Starting phenix.real_space_refine on Wed Feb 4 17:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.map" model { file = "/net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w44_65618/02_2026/9w44_65618.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.127 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 54 5.16 5 C 7269 2.51 5 N 1932 2.21 5 O 2406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11661 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.91, per 1000 atoms: 0.25 Number of scatterers: 11661 At special positions: 0 Unit cell: (93.5, 91.8, 141.1, 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 54 16.00 O 2406 8.00 N 1932 7.00 C 7269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 495 " 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 BETA1-2 " BMA E 5 " - " BMA E 6 " " BMA H 5 " - " BMA H 6 " " BMA K 5 " - " BMA K 6 " BETA1-3 " BMA E 4 " - " BMA E 5 " " BMA H 4 " - " BMA H 5 " " BMA K 4 " - " BMA K 5 " BETA1-4 " NAG D 1 " - " GAL D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " GAL G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " GAL J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " BETA1-6 " BMA E 3 " - " BMA E 4 " " BMA H 3 " - " BMA H 4 " " BMA K 3 " - " BMA K 4 " BETA2-3 " GAL D 2 " - " SIA D 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL G 2 " - " SIA G 3 " " GAL J 2 " - " SIA J 3 " NAG-ASN " NAG A 601 " - " ASN A 35 " " NAG A 602 " - " ASN A 105 " " NAG A 603 " - " ASN A 203 " " NAG A 604 " - " ASN A 486 " " NAG B 601 " - " ASN B 35 " " NAG B 602 " - " ASN B 105 " " NAG B 603 " - " ASN B 203 " " NAG B 604 " - " ASN B 486 " " NAG C 601 " - " ASN C 35 " " NAG C 602 " - " ASN C 105 " " NAG C 603 " - " ASN C 203 " " NAG C 604 " - " ASN C 486 " " NAG E 1 " - " ASN A 124 " " NAG F 1 " - " ASN A 307 " " NAG H 1 " - " ASN B 124 " " NAG I 1 " - " ASN B 307 " " NAG K 1 " - " ASN C 124 " " NAG L 1 " - " ASN C 307 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 554.0 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 33 sheets defined 32.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.688A pdb=" N HIS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.191A pdb=" N ILE A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.598A pdb=" N GLY A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 384 through 415 removed outlier: 4.073A pdb=" N THR A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 433 through 474 removed outlier: 3.612A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.519A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.799A pdb=" N ILE A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.519A pdb=" N HIS B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.117A pdb=" N ILE B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.559A pdb=" N GLY B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 154' Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 384 through 415 removed outlier: 4.074A pdb=" N THR B 388 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 433 through 474 removed outlier: 3.619A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 474 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.589A pdb=" N ARG B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.807A pdb=" N ILE B 510 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.689A pdb=" N HIS C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 116 through 127 removed outlier: 4.121A pdb=" N ILE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.629A pdb=" N GLY C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 384 through 415 removed outlier: 4.058A pdb=" N THR C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 Processing helix chain 'C' and resid 433 through 474 removed outlier: 3.629A pdb=" N GLU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 502 removed outlier: 3.536A pdb=" N SER C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.808A pdb=" N ILE C 510 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.462A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.462A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 486 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 478 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.036A pdb=" N ILE A 312 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 62 removed outlier: 5.784A pdb=" N ILE A 61 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 68 through 70 Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 115 removed outlier: 6.741A pdb=" N ASN A 112 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU A 251 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR A 114 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N SER A 253 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR A 184 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR A 275 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 112 through 115 removed outlier: 6.741A pdb=" N ASN A 112 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU A 251 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR A 114 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N SER A 253 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.988A pdb=" N ARG A 211 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.427A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.427A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 486 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 478 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.020A pdb=" N ILE B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 62 removed outlier: 5.761A pdb=" N ILE B 61 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 70 Processing sheet with id=AC1, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.750A pdb=" N ASN B 112 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU B 251 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 114 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER