Starting phenix.real_space_refine on Sun May 18 18:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwe_47241/05_2025/9dwe_47241_neut.cif" } resolution = 2.8 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= 0.023 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 90 5.16 5 C 10899 2.51 5 N 2970 2.21 5 O 3438 1.98 5 H 3 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17400 Number of models: 1 Model: "" Number of chains: 15 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3987 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "M" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "I" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 807 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 907 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" Number of atoms: 3984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3984 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 20, 'TRANS': 478} Chain breaks: 1 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N SER H 17 " occ=0.59 ... (4 atoms not shown) pdb=" OG SER H 17 " occ=0.59 residue: pdb=" N SER H 24 " occ=0.85 ... (4 atoms not shown) pdb=" OG SER H 24 " occ=0.85 residue: pdb=" N SER I 17 " occ=0.56 ... (4 atoms not shown) pdb=" OG SER I 17 " occ=0.56 residue: pdb=" N SER I 24 " occ=0.79 ... (4 atoms not shown) pdb=" OG SER I 24 " occ=0.79 residue: pdb=" N SER J 17 " occ=0.54 ... (4 atoms not shown) pdb=" OG SER J 17 " occ=0.54 residue: pdb=" N SER J 24 " occ=0.83 ... (4 atoms not shown) pdb=" OG SER J 24 " occ=0.83 Time building chain proxies: 12.09, per 1000 atoms: 0.69 Number of scatterers: 17400 At special positions: 0 Unit cell: (134.125, 129.05, 146.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 3438 8.00 N 2970 7.00 C 10899 6.00 H 3 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.02 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 487 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 476 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.02 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.02 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 487 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA2-3 " GAL D 1 " - " SIA D 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL E 1 " - " SIA E 2 " " GAL P 1 " - " SIA P 2 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 33 " " NAG A 603 " - " ASN A 175 " " NAG A 604 " - " ASN A 296 " " NAG A 605 " - " ASN A 493 " " NAG B 601 " - " ASN B 21 " " NAG B 602 " - " ASN B 33 " " NAG B 603 " - " ASN B 175 " " NAG B 604 " - " ASN B 296 " " NAG B 605 " - " ASN B 493 " " NAG C 601 " - " ASN C 21 " " NAG C 602 " - " ASN C 33 " " NAG C 603 " - " ASN C 175 " " NAG C 604 " - " ASN C 296 " " NAG C 605 " - " ASN C 493 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.0 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 54 sheets defined 20.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.009A pdb=" N ASP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLU A 79 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 376 through 398 removed outlier: 3.590A pdb=" N MET A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 466 Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 497 through 513 removed outlier: 4.019A pdb=" N TYR A 501 " --> pdb=" O ASP A 497 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 81 removed outlier: 3.933A pdb=" N ASP B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 79 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.694A pdb=" N TRP B 132 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 376 through 398 removed outlier: 3.646A pdb=" N MET B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 466 Processing helix chain 'B' and resid 484 through 493 Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.677A pdb=" N ASP N 82 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.012A pdb=" N ASP C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU C 79 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.660A pdb=" N TRP C 132 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 376 through 398 removed outlier: 3.601A pdb=" N MET C 398 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 466 Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 497 through 513 removed outlier: 3.988A pdb=" N TYR C 501 " --> pdb=" O ASP C 497 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU C 503 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU C 504 " --> pdb=" O GLN C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.651A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.527A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 370 through 375 removed outlier: 3.965A pdb=" N ASN