Starting phenix.real_space_refine on Sat Jul 4 01:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.cif" model { file = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kra_23003/07_2026/7kra_23003.cif" } resolution = 3.2 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= 0.008 sd= 1.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 67 5.16 5 C 11141 2.51 5 N 2814 2.21 5 O 3270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17293 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5637 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 32, 'TRANS': 661} Chain breaks: 6 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2362 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 286} Chain: "C" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1522 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 3 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1028 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "F" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "G" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1235 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "I" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1309 Classifications: {'peptide': 170} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 160} Chain breaks: 6 Chain: "J" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1610 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain breaks: 2 Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'X3P': 1} Classifications: {'undetermined': 1} Chain: "G" 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 chiralities: 2 Time building chain proxies: 3.29, per 1000 atoms: 0.19 Number of scatterers: 17293 At special positions: 0 Unit cell: (111.743, 127.097, 194.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1 15.00 O 3270 8.00 N 2814 7.00 C 11141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 701 " - pdb=" SG CYS A 709 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 152 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS J 39 " - pdb=" SG CYS J 109 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 214 " 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 NAG-ASN " NAG A 801 " - " ASN A 192 " " NAG A 802 " - " ASN A 106 " " NAG A 803 " - " ASN A 73 " " NAG G 301 " - " ASN G 115 " " NAG G 302 " - " ASN G 53 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 577.1 milliseconds 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4110 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 28 sheets defined 32.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 3.895A pdb=" N ALA A 30 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 248 through 266 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.060A pdb=" N SER A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 757 removed outlier: 3.645A pdb=" N LEU A 730 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Proline residue: A 746 - end of helix removed outlier: 3.931A pdb=" N TRP A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.961A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 36 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 64 Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 85 through 101 removed outlier: 4.355A pdb=" N GLY B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.526A pdb=" N TYR B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 removed outlier: 3.874A pdb=" N TYR B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 157 removed outlier: 3.717A pdb=" N LEU B 149 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 176 removed outlier: 3.913A pdb=" N TRP B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.679A pdb=" N TYR B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.798A pdb=" N LEU B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 237 removed outlier: 4.288A pdb=" N ARG B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.598A pdb=" N TRP B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 274 Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.838A pdb=" N LEU B 287 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 34 Proline residue: C 14 - end of helix Processing helix chain 'C' and resid 43 through 62 removed outlier: 3.697A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 removed outlier: 4.089A pdb=" N LYS C 75 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE C 77 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 140 Proline residue: C 128 - end of helix Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.741A pdb=" N TYR C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 221 through 232 removed outlier: 3.688A pdb=" N MET C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'D' and resid 9 through 17 removed outlier: 3.597A pdb=" N LYS D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.213A pdb=" N GLY D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'E' and resid 3 