B 253 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR B 184 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR B 275 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 112 through 115 removed outlier: 6.750A pdb=" N ASN B 112 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU B 251 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 114 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER B 253 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.985A pdb=" N ARG B 211 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AC5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.442A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.442A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 486 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 478 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 36 through 39 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC9, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.044A pdb=" N ILE C 312 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.741A pdb=" N ILE C 61 " --> pdb=" O ASP C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AD3, first strand: chain 'C' and resid 112 through 115 removed outlier: 6.765A pdb=" N ASN C 112 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU C 251 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 114 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N SER C 253 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TYR C 184 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 275 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 112 through 115 removed outlier: 6.765A pdb=" N ASN C 112 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU C 251 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 114 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N SER C 253 " --> pdb=" O TYR C 114 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 171 through 176 removed outlier: 3.978A pdb=" N ARG C 211 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 303 through 304 498 hydrogen bonds defined for protein. 1377 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: 1.95 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3732 1.34 - 1.46: 2875 1.46 - 1.58: 5192 1.58 - 1.70: 6 1.70 - 1.82: 72 Bond restraints: 11877 Sorted by residual: bond pdb=" C1 BMA K 5 " pdb=" C2 BMA K 5 " ideal model delta sigma weight residual 1.519 1.585 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C1 BMA E 5 " pdb=" C2 BMA E 5 " ideal model delta sigma weight residual 1.519 1.584 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 BMA H 5 " pdb=" C2 BMA H 5 " ideal model delta sigma weight residual 1.519 1.584 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C2 BMA H 5 " pdb=" O2 BMA H 5 " ideal model delta sigma weight residual 1.402 1.462 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C2 BMA E 5 " pdb=" O2 BMA E 5 " ideal model delta sigma weight residual 1.402 1.462 -0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 11872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15627 1.58 - 3.17: 312 3.17 - 4.75: 97 4.75 - 6.34: 26 6.34 - 7.92: 21 Bond angle restraints: 16083 Sorted by residual: angle pdb=" CA LYS C 379 " pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB LYS C 379 " pdb=" CG LYS C 379 " pdb=" CD LYS C 379 " ideal model delta sigma weight residual 111.30 119.22 -7.92 2.30e+00 1.89e-01 1.19e+01 angle pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " pdb=" CD LYS A 379 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CA LYS A 379 " pdb=" CB LYS A 379 " pdb=" CG LYS A 379 " ideal model delta sigma weight residual 114.10 120.73 -6.63 2.00e+00 2.50e-01 1.10e+01 angle pdb=" CB LYS B 379 " pdb=" CG LYS B 379 " pdb=" CD LYS B 379 " ideal model delta sigma weight residual 111.30 118.35 -7.05 2.30e+00 1.89e-01 9.40e+00 ... (remaining 16078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 6779 22.46 - 44.92: 617 44.92 - 67.37: 152 67.37 - 89.83: 89 89.83 - 112.29: 43 Dihedral angle restraints: 7680 sinusoidal: 3600 harmonic: 4080 Sorted by residual: dihedral pdb=" O4 BMA E 5 " pdb=" C4 BMA E 5 " pdb=" C5 BMA E 5 " pdb=" O5 BMA E 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.42 112.29 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA K 5 " pdb=" C4 BMA K 5 " pdb=" C5 BMA K 5 " pdb=" O5 BMA K 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.46 112.25 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA H 5 " pdb=" C4 BMA H 5 " pdb=" C5 BMA H 5 " pdb=" O5 BMA H 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.47 112.24 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1680 0.067 - 0.134: 225 0.134 - 0.201: 10 0.201 - 0.269: 14 0.269 - 0.336: 3 Chirality restraints: 1932 Sorted by residual: chirality pdb=" C2 SIA G 3 " pdb=" O3 GAL G 2 " pdb=" C1 SIA G 3 " pdb=" O6 SIA G 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.60 0.10 2.00e-02 2.50e+03 2.69e+01 chirality pdb=" C2 SIA D 3 " pdb=" O3 GAL D 2 " pdb=" C1 SIA D 3 " pdb=" O6 SIA D 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.54 0.04 2.00e-02 2.50e+03 3.63e+00 chirality pdb=" C2 SIA J 3 " pdb=" O3 GAL J 2 " pdb=" C1 SIA J 3 " pdb=" O6 SIA J 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.54 0.04 2.00e-02 2.50e+03 3.55e+00 ... (remaining 1929 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 324 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO B 325 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 324 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 325 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 324 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO A 325 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " -0.018 5.00e-02 4.00e+02 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2293 2.77 - 3.30: 10154 3.30 - 3.84: 18767 3.84 - 4.37: 21975 4.37 - 4.90: 38543 Nonbonded interactions: 91732 Sorted by model distance: nonbonded pdb=" OD1 ASP B 209 " pdb=" OG SER B 221 " model vdw 2.241 3.040 nonbonded pdb=" OD1 ASP C 209 " pdb=" OG SER C 221 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP A 209 " pdb=" OG SER A 221 " model vdw 2.257 3.040 nonbonded pdb=" O SER A 493 " pdb=" ND2 ASN A 497 " model vdw 2.320 3.120 nonbonded pdb=" N ASP C 297 " pdb=" OD1 ASP C 297 " model vdw 2.345 3.120 ... (remaining 91727 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.260 Find NCS groups from input model: 0.200 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.004 0.066 11934 Z= 0.208 Angle : 0.692 12.841 16239 Z= 0.303 Chirality : 0.050 0.336 1932 Planarity : 0.003 0.034 2010 Dihedral : 21.211 112.290 5037 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.89 % Allowed : 18.78 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.22), residues: 1425 helix: 3.56 (0.26), residues: 384 sheet: -0.48 (0.30), residues: 252 loop : -0.81 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 501 TYR 0.017 0.001 TYR C 504 PHE 0.013 0.001 PHE A 282 TRP 0.010 0.001 TRP B 208 HIS 0.002 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00439 (11877) covalent geometry : angle 0.66097 (16083) SS BOND : bond 0.00069 ( 15) SS BOND : angle 0.46012 ( 30) hydrogen bonds : bond 0.15127 ( 468) hydrogen bonds : angle 5.22388 ( 1377) link_BETA1-2 : bond 0.00561 ( 3) link_BETA1-2 : angle 4.32063 ( 9) link_BETA1-3 : bond 0.00529 ( 3) link_BETA1-3 : angle 3.66019 ( 9) link_BETA1-4 : bond 0.00320 ( 12) link_BETA1-4 : angle 1.73468 ( 36) link_BETA1-6 : bond 0.01546 ( 3) link_BETA1-6 : angle 0.52554 ( 9) link_BETA2-3 : bond 0.00228 ( 3) link_BETA2-3 : angle 4.59147 ( 9) link_NAG-ASN : bond 0.00298 ( 18) link_NAG-ASN : angle 1.62900 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8211 (ptt) cc_final: 0.7971 (ptt) REVERT: A 93 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7244 (mm) REVERT: A 132 GLU cc_start: 0.7107 (tt0) cc_final: 0.6769 (tm-30) REVERT: A 155 THR cc_start: 0.7423 (OUTLIER) cc_final: 0.6929 (p) REVERT: A 157 LYS cc_start: 0.7537 (mptt) cc_final: 0.7016 (mtmt) REVERT: A 217 GLU cc_start: 0.6411 (mm-30) cc_final: 0.5670 (tm-30) REVERT: A 293 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6512 (p0) REVERT: A 434 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5134 (pp) REVERT: A 456 GLU cc_start: 0.5938 (tp30) cc_final: 0.5470 (tm-30) REVERT: A 464 LYS cc_start: 0.5604 (ttmt) cc_final: 0.5394 (mtmt) REVERT: A 466 LYS cc_start: 0.5679 (tttp) cc_final: 0.5446 (ttpt) REVERT: A 468 GLU cc_start: 0.5697 (tt0) cc_final: 0.5493 (tt0) REVERT: B 93 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7274 (mm) REVERT: B 111 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.5391 (p90) REVERT: B 132 GLU cc_start: 0.7305 (tt0) cc_final: 0.7096 (tm-30) REVERT: B 155 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6669 (p) REVERT: B 157 LYS cc_start: 0.7631 (mptt) cc_final: 0.7072 (mtmt) REVERT: B 216 SER cc_start: 0.7352 (t) cc_final: 0.6981 (m) REVERT: B 217 GLU cc_start: 0.6425 (mm-30) cc_final: 0.5846 (tm-30) REVERT: B 370 TYR cc_start: 0.6817 (m-80) cc_final: 0.6557 (m-80) REVERT: B 456 GLU cc_start: 0.5901 (tt0) cc_final: 0.5335 (tm-30) REVERT: B 463 SER cc_start: 0.6021 (t) cc_final: 0.5736 (m) REVERT: B 466 LYS cc_start: 0.5921 (tmtp) cc_final: 0.5579 (ttpt) REVERT: B 468 GLU cc_start: 0.5685 (tt0) cc_final: 0.5474 (tt0) REVERT: C 59 GLN cc_start: 0.7819 (mm110) cc_final: 0.7591 (mm110) REVERT: C 93 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7264 (mm) REVERT: C 111 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.5441 (p90) REVERT: C 132 GLU cc_start: 0.7078 (tt0) cc_final: 0.6768 (tm-30) REVERT: C 157 LYS cc_start: 0.7823 (mptt) cc_final: 0.7112 (mtmt) REVERT: C 217 GLU cc_start: 0.6371 (mm-30) cc_final: 0.5968 (tm-30) REVERT: C 293 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6649 (p0) REVERT: C 456 GLU cc_start: 0.5977 (tt0) cc_final: 0.5442 (tm-30) REVERT: C 463 SER cc_start: 0.5738 (t) cc_final: 0.5521 (m) REVERT: C 466 LYS cc_start: 0.5751 (tttp) cc_final: 0.5427 (ttmt) outliers start: 47 outliers final: 24 residues processed: 133 average time/residue: 0.4408 time to fit residues: 64.7981 Evaluate side-chains 108 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 514 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103473 restraints weight = 11267.298| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.94 r_work: 0.3059 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11934 Z= 0.135 Angle : 0.639 9.133 16239 Z= 0.306 Chirality : 0.049 0.415 1932 Planarity : 0.003 0.035 2010 Dihedral : 16.525 82.486 2544 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.06 % Allowed : 18.44 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1425 helix: 3.29 (0.25), residues: 396 sheet: 0.29 (0.37), residues: 189 loop : -0.84 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 501 TYR 0.012 0.002 TYR C 184 PHE 0.018 0.002 PHE B 111 TRP 0.011 0.001 TRP B 208 HIS 0.002 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00286 (11877) covalent geometry : angle 0.59330 (16083) SS BOND : bond 0.00134 ( 15) SS BOND : angle 0.62729 ( 30) hydrogen bonds : bond 0.05708 ( 468) hydrogen bonds : angle 4.33217 ( 1377) link_BETA1-2 : bond 0.00899 ( 3) link_BETA1-2 : angle 5.65284 ( 9) link_BETA1-3 : bond 0.00570 ( 3) link_BETA1-3 : angle 5.36736 ( 9) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 2.19053 ( 36) link_BETA1-6 : bond 0.01166 ( 3) link_BETA1-6 : angle 1.52164 ( 9) link_BETA2-3 : bond 0.00856 ( 3) link_BETA2-3 : angle 1.97262 ( 9) link_NAG-ASN : bond 0.00353 ( 18) link_NAG-ASN : angle 1.85621 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.412 Fit side-chains REVERT: A 155 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8158 (p) REVERT: A 217 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7817 (tm-30) REVERT: A 422 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: A 456 GLU cc_start: 0.8326 (tp30) cc_final: 0.8086 (tm-30) REVERT: A 464 LYS cc_start: 0.7459 (ttmt) cc_final: 0.7211 (mtmt) REVERT: A 466 LYS cc_start: 0.7234 (tttp) cc_final: 0.6874 (ttpt) REVERT: A 468 GLU cc_start: 0.6876 (tt0) cc_final: 0.6536 (tt0) REVERT: B 111 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.6708 (p90) REVERT: B 155 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7987 (p) REVERT: B 157 LYS cc_start: 0.8586 (mptt) cc_final: 0.8327 (mtmt) REVERT: B 370 TYR cc_start: 0.8283 (m-80) cc_final: 0.8028 (m-80) REVERT: B 422 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: B 434 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7237 (pp) REVERT: B 456 GLU cc_start: 0.8236 (tt0) cc_final: 0.8021 (tm-30) REVERT: B 463 SER cc_start: 0.8077 (t) cc_final: 0.7864 (m) REVERT: B 466 LYS cc_start: 0.7454 (tmtp) cc_final: 0.6978 (ttmt) REVERT: C 111 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.6662 (p90) REVERT: C 157 LYS cc_start: 0.8630 (mptt) cc_final: 0.8383 (mtmt) REVERT: C 434 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7197 (pp) REVERT: C 456 GLU cc_start: 0.8169 (tt0) cc_final: 0.7936 (tm-30) REVERT: C 466 LYS cc_start: 0.7300 (tttp) cc_final: 0.6843 (ttmt) outliers start: 37 outliers final: 18 residues processed: 103 average time/residue: 0.5094 time to fit residues: 57.2497 Evaluate side-chains 99 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 135 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.139681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.091325 restraints weight = 11447.101| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.82 r_work: 0.2884 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11934 Z= 0.260 Angle : 0.833 10.573 16239 Z= 0.406 Chirality : 0.059 0.442 1932 Planarity : 0.005 0.049 2010 Dihedral : 16.753 83.651 2515 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.80 % Allowed : 16.79 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.21), residues: 1425 helix: 2.53 (0.25), residues: 402 sheet: 0.03 (0.34), residues: 207 loop : -1.03 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 501 TYR 0.019 0.004 TYR C 185 PHE 0.032 0.004 PHE B 111 TRP 0.011 0.002 TRP A 208 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00614 (11877) covalent geometry : angle 0.78429 (16083) SS BOND : bond 0.00357 ( 15) SS BOND : angle 1.18257 ( 30) hydrogen bonds : bond 0.08253 ( 468) hydrogen bonds : angle 4.75797 ( 1377) link_BETA1-2 : bond 0.00369 ( 3) link_BETA1-2 : angle 5.43052 ( 9) link_BETA1-3 : bond 0.00462 ( 3) link_BETA1-3 : angle 5.05218 ( 9) link_BETA1-4 : bond 0.00561 ( 12) link_BETA1-4 : angle 3.19031 ( 36) link_BETA1-6 : bond 0.00533 ( 3) link_BETA1-6 : angle 2.90377 ( 9) link_BETA2-3 : bond 0.00610 ( 3) link_BETA2-3 : angle 2.53735 ( 9) link_NAG-ASN : bond 0.00393 ( 18) link_NAG-ASN : angle 2.47790 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 76 time to evaluate : 0.420 Fit side-chains REVERT: A 155 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 217 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7648 (tm-30) REVERT: A 293 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7121 (p0) REVERT: A 422 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: A 434 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7320 (pp) REVERT: A 456 GLU cc_start: 0.8393 (tp30) cc_final: 0.8146 (tm-30) REVERT: A 464 LYS cc_start: 0.7568 (ttmt) cc_final: 0.7322 (mtmt) REVERT: A 466 LYS cc_start: 0.7302 (tttp) cc_final: 0.6946 (ttpt) REVERT: A 468 GLU cc_start: 0.6922 (tt0) cc_final: 0.6577 (tt0) REVERT: B 85 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7490 (mt-10) REVERT: B 155 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 157 LYS cc_start: 0.8651 (mptt) cc_final: 0.8322 (mtmt) REVERT: B 293 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7142 (p0) REVERT: B 422 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: B 434 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7360 (pp) REVERT: B 456 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8112 (tm-30) REVERT: B 466 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6999 (ttpt) REVERT: B 468 GLU cc_start: 0.7039 (tt0) cc_final: 0.6716 (tt0) REVERT: C 155 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7951 (p) REVERT: C 157 LYS cc_start: 0.8722 (mptt) cc_final: 0.8391 (mmtp) REVERT: C 293 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7201 (p0) REVERT: C 434 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7251 (pp) REVERT: C 456 GLU cc_start: 0.8182 (tt0) cc_final: 0.7912 (tm-30) REVERT: C 463 SER cc_start: 0.8035 (t) cc_final: 0.7764 (m) REVERT: C 464 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7254 (ttmt) REVERT: C 466 LYS cc_start: 0.7369 (tttp) cc_final: 0.6954 (ttmt) outliers start: 58 outliers final: 23 residues processed: 114 average time/residue: 0.4729 time to fit residues: 58.9917 Evaluate side-chains 114 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 77 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN C 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095203 restraints weight = 11403.997| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.83 r_work: 0.2940 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11934 Z= 0.128 Angle : 0.672 10.042 16239 Z= 0.313 Chirality : 0.052 0.422 1932 Planarity : 0.003 0.035 2010 Dihedral : 14.106 78.216 2515 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.64 % Allowed : 18.11 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1425 helix: 3.06 (0.26), residues: 393 sheet: 0.22 (0.34), residues: 204 loop : -0.87 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 501 TYR 0.012 0.002 TYR C 184 PHE 0.019 0.002 PHE B 111 TRP 0.009 0.001 TRP B 208 HIS 0.002 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00272 (11877) covalent geometry : angle 0.61325 (16083) SS BOND : bond 0.00127 ( 15) SS BOND : angle 0.59873 ( 30) hydrogen bonds : bond 0.05856 ( 468) hydrogen bonds : angle 4.40484 ( 1377) link_BETA1-2 : bond 0.00811 ( 3) link_BETA1-2 : angle 6.53779 ( 9) link_BETA1-3 : bond 0.00342 ( 3) link_BETA1-3 : angle 5.82611 ( 9) link_BETA1-4 : bond 0.00590 ( 12) link_BETA1-4 : angle 2.60525 ( 36) link_BETA1-6 : bond 0.00750 ( 3) link_BETA1-6 : angle 2.10338 ( 9) link_BETA2-3 : bond 0.00978 ( 3) link_BETA2-3 : angle 2.10853 ( 9) link_NAG-ASN : bond 0.00249 ( 18) link_NAG-ASN : angle 2.15693 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 75 time to evaluate : 0.348 Fit side-chains REVERT: A 155 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 217 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7646 (tm-30) REVERT: A 401 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 422 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 456 GLU cc_start: 0.8307 (tp30) cc_final: 0.8083 (tm-30) REVERT: A 463 SER cc_start: 0.7849 (t) cc_final: 0.7499 (m) REVERT: A 464 LYS cc_start: 0.7430 (ttmt) cc_final: 0.7180 (mtmt) REVERT: A 466 LYS cc_start: 0.7071 (tttp) cc_final: 0.6713 (ttpt) REVERT: A 468 GLU cc_start: 0.6753 (tt0) cc_final: 0.6455 (tt0) REVERT: B 85 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7429 (mt-10) REVERT: B 157 LYS cc_start: 0.8622 (mptt) cc_final: 0.8292 (mtmt) REVERT: B 293 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 422 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 434 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7217 (pp) REVERT: B 456 GLU cc_start: 0.8253 (tt0) cc_final: 0.8005 (tm-30) REVERT: B 466 LYS cc_start: 0.7253 (tmtp) cc_final: 0.6808 (ttmt) REVERT: B 468 GLU cc_start: 0.6979 (tt0) cc_final: 0.6666 (tt0) REVERT: C 111 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.7015 (p90) REVERT: C 157 LYS cc_start: 0.8705 (mptt) cc_final: 0.8366 (mmtp) REVERT: C 293 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7085 (p0) REVERT: C 434 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7143 (pp) REVERT: C 456 GLU cc_start: 0.8234 (tt0) cc_final: 0.7938 (tm-30) REVERT: C 463 SER cc_start: 0.7889 (t) cc_final: 0.7634 (m) REVERT: C 466 LYS cc_start: 0.7128 (tttp) cc_final: 0.6756 (ttmt) outliers start: 44 outliers final: 28 residues processed: 108 average time/residue: 0.5460 time to fit residues: 64.2276 Evaluate side-chains 107 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.093237 restraints weight = 11405.969| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.81 r_work: 0.2914 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11934 Z= 0.178 Angle : 0.740 10.300 16239 Z= 0.351 Chirality : 0.055 0.410 1932 Planarity : 0.004 0.036 2010 Dihedral : 14.111 80.969 2515 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.30 % Allowed : 17.78 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.21), residues: 1425 helix: 2.96 (0.25), residues: 393 sheet: 0.23 (0.34), residues: 204 loop : -0.90 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 501 TYR 0.015 0.002 TYR C 184 PHE 0.024 0.003 PHE B 111 TRP 0.010 0.002 TRP B 208 HIS 0.003 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00408 (11877) covalent geometry : angle 0.68385 (16083) SS BOND : bond 0.00230 ( 15) SS BOND : angle 0.83075 ( 30) hydrogen bonds : bond 0.06827 ( 468) hydrogen bonds : angle 4.53818 ( 1377) link_BETA1-2 : bond 0.00606 ( 3) link_BETA1-2 : angle 6.40444 ( 9) link_BETA1-3 : bond 0.00717 ( 3) link_BETA1-3 : angle 5.38738 ( 9) link_BETA1-4 : bond 0.00538 ( 12) link_BETA1-4 : angle 2.93291 ( 36) link_BETA1-6 : bond 0.00648 ( 3) link_BETA1-6 : angle 2.54801 ( 9) link_BETA2-3 : bond 0.00756 ( 3) link_BETA2-3 : angle 2.23110 ( 9) link_NAG-ASN : bond 0.00325 ( 18) link_NAG-ASN : angle 2.33926 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 71 time to evaluate : 0.419 Fit side-chains REVERT: A 155 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 217 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7658 (tm-30) REVERT: A 293 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7182 (p0) REVERT: A 422 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 434 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7181 (pp) REVERT: A 456 GLU cc_start: 0.8357 (tp30) cc_final: 0.8122 (tm-30) REVERT: A 463 SER cc_start: 0.7932 (t) cc_final: 0.7552 (m) REVERT: A 464 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7284 (mtmt) REVERT: A 466 LYS cc_start: 0.7184 (tttp) cc_final: 0.6822 (ttpt) REVERT: A 468 GLU cc_start: 0.6814 (tt0) cc_final: 0.6466 (tt0) REVERT: B 85 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7482 (mt-10) REVERT: B 293 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7080 (p0) REVERT: B 422 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: B 434 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7303 (pp) REVERT: B 456 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: B 466 LYS cc_start: 0.7341 (OUTLIER) cc_final: 0.6888 (ttmt) REVERT: C 155 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8001 (p) REVERT: C 157 LYS cc_start: 0.8680 (mptt) cc_final: 0.8305 (mmtp) REVERT: C 293 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7131 (p0) REVERT: C 434 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7210 (pp) REVERT: C 456 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: C 463 SER cc_start: 0.7957 (t) cc_final: 0.7703 (m) REVERT: C 464 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7055 (ttmt) REVERT: C 466 LYS cc_start: 0.7242 (tttp) cc_final: 0.6873 (ttmt) outliers start: 52 outliers final: 29 residues processed: 107 average time/residue: 0.5214 time to fit residues: 60.9670 Evaluate side-chains 115 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 71 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 111 PHE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 23 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.091663 restraints weight = 11440.167| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.81 r_work: 0.2889 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11934 Z= 0.234 Angle : 0.824 10.607 16239 