0.070: 446 0.070 - 0.106: 123 0.106 - 0.141: 43 0.141 - 0.176: 20 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CB VAL B 557 " pdb=" CA VAL B 557 " pdb=" CG1 VAL B 557 " pdb=" CG2 VAL B 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB VAL A 557 " pdb=" CA VAL A 557 " pdb=" CG1 VAL A 557 " pdb=" CG2 VAL A 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB VAL D 6 " pdb=" CA VAL D 6 " pdb=" CG1 VAL D 6 " pdb=" CG2 VAL D 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1243 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 584 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C PRO B 584 " -0.049 2.00e-02 2.50e+03 pdb=" O PRO B 584 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE B 585 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 584 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C PRO A 584 " 0.049 2.00e-02 2.50e+03 pdb=" O PRO A 584 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 585 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 551 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 552 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " -0.030 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2388 2.84 - 3.35: 6505 3.35 - 3.87: 11808 3.87 - 4.38: 13316 4.38 - 4.90: 23069 Nonbonded interactions: 57086 Sorted by model distance: nonbonded pdb=" NH2 ARG A 547 " pdb=" O ALA A 576 " model vdw 2.319 2.520 nonbonded pdb=" NH2 ARG B 547 " pdb=" O ALA B 576 " model vdw 2.319 2.520 nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU B 191 " model vdw 2.344 2.520 nonbonded pdb=" ND2 ASN B 43 " pdb=" OG SER B 521 " model vdw 2.371 2.520 nonbonded pdb=" ND2 ASN A 43 " pdb=" OG SER A 521 " model vdw 2.371 2.520 ... (remaining 57081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.480 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.090 7922 Z= 0.410 Angle : 0.965 23.015 10772 Z= 0.481 Chirality : 0.053 0.176 1246 Planarity : 0.007 0.053 1320 Dihedral : 9.929 74.392 2820 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.76 (0.20), residues: 976 helix: -4.77 (0.08), residues: 512 sheet: -1.41 (0.42), residues: 166 loop : -2.85 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 37 HIS 0.004 0.001 HIS A 9 PHE 0.022 0.002 PHE B 585 TYR 0.022 0.002 TYR C 56 ARG 0.003 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8810 (t0) cc_final: 0.8567 (t0) REVERT: A 196 ILE cc_start: 0.8605 (mt) cc_final: 0.8127 (mt) REVERT: A 468 MET cc_start: 0.8521 (mmm) cc_final: 0.8308 (mmm) REVERT: A 499 MET cc_start: 0.8561 (ttp) cc_final: 0.8353 (ttp) REVERT: A 519 MET cc_start: 0.8565 (mmt) cc_final: 0.8362 (mmm) REVERT: A 538 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7328 (tmt170) REVERT: A 575 GLN cc_start: 0.8996 (pp30) cc_final: 0.8721 (pp30) REVERT: A 599 SER cc_start: 0.9165 (p) cc_final: 0.8964 (p) REVERT: A 615 LEU cc_start: 0.8924 (tp) cc_final: 0.8673 (tp) REVERT: C 51 TRP cc_start: 0.7421 (m-10) cc_final: 0.7029 (m100) REVERT: C 76 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6818 (ttp-110) REVERT: D 42 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8426 (ptm160) REVERT: D 76 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6552 (ttp-170) REVERT: B 62 ASN cc_start: 0.8811 (t0) cc_final: 0.8568 (t0) REVERT: B 196 ILE cc_start: 0.8627 (mt) cc_final: 0.8156 (mt) REVERT: B 468 MET cc_start: 0.8523 (mmm) cc_final: 0.8295 (mmm) REVERT: B 499 MET cc_start: 0.8558 (ttp) cc_final: 0.8351 (ttp) REVERT: B 519 MET cc_start: 0.8552 (mmt) cc_final: 0.8292 (mmm) REVERT: B 615 LEU cc_start: 0.8936 (tp) cc_final: 0.8690 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2457 time to fit residues: 71.9040 Evaluate side-chains 157 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 43 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS C 7 GLN B 9 HIS B 43 ASN B 127 ASN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7922 Z= 0.308 Angle : 0.669 6.427 10772 Z= 0.345 Chirality : 0.044 0.150 1246 Planarity : 0.006 0.046 1320 Dihedral : 5.648 34.047 1084 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.86 % Allowed : 10.51 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.53 (0.22), residues: 976 helix: -3.44 (0.15), residues: 500 sheet: -0.88 (0.44), residues: 158 loop : -2.99 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 144 HIS 0.003 0.001 HIS A 9 PHE 0.027 0.002 PHE A 128 TYR 0.026 0.001 TYR C 56 ARG 0.007 