through 29 Processing helix chain 'E' and resid 31 through 37 Processing helix chain 'E' and resid 46 through 66 Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.950A pdb=" N ILE E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 116 through 128 removed outlier: 3.689A pdb=" N VAL E 120 " --> pdb=" O THR E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.885A pdb=" N ASN F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 42 Processing helix chain 'F' and resid 45 through 68 removed outlier: 3.632A pdb=" N PHE F 50 " --> pdb=" O SER F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 85 removed outlier: 3.887A pdb=" N PHE F 85 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'J' and resid 202 through 208 removed outlier: 4.187A pdb=" N LYS J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 21 Processing helix chain 'N' and resid 2 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 48 removed outlier: 3.888A pdb=" N PHE A 81 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 180 removed outlier: 3.626A pdb=" N LYS A 175 " --> pdb=" O ASN A 190 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 188 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A 179 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA A 186 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR A 196 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLN A 211 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY A 198 " --> pdb=" O VAL A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 226 removed outlier: 3.554A pdb=" N ASP A 221 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TRP A 324 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP A 315 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 322 " --> pdb=" O ASP A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 338 removed outlier: 6.899A pdb=" N PHE A 349 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 336 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 347 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRP A 338 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLU A 345 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU A 359 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 367 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 384 Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 428 removed outlier: 3.886A pdb=" N ILE A 426 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AB1, first strand: chain 'A' and resid 458 through 465 removed outlier: 5.521A pdb=" N MET A 460 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 498 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 462 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.713A pdb=" N SER A 548 " --> pdb=" O GLU A 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 604 through 608 removed outlier: 3.836A pdb=" N ILE A 630 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 691 Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.829A pdb=" N MET C 146 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'G' and resid 61 through 64 removed outlier: 3.533A pdb=" N PHE G 46 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA G 95 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 61 through 64 removed outlier: 3.533A pdb=" N PHE G 46 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR G 89 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU G 107 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA G 122 " --> pdb=" O MET G 146 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET G 146 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN G 144 " --> pdb=" O LYS G 124 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 48 through 55 removed outlier: 5.318A pdb=" N VAL H 50 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP H 41 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR H 52 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU H 39 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR H 25 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP H 19 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 48 through 55 removed outlier: 5.318A pdb=" N VAL H 50 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP H 41 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR H 52 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLU H 39 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N TYR H 25 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP H 19 " --> pdb=" O ILE H 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 102 through 109 removed outlier: 3.649A pdb=" N THR H 117 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 7 through 9 Processing sheet with id=AC4, first strand: chain 'I' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'I' and resid 133 through 134 removed outlier: 5.202A pdb=" N LYS I 155 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU I 190 " --> pdb=" O LYS