Z= 0.394 Chirality : 0.058 0.405 1932 Planarity : 0.005 0.038 2010 Dihedral : 14.776 82.306 2515 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.80 % Allowed : 16.96 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.21), residues: 1425 helix: 2.66 (0.25), residues: 393 sheet: 0.04 (0.31), residues: 222 loop : -0.95 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 239 TYR 0.018 0.003 TYR C 185 PHE 0.025 0.003 PHE C 111 TRP 0.011 0.002 TRP A 208 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00551 (11877) covalent geometry : angle 0.76985 (16083) SS BOND : bond 0.00322 ( 15) SS BOND : angle 1.11567 ( 30) hydrogen bonds : bond 0.07810 ( 468) hydrogen bonds : angle 4.74164 ( 1377) link_BETA1-2 : bond 0.00357 ( 3) link_BETA1-2 : angle 6.20498 ( 9) link_BETA1-3 : bond 0.01026 ( 3) link_BETA1-3 : angle 5.22798 ( 9) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 3.22934 ( 36) link_BETA1-6 : bond 0.00479 ( 3) link_BETA1-6 : angle 3.12573 ( 9) link_BETA2-3 : bond 0.00699 ( 3) link_BETA2-3 : angle 2.40307 ( 9) link_NAG-ASN : bond 0.00362 ( 18) link_NAG-ASN : angle 2.50814 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 81 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7550 (mt-10) REVERT: A 155 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 175 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9056 (tptm) REVERT: A 217 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7678 (tm-30) REVERT: A 293 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7241 (p0) REVERT: A 422 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: A 434 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7388 (pp) REVERT: A 456 GLU cc_start: 0.8387 (tp30) cc_final: 0.8161 (tm-30) REVERT: A 464 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7338 (mtmt) REVERT: A 466 LYS cc_start: 0.7212 (tttp) cc_final: 0.6851 (ttpt) REVERT: A 468 GLU cc_start: 0.6899 (tt0) cc_final: 0.6543 (tt0) REVERT: B 85 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 155 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (p) REVERT: B 293 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7165 (p0) REVERT: B 422 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: B 434 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7349 (pp) REVERT: B 456 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 466 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.6893 (ttmt) REVERT: C 85 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7551 (mt-10) REVERT: C 155 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8167 (p) REVERT: C 157 LYS cc_start: 0.8679 (mptt) cc_final: 0.8345 (mmtp) REVERT: C 293 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7168 (p0) REVERT: C 434 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7288 (pp) REVERT: C 456 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: C 463 SER cc_start: 0.8002 (t) cc_final: 0.7752 (m) REVERT: C 464 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7153 (ttmt) REVERT: C 466 LYS cc_start: 0.7285 (tttp) cc_final: 0.6907 (ttmt) outliers start: 58 outliers final: 28 residues processed: 119 average time/residue: 0.4827 time to fit residues: 62.6529 Evaluate side-chains 125 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 80 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 128 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.092145 restraints weight = 11385.502| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.79 r_work: 0.2894 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 11934 Z= 0.214 Angle : 0.796 10.544 16239 Z= 0.379 Chirality : 0.057 0.411 1932 Planarity : 0.004 0.037 2010 Dihedral : 14.336 80.866 2511 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.38 % Allowed : 17.29 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.21), residues: 1425 helix: 2.62 (0.25), residues: 393 sheet: 0.38 (0.33), residues: 201 loop : -0.95 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 471 TYR 0.019 0.003 TYR C 185 PHE 0.023 0.003 PHE B 111 TRP 0.011 0.002 TRP A 208 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00500 (11877) covalent geometry : angle 0.73947 (16083) SS BOND : bond 0.00286 ( 15) SS BOND : angle 1.00969 ( 30) hydrogen bonds : bond 0.07437 ( 468) hydrogen bonds : angle 4.68114 ( 1377) link_BETA1-2 : bond 0.00408 ( 3) link_BETA1-2 : angle 6.42012 ( 9) link_BETA1-3 : bond 0.01050 ( 3) link_BETA1-3 : angle 5.57996 ( 9) link_BETA1-4 : bond 0.00562 ( 12) link_BETA1-4 : angle 3.15360 ( 36) link_BETA1-6 : bond 0.00421 ( 3) link_BETA1-6 : angle 3.02474 ( 9) link_BETA2-3 : bond 0.00811 ( 3) link_BETA2-3 : angle 2.39584 ( 9) link_NAG-ASN : bond 0.00334 ( 18) link_NAG-ASN : angle 2.47891 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 79 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7493 (mt-10) REVERT: A 155 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8200 (p) REVERT: A 217 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7664 (tm-30) REVERT: A 293 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7197 (p0) REVERT: A 422 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: A 434 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7323 (pp) REVERT: A 456 GLU cc_start: 0.8375 (tp30) cc_final: 0.8158 (tm-30) REVERT: A 464 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7270 (mtmt) REVERT: A 466 LYS cc_start: 0.7167 (tttp) cc_final: 0.6804 (ttpt) REVERT: A 468 GLU cc_start: 0.6783 (tt0) cc_final: 0.6438 (tt0) REVERT: B 85 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7482 (mt-10) REVERT: B 155 THR cc_start: 0.8569 (m) cc_final: 0.8277 (p) REVERT: B 293 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7251 (p0) REVERT: B 422 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: B 434 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7317 (pp) REVERT: B 456 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: B 466 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6848 (ttmt) REVERT: C 85 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7541 (mt-10) REVERT: C 155 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 157 LYS cc_start: 0.8657 (mptt) cc_final: 0.8348 (mmtp) REVERT: C 293 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7191 (p0) REVERT: C 434 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7266 (pp) REVERT: C 463 SER cc_start: 0.7950 (t) cc_final: 0.7704 (m) REVERT: C 464 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7055 (ttmt) REVERT: C 466 LYS cc_start: 0.7239 (tttp) cc_final: 0.6849 (ttmt) outliers start: 53 outliers final: 27 residues processed: 115 average time/residue: 0.4887 time to fit residues: 61.3032 Evaluate side-chains 120 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 293 ASP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 466 LYS Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 293 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 464 LYS Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096405 restraints weight = 11450.125| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.82 r_work: 0.2959 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11934 Z= 0.115 Angle : 0.654 10.406 16239 Z= 0.300 Chirality : 0.051 0.452 1932 Planarity : 0.003 0.035 2010 Dihedral : 11.916 77.619 2510 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.98 % Allowed : 18.69 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.22), residues: 1425 helix: 3.11 (0.26), residues: 393 sheet: -0.42 (0.29), residues: 258 loop : -0.85 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 202 TYR 0.012 0.001 TYR B 370 PHE 0.014 0.002 PHE B 111 TRP 0.010 0.001 TRP A 208 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00239 (11877) covalent geometry : angle 0.59239 (16083) SS BOND : bond 0.00095 ( 15) SS BOND : angle 0.46346 ( 30) hydrogen bonds : bond 0.05410 ( 468) hydrogen bonds : angle 4.34040 ( 1377) link_BETA1-2 : bond 0.00706 ( 3) link_BETA1-2 : angle 7.16658 ( 9) link_BETA1-3 : bond 0.00466 ( 3) link_BETA1-3 : angle 5.75134 ( 9) link_BETA1-4 : bond 0.00574 ( 12) link_BETA1-4 : angle 2.52076 ( 36) link_BETA1-6 : bond 0.00602 ( 3) link_BETA1-6 : angle 1.98357 ( 9) link_BETA2-3 : bond 0.01019 ( 3) link_BETA2-3 : angle 2.11317 ( 9) link_NAG-ASN : bond 0.00266 ( 18) link_NAG-ASN : angle 2.06905 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.445 Fit side-chains REVERT: A 85 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7392 (mt-10) REVERT: A 155 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 175 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9038 (tptm) REVERT: A 217 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7661 (tm-30) REVERT: A 422 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8364 (tt0) REVERT: A 434 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 463 SER cc_start: 0.7823 (t) cc_final: 0.7468 (m) REVERT: A 464 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7133 (mtmt) REVERT: A 466 LYS cc_start: 0.7041 (tttp) cc_final: 0.6674 (ttpt) REVERT: B 85 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7445 (mt-10) REVERT: B 155 THR cc_start: 0.8508 (m) cc_final: 0.8207 (p) REVERT: B 422 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8440 (tt0) REVERT: B 434 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7164 (pp) REVERT: B 456 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: B 466 LYS cc_start: 0.7253 (tmtp) cc_final: 0.6807 (ttmt) REVERT: C 58 MET cc_start: 0.9025 (mtp) cc_final: 0.8820 (mtp) REVERT: C 85 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7425 (mt-10) REVERT: C 155 THR cc_start: 0.8382 (m) cc_final: 0.8064 (p) REVERT: C 434 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7131 (pp) REVERT: C 463 SER cc_start: 0.7887 (t) cc_final: 0.7623 (m) REVERT: C 466 LYS cc_start: 0.7059 (tttp) cc_final: 0.6696 (ttmt) outliers start: 36 outliers final: 19 residues processed: 99 average time/residue: 0.5054 time to fit residues: 54.6412 Evaluate side-chains 99 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 514 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 114 optimal weight: 0.0060 chunk 107 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN C 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094858 restraints weight = 11326.423| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.80 r_work: 0.2954 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11934 Z= 0.138 Angle : 0.685 10.103 16239 Z= 0.320 Chirality : 0.052 0.438 1932 Planarity : 0.004 0.035 2010 Dihedral : 11.848 79.902 2509 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.14 % Allowed : 18.44 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.21), residues: 1425 helix: 3.12 (0.26), residues: 393 sheet: 0.26 (0.33), residues: 204 loop : -0.88 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 501 TYR 0.012 0.002 TYR C 184 PHE 0.017 0.002 PHE B 111 TRP 0.011 0.001 TRP A 208 HIS 0.002 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00305 (11877) covalent geometry : angle 0.62735 (16083) SS BOND : bond 0.00155 ( 15) SS BOND : angle 0.64940 ( 30) hydrogen bonds : bond 0.05958 ( 468) hydrogen bonds : angle 4.39665 ( 1377) link_BETA1-2 : bond 0.00635 ( 3) link_BETA1-2 : angle 6.94539 ( 9) link_BETA1-3 : bond 0.00533 ( 3) link_BETA1-3 : angle 5.23319 ( 9) link_BETA1-4 : bond 0.00511 ( 12) link_BETA1-4 : angle 2.66417 ( 36) link_BETA1-6 : bond 0.00696 ( 3) link_BETA1-6 : angle 2.14799 ( 9) link_BETA2-3 : bond 0.00835 ( 3) link_BETA2-3 : angle 2.10038 ( 9) link_NAG-ASN : bond 0.00324 ( 18) link_NAG-ASN : angle 2.20054 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7437 (mt-10) REVERT: A 155 THR cc_start: 0.8442 (m) cc_final: 0.8193 (p) REVERT: A 175 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (tptm) REVERT: A 217 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7629 (tm-30) REVERT: A 401 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8112 (mt-10) REVERT: A 422 