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 196 ILE cc_start: 0.8520 (mt) cc_final: 0.8224 (mt) REVERT: A 468 MET cc_start: 0.8733 (mmm) cc_final: 0.8397 (mmm) REVERT: A 538 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7356 (tmt170) REVERT: C 51 TRP cc_start: 0.7438 (m-10) cc_final: 0.7100 (m100) REVERT: C 76 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6308 (ttm110) REVERT: D 76 ARG cc_start: 0.7035 (ttp-170) cc_final: 0.5868 (ttp-110) REVERT: B 195 GLU cc_start: 0.7275 (tp30) cc_final: 0.6960 (tm-30) REVERT: B 196 ILE cc_start: 0.8525 (mt) cc_final: 0.8004 (mt) REVERT: B 468 MET cc_start: 0.8710 (mmm) cc_final: 0.8355 (mmm) REVERT: B 538 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7270 (tmt170) outliers start: 32 outliers final: 23 residues processed: 201 average time/residue: 0.1935 time to fit residues: 52.0436 Evaluate side-chains 171 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7922 Z= 0.160 Angle : 0.571 7.384 10772 Z= 0.288 Chirality : 0.042 0.141 1246 Planarity : 0.005 0.039 1320 Dihedral : 5.072 32.071 1084 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.14 % Allowed : 13.04 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.32 (0.24), residues: 976 helix: -2.31 (0.19), residues: 490 sheet: -0.40 (0.44), residues: 142 loop : -2.57 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 144 HIS 0.001 0.000 HIS B 203 PHE 0.020 0.001 PHE A 128 TYR 0.022 0.001 TYR C 56 ARG 0.005 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8708 (p) REVERT: A 195 GLU cc_start: 0.7311 (tm-30) cc_final: 0.6594 (tm-30) REVERT: A 196 ILE cc_start: 0.8212 (mt) cc_final: 0.7628 (mt) REVERT: A 468 MET cc_start: 0.8755 (mmm) cc_final: 0.8279 (mmm) REVERT: A 538 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7321 (tmt170) REVERT: A 616 TYR cc_start: 0.8339 (m-80) cc_final: 0.7957 (m-80) REVERT: C 51 TRP cc_start: 0.7411 (m-10) cc_final: 0.6927 (m-90) REVERT: C 76 ARG cc_start: 0.6638 (ttp-170) cc_final: 0.6278 (ttm170) REVERT: D 71 ARG cc_start: 0.4788 (ttp-110) cc_final: 0.4527 (ttp-170) REVERT: D 76 ARG cc_start: 0.7193 (ttp-170) cc_final: 0.5742 (ttp-110) REVERT: B 168 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (p) REVERT: B 195 GLU cc_start: 0.7192 (tp30) cc_final: 0.6837 (tm-30) REVERT: B 468 MET cc_start: 0.8758 (mmm) cc_final: 0.8271 (mmm) REVERT: B 538 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7272 (tmt170) outliers start: 26 outliers final: 12 residues processed: 174 average time/residue: 0.2307 time to fit residues: 53.5255 Evaluate side-chains 160 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.0070 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7922 Z= 0.155 Angle : 0.559 8.006 10772 Z= 0.279 Chirality : 0.041 0.141 1246 Planarity : 0.004 0.034 1320 Dihedral : 4.780 30.687 1084 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.90 % Allowed : 13.16 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.52 (0.25), residues: 976 helix: -1.55 (0.21), residues: 492 sheet: -0.34 (0.44), residues: 140 loop : -2.20 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.017 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.006 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9094 (m-10) cc_final: 0.8840 (m-10) REVERT: A 168 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 468 MET cc_start: 0.8786 (mmm) cc_final: 0.8576 (mmm) REVERT: A 538 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7324 (tmt170) REVERT: A 616 TYR cc_start: 0.8379 (m-80) cc_final: 0.8119 (m-80) REVERT: C 51 TRP cc_start: 0.7396 (m-10) cc_final: 0.6980 (m-90) REVERT: C 76 ARG cc_start: 0.6629 (ttp-170) cc_final: 0.6229 (ttm170) REVERT: D 41 TYR cc_start: 0.7808 (p90) cc_final: 0.6876 (p90) REVERT: B 145 TYR cc_start: 0.9099 (m-10) cc_final: 0.8867 (m-10) REVERT: B 168 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 468 MET cc_start: 0.8793 (mmm) cc_final: 0.8563 (mmm) REVERT: B 538 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7279 (tmt170) REVERT: B 616 TYR cc_start: 0.8339 (m-80) cc_final: 0.8076 (m-80) outliers start: 24 outliers final: 19 residues processed: 171 average time/residue: 0.1964 time to fit residues: 44.9344 Evaluate side-chains 164 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7922 Z= 0.179 Angle : 0.566 8.467 10772 Z= 0.279 Chirality : 0.042 0.129 1246 Planarity : 0.004 0.035 1320 Dihedral : 4.644 29.550 1084 