I 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 208 through 212 Processing sheet with id=AC7, first strand: chain 'J' and resid 20 through 22 Processing sheet with id=AC8, first strand: chain 'J' and resid 65 through 69 removed outlier: 5.284A pdb=" N LEU J 67 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU J 58 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE J 69 " --> pdb=" O TRP J 56 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY J 105 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL J 124 " --> pdb=" O GLY J 105 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY J 120 " --> pdb=" O CYS J 109 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 134 through 138 removed outlier: 3.866A pdb=" N VAL J 153 " --> pdb=" O PHE J 138 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR J 193 " --> pdb=" O ASN J 158 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER J 194 " --> pdb=" O THR J 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 173 through 174 removed outlier: 3.623A pdb=" N LYS J 165 " --> pdb=" O THR J 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR J 217 " --> pdb=" O LYS J 165 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2082 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: 2.77 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2848 1.31 - 1.44: 4736 1.44 - 1.56: 9964 1.56 - 1.69: 5 1.69 - 1.81: 111 Bond restraints: 17664 Sorted by residual: bond pdb=" C31 X3P C 301 " pdb=" O31 X3P C 301 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C21 X3P C 301 " pdb=" O22 X3P C 301 " ideal model delta sigma weight residual 1.280 1.184 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11 X3P C 301 " pdb=" C12 X3P C 301 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.00e-02 2.50e+03 8.40e+00 bond pdb=" N LEU H 74 " pdb=" CA LEU H 74 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.15e+00 bond pdb=" N X3P C 301 " pdb=" C15 X3P C 301 " ideal model delta sigma weight residual 1.491 1.443 0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 17659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 23426 2.36 - 4.72: 441 4.72 - 7.08: 79 7.08 - 9.44: 6 9.44 - 11.80: 4 Bond angle restraints: 23956 Sorted by residual: angle pdb=" N TRP A 35 " pdb=" CA TRP A 35 " pdb=" CB TRP A 35 " ideal model delta sigma weight residual 111.51 104.18 7.33 1.48e+00 4.57e-01 2.45e+01 angle pdb=" N LYS H 73 " pdb=" CA LYS H 73 " pdb=" C LYS H 73 " ideal model delta sigma weight residual 110.65 116.37 -5.72 1.26e+00 6.30e-01 2.06e+01 angle pdb=" C22 X3P C 301 " pdb=" C21 X3P C 301 " pdb=" O21 X3P C 301 " ideal model delta sigma weight residual 108.34 120.14 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" C PRO D 166 " pdb=" N ASN D 167 " pdb=" CA ASN D 167 " ideal model delta sigma weight residual 124.82 131.75 -6.93 1.78e+00 3.16e-01 1.52e+01 angle pdb=" O13 X3P C 301 " pdb=" P X3P C 301 " pdb=" O14 X3P C 301 " ideal model delta sigma weight residual 120.95 109.62 11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 23951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 9303 18.08 - 36.15: 1015 36.15 - 54.23: 135 54.23 - 72.31: 29 72.31 - 90.38: 10 Dihedral angle restraints: 10492 sinusoidal: 4153 harmonic: 6339 Sorted by residual: dihedral pdb=" CB CYS J 39 " pdb=" SG CYS J 39 " pdb=" SG CYS J 109 " pdb=" CB CYS J 109 " ideal model delta sinusoidal sigma weight residual 93.00 167.19 -74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CA ASP A 34 " pdb=" C ASP A 34 " pdb=" N TRP A 35 " pdb=" CA TRP A 35 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU A 397 " pdb=" C GLU A 397 " pdb=" N ASP A 398 " pdb=" CA ASP A 398 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 10489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2679 0.124 - 0.249: 57 0.249 - 0.373: 0 0.373 - 0.498: 0 0.498 - 0.622: 1 Chirality restraints: 2737 Sorted by residual: chirality pdb=" C1 NAG G 301 " pdb=" ND2 ASN G 115 " pdb=" C2 NAG G 301 " pdb=" O5 NAG G 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.68e+00 chirality pdb=" C1 NAG A 803 " pdb=" ND2 ASN A 73 " pdb=" C2 NAG A 803 " pdb=" O5 NAG A 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.51e-01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 106 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 2734 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 166 " 0.012 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP B 166 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 166 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP B 166 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP B 166 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 166 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 166 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 166 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 166 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " 0.023 