A 367 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY A 362 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.880A pdb=" N LEU A 51 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS A 284 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.585A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 89 " --> pdb=" O MET A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 185 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 262 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS A 120 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 269 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE A 118 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 105 removed outlier: 6.480A pdb=" N SER A 104 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N TRP A 240 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 135 through 136 Processing sheet with id=AB7, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.631A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB9, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.018A pdb=" N CYS A 288 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 9 through 13 removed outlier: 6.660A pdb=" N VAL M 11 " --> pdb=" O THR M 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.618A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.533A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 370 through 375 removed outlier: 3.504A pdb=" N GLY B 362 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AC9, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD1, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD2, first strand: chain 'B' and resid 51 through 54 removed outlier: 6.860A pdb=" N LEU B 51 " --> pdb=" O GLY B 282 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYS B 284 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.606A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 89 " --> pdb=" O MET B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LEU B 185 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B 262 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS B 120 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS B 269 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 118 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.528A pdb=" N SER B 104 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TRP B 240 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 135 through 136 Processing sheet with id=AD7, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.644A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AD9, first strand: chain 'B' and resid 288 through 289 Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.641A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.623A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.524A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.518A pdb=" N GLY C 362 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AE9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AF1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.867A pdb=" N LEU C 51 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N CYS C 284 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.595A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 89 " --> pdb=" O MET C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 185 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 262 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS C 120 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 269 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 118 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.482A pdb=" N SER C 104 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TRP C 240 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 135 through 136 Processing sheet with id=AF7, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.639A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AF9, first strand: chain 'C' and resid 288 through 289 747 hydrogen bonds defined for protein. 