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: A 434 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7063 (pp) REVERT: A 456 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7725 (tt0) REVERT: A 463 SER cc_start: 0.7827 (t) cc_final: 0.7460 (m) REVERT: A 464 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7150 (mtmt) REVERT: A 466 LYS cc_start: 0.7058 (tttp) cc_final: 0.6690 (ttpt) REVERT: B 85 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7462 (mt-10) REVERT: B 155 THR cc_start: 0.8522 (m) cc_final: 0.8226 (p) REVERT: B 422 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: B 434 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7194 (pp) REVERT: B 456 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: B 466 LYS cc_start: 0.7266 (tmtp) cc_final: 0.6815 (ttmt) REVERT: C 85 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7487 (mt-10) REVERT: C 155 THR cc_start: 0.8387 (m) cc_final: 0.8081 (p) REVERT: C 434 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7159 (pp) REVERT: C 463 SER cc_start: 0.7866 (t) cc_final: 0.7592 (m) REVERT: C 466 LYS cc_start: 0.7043 (tttp) cc_final: 0.6676 (ttmt) outliers start: 38 outliers final: 22 residues processed: 103 average time/residue: 0.4709 time to fit residues: 52.6628 Evaluate side-chains 105 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 111 PHE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.140553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092545 restraints weight = 11440.634| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.81 r_work: 0.2904 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11934 Z= 0.195 Angle : 0.773 10.392 16239 Z= 0.366 Chirality : 0.055 0.424 1932 Planarity : 0.004 0.036 2010 Dihedral : 12.608 81.572 2506 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.31 % Allowed : 18.44 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1425 helix: 2.86 (0.26), residues: 393 sheet: 0.27 (0.33), residues: 204 loop : -0.91 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 202 TYR 0.018 0.003 TYR C 185 PHE 0.021 0.003 PHE B 111 TRP 0.011 0.002 TRP A 208 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00454 (11877) covalent geometry : angle 0.71778 (16083) SS BOND : bond 0.00266 ( 15) SS BOND : angle 0.93941 ( 30) hydrogen bonds : bond 0.07038 ( 468) hydrogen bonds : angle 4.58612 ( 1377) link_BETA1-2 : bond 0.00364 ( 3) link_BETA1-2 : angle 6.76630 ( 9) link_BETA1-3 : bond 0.00862 ( 3) link_BETA1-3 : angle 4.89624 ( 9) link_BETA1-4 : bond 0.00524 ( 12) link_BETA1-4 : angle 3.03898 ( 36) link_BETA1-6 : bond 0.00660 ( 3) link_BETA1-6 : angle 2.69429 ( 9) link_BETA2-3 : bond 0.00779 ( 3) link_BETA2-3 : angle 2.29643 ( 9) link_NAG-ASN : bond 0.00369 ( 18) link_NAG-ASN : angle 2.38466 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7507 (mt-10) REVERT: A 155 THR cc_start: 0.8545 (m) cc_final: 0.8279 (p) REVERT: A 175 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9047 (tptm) REVERT: A 217 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7682 (tm-30) REVERT: A 401 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 422 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: A 434 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7276 (pp) REVERT: A 463 SER cc_start: 0.7929 (t) cc_final: 0.7555 (m) REVERT: A 464 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7270 (mtmt) REVERT: A 466 LYS cc_start: 0.7155 (tttp) cc_final: 0.6816 (ttpt) REVERT: B 85 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7479 (mt-10) REVERT: B 155 THR cc_start: 0.8559 (m) cc_final: 0.8273 (p) REVERT: B 422 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 434 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7299 (pp) REVERT: B 456 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: B 466 LYS cc_start: 0.7337 (tmtp) cc_final: 0.6890 (ttmt) REVERT: C 85 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7515 (mt-10) REVERT: C 155 THR cc_start: 0.8516 (m) cc_final: 0.8234 (p) REVERT: C 434 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7248 (pp) REVERT: C 463 SER cc_start: 0.7914 (t) cc_final: 0.7652 (m) REVERT: C 466 LYS cc_start: 0.7190 (tttp) cc_final: 0.6831 (ttmt) outliers start: 40 outliers final: 23 residues processed: 103 average time/residue: 0.5474 time to fit residues: 61.3698 Evaluate side-chains 105 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 495 CYS Chi-restraints excluded: chain C residue 514 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.095240 restraints weight = 11444.129| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.82 r_work: 0.2961 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11934 Z= 0.125 Angle : 0.670 10.310 16239 Z= 0.311 Chirality : 0.051 0.450 1932 Planarity : 0.003 0.035 2010 Dihedral : 11.370 78.746 2504 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.56 % Allowed : 19.11 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1425 helix: 3.10 (0.26), residues: 393 sheet: 0.24 (0.33), residues: 204 loop : -0.87 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 501 TYR 0.012 0.002 TYR B 370 PHE 0.017 0.002 PHE B 111 TRP 0.010 0.001 TRP A 208 HIS 0.002 0.001 HIS A 69 Details of bonding type rmsd covalent geometry : bond 0.00268 (11877) covalent geometry : angle 0.61211 (16083) SS BOND : bond 0.00136 ( 15) SS BOND : angle 0.54999 ( 30) hydrogen bonds : bond 0.05717 ( 468) hydrogen bonds : angle 4.37796 ( 1377) link_BETA1-2 : bond 0.00619 ( 3) link_BETA1-2 : angle 7.06331 ( 9) link_BETA1-3 : bond 0.00492 ( 3) link_BETA1-3 : angle 5.13152 ( 9) link_BETA1-4 : bond 0.00512 ( 12) link_BETA1-4 : angle 2.59441 ( 36) link_BETA1-6 : bond 0.00796 ( 3) link_BETA1-6 : angle 1.97559 ( 9) link_BETA2-3 : bond 0.00956 ( 3) link_BETA2-3 : angle 2.10141 ( 9) link_NAG-ASN : bond 0.00310 ( 18) link_NAG-ASN : angle 2.14894 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3997.17 seconds wall clock time: 68 minutes 52.12 seconds (4132.12 seconds total)