2.00e-02 2.50e+03 1.92e-02 9.25e+00 pdb=" CG TRP A 35 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 72 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C GLY H 72 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY H 72 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS H 73 " -0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1017 2.73 - 3.27: 17251 3.27 - 3.81: 26151 3.81 - 4.36: 31469 4.36 - 4.90: 56018 Nonbonded interactions: 131906 Sorted by model distance: nonbonded pdb=" O THR B 12 " pdb=" OG1 THR B 16 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP J 190 " pdb=" OG1 THR J 192 " model vdw 2.187 3.040 nonbonded pdb=" OE2 GLU J 125 " pdb=" OH TYR J 193 " model vdw 2.205 3.040 nonbonded pdb=" O THR B 156 " pdb=" OH TYR C 52 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR J 206 " pdb=" NH2 ARG J 231 " model vdw 2.229 3.120 ... (remaining 131901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'N' and resid 4 through 24) } 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: 7.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.330 Find NCS groups from input model: 0.090 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17674 Z= 0.226 Angle : 0.839 12.863 23981 Z= 0.435 Chirality : 0.048 0.622 2737 Planarity : 0.005 0.065 3007 Dihedral : 14.895 90.383 6367 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -2.08 (0.17), residues: 2061 helix: -0.33 (0.20), residues: 579 sheet: -0.30 (0.22), residues: 536 loop : -2.78 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 95 TYR 0.030 0.002 TYR E 54 PHE 0.023 0.002 PHE A 537 TRP 0.061 0.002 TRP B 166 HIS 0.006 0.001 HIS C 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (17664) covalent geometry : angle 0.82190 / 0.43 (23956) SS BOND : bond 0.00218 / 0.10 ( 5) SS BOND : angle 1.05552 / 0.57 ( 10) hydrogen bonds : bond 0.13278 / 9.03 ( 718) hydrogen bonds : angle 6.43751 / 4.49 ( 2082) link_NAG-ASN : bond 0.01403 / 0.77 ( 5) link_NAG-ASN : angle 6.67227 / 4.68 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 14 MET cc_start: 0.6918 (ttm) cc_final: 0.6652 (ttm) REVERT: C 19 MET cc_start: 0.8295 (mmm) cc_final: 0.7998 (mtp) REVERT: E 54 TYR cc_start: 0.8181 (m-80) cc_final: 0.7973 (m-80) REVERT: E 91 LYS cc_start: 0.8706 (mttm) cc_final: 0.8354 (mttt) REVERT: F 83 ASP cc_start: 0.8458 (m-30) cc_final: 0.8026 (m-30) REVERT: G 86 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7987 (mt-10) REVERT: J 33 GLU cc_start: 0.8764 (mp0) cc_final: 0.8548 (mp0) REVERT: J 162 ARG cc_start: 0.8714 (tmm-80) cc_final: 0.8051 (tpm170) REVERT: J 168 TRP cc_start: 0.4792 (m100) cc_final: 0.4196 (m100) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.1382 time to fit residues: 48.9246 Evaluate side-chains 193 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 GLN A 502 HIS A 717 GLN C 51 GLN E 86 GLN H 56 GLN I 212 HIS J 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.120892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080212 restraints weight = 36801.704| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.01 r_work: 0.3238 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 17674 Z= 0.294 Angle : 0.772 20.321 23981 Z= 0.397 Chirality : 0.049 0.590 2737 Planarity : 0.005 0.056 3007 Dihedral : 6.629 50.993 2315 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.00 % Allowed : 9.77 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.79 (0.18), residues: 2061 helix: 0.20 (0.21), residues: 599 sheet: -0.31 (0.22), residues: 542 loop : -2.77 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 82 TYR 0.027 0.002 TYR J 160 PHE 0.018 0.002 PHE D 188 TRP 0.046 0.002 TRP A 35 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.29 (17664) covalent geometry : angle 0.74337 / 0.39 (23956) SS BOND : bond 0.01162 / 0.43 ( 5) SS BOND : angle 0.91895 / 0.49 ( 10) hydrogen bonds : bond 0.04841 / 3.25 ( 718) hydrogen bonds : angle 5.40960 / 3.75 ( 2082) link_NAG-ASN : bond 0.01246 / 0.67 ( 5) link_NAG-ASN : angle 8.32381 / 6.36 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 14 MET cc_start: 0.7244 (ttm) cc_final: 0.7000 (mtt) REVERT: E 91 LYS cc_start: 0.8697 (mttm) cc_final: 0.8296 (mttt) REVERT: F 92 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 86 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8180 (mt-10) REVERT: G 167 GLN cc_start: 0.9044 (tp40) cc_final: 0.8825 (tp40) REVERT: J 33 GLU cc_start: 0.8895 (mp0) cc_final: 0.8498 (mp0) REVERT: J 111 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: J 162 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8002 (tpm170) outliers start: 19 outliers final: 15 residues processed: 213 average time/residue: 0.1385 time to fit residues: 43.8114 Evaluate side-chains 197 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain J residue 111 GLN Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 46 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.0570 chunk 