1935 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: 6.47 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 3 1.17 - 1.33: 5026 1.33 - 1.49: 5544 1.49 - 1.66: 7082 1.66 - 1.82: 132 Bond restraints: 17787 Sorted by residual: bond pdb=" N GLY A 340 " pdb=" H GLY A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CA GLY A 340 " pdb=" HA3 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA GLY A 340 " pdb=" HA2 GLY A 340 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C1 SIA P 2 " pdb=" O1A SIA P 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C1 SIA E 2 " pdb=" O1A SIA E 2 " ideal model delta sigma weight residual 1.262 1.197 0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 17782 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23486 2.12 - 4.24: 558 4.24 - 6.35: 39 6.35 - 8.47: 17 8.47 - 10.59: 11 Bond angle restraints: 24111 Sorted by residual: angle pdb=" C SER N 2 " pdb=" N ALA N 3 " pdb=" CA ALA N 3 " ideal model delta sigma weight residual 121.54 128.70 -7.16 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER M 2 " pdb=" N ALA M 3 " pdb=" CA ALA M 3 " ideal model delta sigma weight residual 121.54 128.69 -7.15 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C SER L 2 " pdb=" N ALA L 3 " pdb=" CA ALA L 3 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" C1 SIA P 2 " pdb=" C2 SIA P 2 " pdb=" C3 SIA P 2 " ideal model delta sigma weight residual 115.48 104.89 10.59 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA ARG C 117 " pdb=" CB ARG C 117 " pdb=" CG ARG C 117 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 ... (remaining 24106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.52: 10419 26.52 - 53.05: 421 53.05 - 79.57: 52 79.57 - 106.09: 14 106.09 - 132.62: 1 Dihedral angle restraints: 10907 sinusoidal: 4628 harmonic: 6279 Sorted by residual: dihedral pdb=" C9 SIA E 2 " pdb=" C7 SIA E 2 " pdb=" C8 SIA E 2 " pdb=" O7 SIA E 2 " ideal model delta sinusoidal sigma weight residual -44.94 87.68 -132.62 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " pdb=" CB CYS I 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.68 35.32 1 1.00e+01 1.00e-02 1.77e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 58.04 34.96 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 10904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2575 0.120 - 0.240: 60 0.240 - 0.359: 3 0.359 - 0.479: 4 0.479 - 0.599: 1 Chirality restraints: 2643 Sorted by residual: chirality pdb=" C2 SIA P 2 " pdb=" O3 GAL P 1 " pdb=" C1 SIA P 2 " pdb=" O6 SIA P 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.70e+02 chirality pdb=" C2 SIA D 2 " pdb=" O3 GAL D 1 " pdb=" C1 SIA D 2 " pdb=" O6 SIA D 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.33 2.00e-02 2.50e+03 2.69e+02 chirality pdb=" C2 SIA E 2 " pdb=" O3 GAL E 1 " pdb=" C1 SIA E 2 " pdb=" O6 SIA E 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.74 0.24 2.00e-02 2.50e+03 1.46e+02 ... (remaining 2640 not shown) Planarity restraints: 3135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SIA P 2 " 0.016 2.00e-02 2.50e+03 4.79e-02 2.86e+01 pdb=" C11 SIA P 2 " -0.044 2.00e-02 2.50e+03 pdb=" C5 SIA P 2 " -0.058 2.00e-02 2.50e+03 pdb=" N5 SIA P 2 " 0.076 2.00e-02 2.50e+03 pdb=" O10 SIA P 2 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 290 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 291 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 291 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 291 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 SIA D 2 " 0.007 2.00e-02 2.50e+03 2.42e-02 7.31e+00 pdb=" C11 SIA D 2 " -0.022 2.00e-02 2.50e+03 pdb=" C5 SIA D 2 " -0.029 2.00e-02 2.50e+03 pdb=" N5 SIA D 2 " 0.039 2.00e-02 2.50e+03 pdb=" O10 SIA D 2 " 0.006 2.00e-02 2.50e+03 ... (remaining 3132 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 3 2.11 - 2.73: 1099 2.73 - 3.35: 18934 3.35 - 3.98: 38221 3.98 - 4.60: 53340 Nonbonded interactions: 111597 Sorted by model distance: nonbonded pdb=" O SER B 513 " pdb=" CZ ARG C 506 " model vdw 1.485 3.100 nonbonded pdb=" O SER B 513 " pdb=" NH1 ARG C 506 " model vdw 1.624 2.950 nonbonded pdb=" O SER B 513 " pdb=" NE ARG C 506 " model vdw 1.921 2.950 nonbonded pdb=" OH TYR A 101 " pdb=" O9 SIA E 2 " model vdw 2.279 2.800 nonbonded pdb=" OG1 THR B 290 " pdb=" O GLY B 293 " model vdw 2.279 2.800 ... (remaining 111592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 332 or (resid 340 and (name N or name CA or name \ C or name O )) or resid 341 through 513 or resid 601 through 605)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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=0.54 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: 14.630 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: 0.490 Extract box with map and model: 0.800 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 41.