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.26 % Allowed : 13.77 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.26), residues: 976 helix: -1.00 (0.22), residues: 490 sheet: 0.92 (0.52), residues: 100 loop : -2.09 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 37 HIS 0.002 0.000 HIS A 203 PHE 0.018 0.001 PHE D 72 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 142 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.9148 (t80) cc_final: 0.8948 (t80) REVERT: A 168 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 468 MET cc_start: 0.8845 (mmm) cc_final: 0.8625 (mmm) REVERT: A 538 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7325 (tmt170) REVERT: C 51 TRP cc_start: 0.7172 (m-10) cc_final: 0.6836 (m-90) REVERT: D 41 TYR cc_start: 0.7635 (p90) cc_final: 0.6698 (p90) REVERT: D 76 ARG cc_start: 0.7267 (ttp-170) cc_final: 0.6944 (ttm170) REVERT: B 145 TYR cc_start: 0.9083 (m-10) cc_final: 0.8860 (m-10) REVERT: B 168 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8617 (p) REVERT: B 468 MET cc_start: 0.8851 (mmm) cc_final: 0.8617 (mmm) REVERT: B 538 ARG cc_start: 0.7727 (mtt180) cc_final: 0.7273 (tmt170) outliers start: 27 outliers final: 20 residues processed: 161 average time/residue: 0.1904 time to fit residues: 41.2893 Evaluate side-chains 160 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7922 Z= 0.144 Angle : 0.531 8.569 10772 Z= 0.262 Chirality : 0.041 0.119 1246 Planarity : 0.004 0.035 1320 Dihedral : 4.393 28.416 1084 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.90 % Allowed : 14.37 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.27), residues: 976 helix: -0.48 (0.23), residues: 486 sheet: -0.16 (0.45), residues: 140 loop : -1.80 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 144 HIS 0.001 0.000 HIS B 203 PHE 0.013 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.002 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8546 (p) REVERT: A 538 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7370 (tmt170) REVERT: C 51 TRP cc_start: 0.7112 (m-10) cc_final: 0.6834 (m-90) REVERT: D 41 TYR cc_start: 0.7540 (p90) cc_final: 0.6561 (p90) REVERT: D 76 ARG cc_start: 0.7246 (ttp-170) cc_final: 0.6932 (ttm170) REVERT: B 168 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8546 (p) REVERT: B 538 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7302 (tmt170) outliers start: 24 outliers final: 15 residues processed: 165 average time/residue: 0.2224 time to fit residues: 48.7346 Evaluate side-chains 154 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7922 Z= 0.225 Angle : 0.589 8.081 10772 Z= 0.286 Chirality : 0.043 0.141 1246 Planarity : 0.004 0.036 1320 Dihedral : 4.547 28.284 1084 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.02 % Allowed : 14.73 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.27), residues: 976 helix: -0.32 (0.24), residues: 488 sheet: -0.04 (0.45), residues: 140 loop : -1.89 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 37 HIS 0.001 0.000 HIS A 203 PHE 0.014 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.002 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 538 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7417 (tmt170) REVERT: C 51 TRP cc_start: 0.7085 (m-10) cc_final: 0.6840 (m-90) REVERT: C 87 MET cc_start: 0.7740 (mmm) cc_final: 0.7526 (mmm) REVERT: D 41 TYR cc_start: 0.7469 (p90) cc_final: 0.6442 (p90) REVERT: D 76 ARG cc_start: 0.7383 (ttp-170) cc_final: 0.6967 (ttm170) REVERT: B 168 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8678 (p) REVERT: B 538 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7345 (tmt170) REVERT: B 555 MET cc_start: 0.8143 (tpp) cc_final: 0.7170 (tpp) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.1971 time to fit residues: 41.8595 Evaluate side-chains 157 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7922 Z= 0.210 Angle : 0.583 7.709 10772 Z= 0.283 Chirality : 0.043 0.142 1246 Planarity : 0.004 0.037 1320 Dihedral : 4.557 28.852 1084 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.50 % Allowed : 15.10 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.27), residues: 976 helix: -0.14 (0.24), residues: 492 sheet: 0.09 (0.45), residues: 140 loop : -1.89 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 37 HIS 0.002 0.000 HIS B 570 PHE 0.013 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.005 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8649 (p) REVERT: A 538 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7487 (tmt170) REVERT: D 41 TYR cc_start: 0.7414 (p90) cc_final: 0.5938 (p90) REVERT: D 42 ARG cc_start: 0.8003 (ptm160) cc_final: 0.7607 (ptm160) REVERT: D 49 ARG cc_start: 0.8206 (ptp-170) cc_final: 0.7986 (ptm160) REVERT: D 76 ARG cc_start: 0.7342 (ttp-170) cc_final: 0.6905 (ttm170) REVERT: B 168 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8618 (p) REVERT: B 538 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7444 (tmt170) outliers start: 29 outliers final: 24 residues processed: 158 average time/residue: 0.2161 time to fit residues: 45.8087 Evaluate side-chains 159 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.0010 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7922 Z= 0.155 Angle : 0.577 9.624 10772 Z= 0.276 Chirality : 0.042 0.139 1246 Planarity : 0.004 0.037 1320 Dihedral : 4.422 28.784 1084 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.90 % Allowed : 15.82 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.28), residues: 976 helix: 0.20 (0.25), residues: 482 sheet: 0.15 (0.46), residues: 140 loop : -1.64 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 37 HIS 0.001 0.000 HIS A 203 PHE 0.012 0.001 PHE A 128 TYR 0.028 0.001 TYR C 56 ARG 0.002 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 0.942 Fit side-chains REVERT: A 168 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 196 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9005 (mp) REVERT: A 538 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7382 (tmt170) REVERT: C 76 ARG cc_start: 0.6828 (ttp-170) cc_final: 0.6322 (ttm170) REVERT: D 76 ARG cc_start: 0.7320 (ttp-170) cc_final: 0.6860 (ttm170) REVERT: D 87 MET cc_start: 0.7911 (mmm) cc_final: 0.7066 (mmm) REVERT: B 168 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 538 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7299 (tmt170) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.2361 time to fit residues: 50.6793 Evaluate side-chains 165 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7922 Z= 0.123 Angle : 0.569 8.975 10772 Z= 0.270 Chirality : 0.041 0.134 1246 Planarity : 0.004 0.037 1320 Dihedral : 4.217 27.132 1084 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 17.15 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.28), residues: 976 helix: 0.60 (0.25), residues: 476 sheet: 0.30 (0.46), residues: 140 loop : -1.36 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.011 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG C 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 TYR cc_start: 0.9108 (t80) cc_final: 0.8905 (t80) REVERT: A 168 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 538 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7336 (tmt170) REVERT: C 41 TYR cc_start: 0.7917 (p90) cc_final: 0.7594 (p90) REVERT: C 76 ARG cc_start: 0.6808 (ttp-170) cc_final: 0.6277 (ttm170) REVERT: D 41 TYR cc_start: 0.7384 (p90) cc_final: 0.6435 (p90) REVERT: D 76 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6981 (ptp-170) REVERT: B 45 PHE cc_start: 0.9117 (t80) cc_final: 0.8651 (t80) REVERT: B 168 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 538 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7333 (tmt170) REVERT: B 619 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8523 (mm) outliers start: 16 outliers final: 12 residues processed: 164 average time/residue: 0.2043 time to fit residues: 44.3799 Evaluate side-chains 156 residues out of total 828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103140 restraints weight = 12434.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106318 restraints weight = 6610.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108291 restraints weight = 4482.615| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7922 Z= 0.136 Angle : 0.583 8.846 10772 Z= 0.276 Chirality : 0.041 0.126 1246 Planarity : 0.004 0.038 1320 Dihedral : 4.157 27.006 1084 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 18.24 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 976 helix: 0.69 (0.25), residues: 480 sheet: 0.37 (0.46), residues: 140 loop : -1.27 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.001 0.000 HIS A 203 PHE 0.011 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.36 seconds wall clock time: 34 minutes 9.68 seconds (2049.68 seconds total)