139 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.124029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083611 restraints weight = 37033.813| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.07 r_work: 0.3299 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17674 Z= 0.134 Angle : 0.655 17.727 23981 Z= 0.333 Chirality : 0.044 0.513 2737 Planarity : 0.004 0.046 3007 Dihedral : 6.161 46.535 2315 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.32 % Allowed : 12.83 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.45 (0.18), residues: 2061 helix: 0.58 (0.21), residues: 604 sheet: -0.13 (0.22), residues: 538 loop : -2.64 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 48 TYR 0.025 0.001 TYR E 24 PHE 0.014 0.001 PHE A 708 TRP 0.032 0.001 TRP A 35 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (17664) covalent geometry : angle 0.62708 / 0.33 (23956) SS BOND : bond 0.00973 / 0.36 ( 5) SS BOND : angle 0.61403 / 0.33 ( 10) hydrogen bonds : bond 0.03857 / 2.59 ( 718) hydrogen bonds : angle 5.01761 / 3.49 ( 2082) link_NAG-ASN : bond 0.01407 / 0.84 ( 5) link_NAG-ASN : angle 7.63450 / 5.71 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.6871 (ptt) cc_final: 0.6540 (ptt) REVERT: B 91 MET cc_start: 0.7949 (mtp) cc_final: 0.7535 (mtp) REVERT: B 108 TYR cc_start: 0.7846 (t80) cc_final: 0.7106 (t80) REVERT: B 227 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7845 (tp) REVERT: C 133 MET cc_start: 0.8664 (mtp) cc_final: 0.8401 (mtp) REVERT: E 69 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 91 LYS cc_start: 0.8743 (mttm) cc_final: 0.8347 (mttt) REVERT: G 86 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 167 GLN cc_start: 0.9027 (tp40) cc_final: 0.8806 (tp40) REVERT: J 33 GLU cc_start: 0.8943 (mp0) cc_final: 0.8588 (mp0) REVERT: J 100 GLU cc_start: 0.8415 (mp0) cc_final: 0.8136 (mp0) REVERT: J 162 ARG cc_start: 0.8796 (tmm-80) cc_final: 0.7988 (tpm170) outliers start: 25 outliers final: 15 residues processed: 212 average time/residue: 0.1377 time to fit residues: 44.2207 Evaluate side-chains 194 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 156 optimal weight: 0.0670 chunk 150 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 157 optimal weight: 0.0670 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 574 ASN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.084028 restraints weight = 36982.357| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.15 r_work: 0.3304 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17674 Z= 0.131 Angle : 0.638 20.024 23981 Z= 0.321 Chirality : 0.044 0.535 2737 Planarity : 0.004 0.045 3007 Dihedral : 5.818 42.381 2315 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.95 % Allowed : 14.36 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.22 (0.18), residues: 2061 helix: 0.80 (0.21), residues: 605 sheet: 0.04 (0.23), residues: 538 loop : -2.55 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 48 TYR 0.022 0.001 TYR E 24 PHE 0.015 0.001 PHE B 58 TRP 0.043 0.001 TRP A 35 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (17664) covalent geometry : angle 0.60599 / 0.31 (23956) SS BOND : bond 0.00218 / 0.08 ( 5) SS BOND : angle 0.48924 / 0.25 ( 10) hydrogen bonds : bond 0.03644 / 2.44 ( 718) hydrogen bonds : angle 4.81649 / 3.34 ( 2082) link_NAG-ASN : bond 0.01489 / 0.91 ( 5) link_NAG-ASN : angle 7.98828 / 6.21 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7755 (tp30) cc_final: 0.7305 (pt0) REVERT: C 133 MET cc_start: 0.8664 (mtp) cc_final: 0.8336 (mtp) REVERT: E 69 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8615 (mm-30) REVERT: E 91 LYS cc_start: 0.8756 (mttm) cc_final: 0.8365 (mttt) REVERT: G 86 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8237 (mt-10) REVERT: H 76 MET cc_start: 0.8731 (mpp) cc_final: 0.8514 (mtm) REVERT: J 33 GLU cc_start: 0.8958 (mp0) cc_final: 0.8584 (mp0) REVERT: J 95 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8208 (ptp-110) REVERT: J 162 ARG cc_start: 0.8817 (tmm-80) cc_final: 0.7995 (tpm170) outliers start: 37 outliers final: 24 residues processed: 208 average time/residue: 0.1210 time to fit residues: 38.9508 Evaluate side-chains 204 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 158 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 71 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN F 82 HIS I 5 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.123214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082773 restraints weight = 36754.399| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.07 r_work: 0.3281 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17674 Z= 0.182 Angle : 0.665 19.248 23981 Z= 0.336 Chirality : 0.045 0.508 2737 Planarity : 0.004 0.047 3007 Dihedral : 5.841 40.550 2315 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.16 % Allowed : 15.84 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.14 (0.19), residues: 