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.005 0.066 17826 Z= 0.228 Angle : 0.825 25.685 24207 Z= 0.410 Chirality : 0.054 0.599 2643 Planarity : 0.006 0.070 3120 Dihedral : 14.212 132.617 6831 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.83 (0.17), residues: 2163 helix: -0.46 (0.23), residues: 396 sheet: -0.06 (0.21), residues: 615 loop : -0.78 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 70 HIS 0.009 0.001 HIS B 450 PHE 0.032 0.002 PHE C 121 TYR 0.013 0.002 TYR A 496 ARG 0.006 0.001 ARG B 407 Details of bonding type rmsd link_BETA2-3 : bond 0.05950 ( 3) link_BETA2-3 : angle 7.04086 ( 9) link_NAG-ASN : bond 0.01456 ( 15) link_NAG-ASN : angle 7.05533 ( 45) hydrogen bonds : bond 0.18375 ( 690) hydrogen bonds : angle 7.94420 ( 1935) SS BOND : bond 0.00384 ( 24) SS BOND : angle 1.01421 ( 48) covalent geometry : bond 0.00482 (17784) covalent geometry : angle 0.75554 (24105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8466 (mt0) cc_final: 0.8064 (tt0) REVERT: A 287 LYS cc_start: 0.8198 (mttm) cc_final: 0.7788 (mptt) REVERT: A 311 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8277 (mm-30) REVERT: A 507 LEU cc_start: 0.8018 (tp) cc_final: 0.7772 (mp) REVERT: M 79 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6547 (mt0) REVERT: I 3 GLN cc_start: 0.8453 (mt0) cc_final: 0.7994 (tt0) REVERT: B 287 LYS cc_start: 0.8108 (mttm) cc_final: 0.7713 (mptt) REVERT: B 311 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8220 (mm-30) REVERT: B 392 ASN cc_start: 0.8336 (m-40) cc_final: 0.8043 (m-40) REVERT: B 414 ARG cc_start: 0.8550 (mmm160) cc_final: 0.8273 (mtm180) REVERT: B 470 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7362 (tttt) REVERT: B 500 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (tt0) REVERT: B 508 LYS cc_start: 0.7429 (tttm) cc_final: 0.6812 (mmmt) REVERT: J 3 GLN cc_start: 0.8474 (mt0) cc_final: 0.7905 (mp10) REVERT: C 287 LYS cc_start: 0.8136 (mttm) cc_final: 0.7674 (mptt) REVERT: C 311 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8173 (mm-30) REVERT: C 414 ARG cc_start: 0.8290 (mmt-90) cc_final: 0.8050 (mtm180) REVERT: C 417 GLU cc_start: 0.8628 (tt0) cc_final: 0.8347 (tt0) REVERT: C 501 TYR cc_start: 0.8740 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 1.3132 time to fit residues: 602.1746 Evaluate side-chains 250 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 196 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 230 ASN A 250 HIS A 364 HIS A 365 HIS A 389 ASN ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 ASN B 399 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127213 restraints weight = 19386.537| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.85 r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 17826 Z= 0.319 Angle : 0.704 23.326 24207 Z= 0.344 Chirality : 0.053 0.475 2643 Planarity : 0.005 0.064 3120 Dihedral : 8.078 128.775 2826 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.21 % Allowed : 10.49 % Favored : 86.30 % 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: -0.51 (0.17), residues: 2163 helix: 0.39 (0.25), residues: 390 sheet: 0.01 (0.21), residues: 576 loop : -0.73 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.010 0.002 HIS C 302 PHE 0.023 0.003 PHE A 342 TYR 0.016 0.002 TYR I 100A ARG 0.005 0.001 ARG B 415 Details of bonding type rmsd link_BETA2-3 : bond 0.01158 ( 3) link_BETA2-3 : angle 1.77673 ( 9) link_NAG-ASN : bond 0.00821 ( 15) link_NAG-ASN : angle 6.23022 ( 45) hydrogen bonds : bond 0.04651 ( 690) hydrogen bonds : angle 6.02907 ( 1935) SS BOND : bond 0.01132 ( 24) SS BOND : angle 0.86407 ( 48) covalent geometry : bond 0.00741 (17784) covalent geometry : angle 0.65006 (24105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.9038 (mtt) cc_final: 0.8824 (mtt) REVERT: A 287 LYS cc_start: 0.8053 (mttm) cc_final: 0.7496 (mptt) REVERT: A 311 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7904 (mm-30) REVERT: A 398 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7685 (mtp) REVERT: A 507 LEU cc_start: 0.7976 (tp) cc_final: 0.7679 (mp) REVERT: I 3 GLN cc_start: 0.8389 (mt0) cc_final: 0.7835 (tt0) REVERT: B 180 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: B 287 LYS cc_start: 0.8054 (mttm) cc_final: 0.7499 (mptt) REVERT: B 311 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7824 (mm-30) REVERT: B 414 ARG cc_start: 0.8493 (mmm160) cc_final: 0.7742 (mpp-170) REVERT: B 497 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7955 (t0) REVERT: B 500 GLN cc_start: 0.7883 (mt0) cc_final: 0.7518 (tt0) REVERT: J 3 GLN cc_start: 0.8406 (mt0) cc_final: 0.7851 (tt0) REVERT: C 122 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: C 193 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8269 (p0) REVERT: C 202 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7803 (tppt) REVERT: C 287 LYS cc_start: 0.8028 (mttm) cc_final: 0.7482 (mptt) REVERT: C 311 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7822 (mm-30) REVERT: C 398 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7730 (mtp) REVERT: C 414 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7617 (mtm180) REVERT: C 417 GLU cc_start: 0.8582 (tt0) cc_final: 0.8161 (tt0) REVERT: C 470 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6758 (tttt) REVERT: C 501 TYR cc_start: 0.8611 (m-80) cc_final: 0.8301 (m-80) outliers start: 60 outliers final: 33 residues processed: 278 average time/residue: 1.3891 time to fit residues: 429.2148 Evaluate side-chains 267 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 226 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 470 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 0.5980 chunk 6 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN B 97 ASN B 176 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.127124 restraints weight = 19107.333| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.89 r_work: 0.3423 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17826 Z= 0.138 Angle : 0.551 20.121 24207 Z= 0.263 Chirality : 0.046 0.384 2643 Planarity : 0.003 0.043 3120 Dihedral : 7.535 121.857 2826 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 13.00 % Favored : 84.38 % 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: -0.15 (0.18), residues: 2163 helix: 1.11 (0.26), residues: 396 sheet: 0.04 (0.22), residues: 558 loop : -0.53 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 431 HIS 0.004 0.001 HIS B 302 PHE 0.013 0.001 PHE A 342 TYR 0.009 0.001 TYR J 100A ARG 0.003 0.000 ARG A 506 Details of bonding type rmsd link_BETA2-3 : bond 0.00141 ( 3) link_BETA2-3 : angle 1.30688 ( 9) link_NAG-ASN : bond 0.00605 ( 15) link_NAG-ASN : angle 6.26145 ( 45) hydrogen bonds : bond 0.03495 ( 690) hydrogen bonds : angle 5.41171 ( 1935) SS BOND : bond 0.00217 ( 24) SS BOND : angle 0.95846 ( 48) covalent geometry : bond 0.00308 (17784) covalent geometry : angle 0.47884 (24105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 287 LYS cc_start: 0.8043 (mttm) cc_final: 0.7505 (mptt) REVERT: A 311 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7863 (mm-30) REVERT: A 482 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8181 (tptt) REVERT: A 507 LEU cc_start: 0.7971 (tp) cc_final: 0.7656 (mp) REVERT: M 69 THR cc_start: 0.8327 (p) cc_final: 0.7854 (t) REVERT: I 3 GLN cc_start: 0.8360 (mt0) cc_final: 0.7794 (tt0) REVERT: B 180 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: B 287 LYS cc_start: 0.8036 (mttm) cc_final: 0.7509 (mptt) REVERT: B 311 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7836 (mm-30) REVERT: B 356 MET cc_start: 0.8858 (ttp) cc_final: 0.8603 (ttm) REVERT: B 414 ARG cc_start: 0.8583 (mmm160) cc_final: 0.7940 (mtm180) REVERT: B 422 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8173 (mmtp) REVERT: B 444 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: B 500 GLN cc_start: 0.7871 (mt0) cc_final: 0.7508 (tt0) REVERT: N 53 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7248 (mp10) REVERT: C 76 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (mmp) REVERT: C 122 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: C 202 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7807 (tppt) REVERT: C 287 LYS cc_start: 0.8092 (mttm) cc_final: 0.7560 (mptt) REVERT: C 398 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: C 414 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.7643 (mtm180) REVERT: C 417 GLU cc_start: 0.8548 (tt0) cc_final: 0.8224 (tt0) REVERT: C 501 TYR cc_start: 0.8604 (m-80) cc_final: 0.8299 (m-80) outliers start: 49 outliers final: 24 residues processed: 278 average time/residue: 1.3324 time to fit residues: 412.6340 Evaluate side-chains 266 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 482 LYS Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 212 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 0.0770 chunk 210 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 ASN A 199 ASN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 ASN C 176 ASN C 250 HIS ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 500 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.128519 restraints weight = 19274.498| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.89 r_work: 0.3419 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17826 Z= 0.193 Angle : 0.574 19.432 24207 Z= 0.276 Chirality : 0.047 0.398 2643 Planarity : 0.003 0.038 3120 Dihedral : 7.497 122.038 2826 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.12 % Allowed : 13.38 % Favored : 82.50 % 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: -0.06 (0.18), residues: 2163 helix: 1.24 (0.26), residues: 396 sheet: 0.17 (0.22), residues: 561 loop : -0.55 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 431 HIS 0.006 0.001 HIS C 18 PHE 0.016 0.002 PHE A 342 TYR 0.011 0.001 TYR A 496 ARG 0.003 0.000 ARG B 415 Details of bonding type rmsd link_BETA2-3 : bond 0.00245 ( 3) link_BETA2-3 : angle 1.39285 ( 9) link_NAG-ASN : bond 0.00608 ( 15) link_NAG-ASN : angle 5.88866 ( 45) hydrogen bonds : bond 0.03553 ( 690) hydrogen bonds : angle 5.37453 ( 1935) SS BOND : bond 0.00610 ( 24) SS BOND : angle 1.31877 ( 48) covalent geometry : bond 0.00443 (17784) covalent geometry : angle 0.51168 (24105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 242 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 69 THR cc_start: 0.8411 (p) cc_final: 0.7953 (t) REVERT: A 122 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: A 180 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: A 287 LYS cc_start: 0.8062 (mttm) cc_final: 0.7510 (mptt) REVERT: A 311 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7768 (mm-30) REVERT: A 398 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: A 507 LEU cc_start: 0.7986 (tp) cc_final: 0.7675 (mp) REVERT: M 69 THR cc_start: 0.8364 (p) cc_final: 0.7861 (t) REVERT: B 122 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: B 180 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: B 287 LYS cc_start: 0.8092 (mttm) cc_final: 0.7521 (mptt) REVERT: B 311 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7759 (mm-30) REVERT: B 398 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7662 (mmt) REVERT: B 414 ARG cc_start: 0.8595 (mmm160) cc_final: 0.7836 (mtm180) REVERT: B 500 GLN cc_start: 0.7889 (mt0) cc_final: 0.7460 (tt0) REVERT: N 53 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7160 (mp10) REVERT: C 76 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8417 (mmp) REVERT: C 122 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: C 202 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7787 (tppt) REVERT: C 287 LYS cc_start: 0.8036 (mttm) cc_final: 0.7537 (mptt) REVERT: C 398 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7775 (mtp) REVERT: C 414 ARG cc_start: 0.7981 (mmt-90) cc_final: 0.7639 (mtm180) REVERT: C 417 GLU cc_start: 0.8562 (tt0) cc_final: 0.8205 (tt0) REVERT: C 470 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.6774 (tttt) REVERT: C 501 TYR cc_start: 0.8632 (m-80) cc_final: 0.8298 (m-80) REVERT: C 506 ARG cc_start: 0.7718 (ttp80) cc_final: 0.6976 (ttp80) outliers start: 77 outliers final: 43 residues processed: 281 average time/residue: 1.2750 time to fit residues: 399.9530 Evaluate side-chains 285 residues out of total 1869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain M residue 37 GLN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 421 LYS Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 122 GLU Chi-restraints excluded: chain C residue 193 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 415 ARG Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7822 > 50: distance: 78 - 125: 37.614 distance: 83 - 88: 33.919 distance: 88 - 116: 40.092 distance: 91 - 113: 40.331 distance: 93 - 95: 12.270 distance: 94 - 96: 34.540 distance: 95 - 97: 21.875 distance: 96 - 98: 57.716 distance: 97 - 98: 38.115 distance: 98 - 99: 31.839 distance: 100 - 101: 39.595 distance: 101 - 104: 38.949 distance: 102 - 103: 47.780 distance: 102 - 109: 39.751 distance: 104 - 105: 40.809 distance: 105 - 106: 23.013 distance: 106 - 107: 43.426 distance: 106 - 108: 46.240 distance: 110 - 111: 40.354 distance: 111 - 112: 38.588 distance: 113 - 114: 40.951 distance: 114 - 115: 5.607 distance: 114 - 117: 51.184 distance: 115 - 116: 35.180 distance: 115 - 118: 35.921 distance: 118 - 124: 68.673 distance: 122 - 123: 32.928 distance: 123 - 124: 57.036 distance: 125 - 126: 60.290 distance: 126 - 127: 25.848 distance: 126 - 129: 18.010 distance: 127 - 128: 35.608 distance: 127 - 131: 33.554 distance: 129 - 130: 28.127 distance: 131 - 132: 30.297 distance: 132 - 133: 33.849 distance: 132 - 135: 10.100 distance: 133 - 134: 27.572 distance: 133 - 142: 48.012 distance: 135 - 136: 14.936 distance: 136 - 137: 14.303 distance: 136 - 138: 22.932 distance: 137 - 139: 26.428 distance: 138 - 140: 17.864 distance: 139 - 141: 20.005 distance: 140 - 141: 15.153 distance: 142 - 143: 42.186 distance: 143 - 144: 30.273 distance: 143 - 146: 29.241 distance: 144 - 153: 20.099 distance: 146 - 147: 28.545 distance: 147 - 148: 36.924 distance: 147 - 149: 10.785 distance: 148 - 150: 32.156 distance: 150 - 152: 30.234 distance: 151 - 152: 11.319 distance: 153 - 154: 44.400 distance: 154 - 157: 39.824 distance: 155 - 156: 40.891 distance: 157 - 158: 3.142 distance: 159 - 160: 13.277 distance: 160 - 161: 16.054 distance: 161 - 162: 48.845 distance: 161 - 163: 12.380 distance: 164 - 165: 26.879 distance: 165 - 166: 26.718 distance: 165 - 168: 19.079 distance: 166 - 167: 5.970 distance: 166 - 172: 30.821 distance: 168 - 169: 18.780 distance: 169 - 171: 41.568