2061 helix: 0.92 (0.22), residues: 603 sheet: 0.07 (0.23), residues: 538 loop : -2.53 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 98 TYR 0.021 0.001 TYR J 160 PHE 0.016 0.001 PHE A 708 TRP 0.046 0.002 TRP B 166 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (17664) covalent geometry : angle 0.63509 / 0.33 (23956) SS BOND : bond 0.00154 / 0.07 ( 5) SS BOND : angle 0.58655 / 0.30 ( 10) hydrogen bonds : bond 0.03841 / 2.56 ( 718) hydrogen bonds : angle 4.81151 / 3.33 ( 2082) link_NAG-ASN : bond 0.01415 / 0.85 ( 5) link_NAG-ASN : angle 7.90244 / 6.06 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7775 (tp30) cc_final: 0.7329 (pt0) REVERT: E 69 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8573 (mm-30) REVERT: E 91 LYS cc_start: 0.8771 (mttm) cc_final: 0.8361 (mttt) REVERT: F 83 ASP cc_start: 0.8671 (m-30) cc_final: 0.8313 (m-30) REVERT: G 86 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8234 (mt-10) REVERT: G 105 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.6304 (mtt90) REVERT: J 33 GLU cc_start: 0.8948 (mp0) cc_final: 0.8562 (mp0) REVERT: J 95 ARG cc_start: 0.8427 (ptp-110) cc_final: 0.8144 (ptp-110) REVERT: J 100 GLU cc_start: 0.8414 (mp0) cc_final: 0.8084 (mp0) REVERT: J 162 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8066 (tpm170) outliers start: 41 outliers final: 29 residues processed: 210 average time/residue: 0.1289 time to fit residues: 42.0925 Evaluate side-chains 206 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 34 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.123824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083543 restraints weight = 36892.092| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.07 r_work: 0.3295 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 : 0.003 0.050 17674 Z= 0.149 Angle : 0.643 18.551 23981 Z= 0.324 Chirality : 0.044 0.500 2737 Planarity : 0.004 0.045 3007 Dihedral : 5.712 38.565 2315 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.11 % Allowed : 16.95 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -1.05 (0.19), residues: 2061 helix: 0.99 (0.22), residues: 600 sheet: 0.15 (0.23), residues: 538 loop : -2.47 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 48 TYR 0.016 0.001 TYR E 24 PHE 0.014 0.001 PHE A 708 TRP 0.049 0.001 TRP B 166 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (17664) covalent geometry : angle 0.61342 / 0.32 (23956) SS BOND : bond 0.00182 / 0.08 ( 5) SS BOND : angle 0.50793 / 0.26 ( 10) hydrogen bonds : bond 0.03650 / 2.44 ( 718) hydrogen bonds : angle 4.73017 / 3.28 ( 2082) link_NAG-ASN : bond 0.01440 / 0.87 ( 5) link_NAG-ASN : angle 7.75048 / 5.88 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8947 (mmm) cc_final: 0.8706 (tpp) REVERT: C 49 GLU cc_start: 0.7707 (tp30) cc_final: 0.7294 (pt0) REVERT: E 69 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8549 (mm-30) REVERT: E 91 LYS cc_start: 0.8777 (mttm) cc_final: 0.8366 (mttt) REVERT: F 83 ASP cc_start: 0.8694 (m-30) cc_final: 0.8306 (m-30) REVERT: G 86 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8251 (mt-10) REVERT: G 105 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.6293 (mtt90) REVERT: J 33 GLU cc_start: 0.8947 (mp0) cc_final: 0.8554 (mp0) REVERT: J 95 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8205 (ptp-110) REVERT: J 100 GLU cc_start: 0.8399 (mp0) cc_final: 0.8119 (mp0) REVERT: J 162 ARG cc_start: 0.8860 (tmm-80) cc_final: 0.8064 (tpm170) outliers start: 40 outliers final: 33 residues processed: 210 average time/residue: 0.1196 time to fit residues: 38.8953 Evaluate side-chains 215 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.121615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081046 restraints weight = 37085.695| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.06 r_work: 0.3251 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17674 Z= 0.231 Angle : 0.705 18.725 23981 Z= 0.358 Chirality : 0.046 0.530 2737 Planarity : 0.004 0.048 3007 Dihedral : 5.983 38.996 2315 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.80 % Allowed : 17.21 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.19), residues: 2061 helix: 0.97 (0.22), residues: 601 sheet: 0.09 (0.23), residues: 538 loop : -2.53 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 48 TYR 0.022 0.002 TYR J 160 PHE 0.016 0.002 PHE A 708 TRP 0.052 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (17664) covalent geometry : angle 0.67653 / 0.35 (23956) SS BOND : bond 0.00148 / 0.07 ( 5) SS BOND : angle 0.69057 / 0.34 ( 10) hydrogen bonds : bond 0.04131 / 2.75 ( 718) hydrogen bonds : angle 4.88311 / 3.37 ( 2082) link_NAG-ASN : bond 0.01348 / 0.79 ( 5) link_NAG-ASN : angle 7.92379 / 5.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7810 (tp30) cc_final: 0.7351 (pt0) REVERT: E 50 MET cc_start: 0.7578 (mtp) cc_final: 0.6873 (mtm) REVERT: E 54 TYR cc_start: 0.8210 (m-80) cc_final: 0.7884 (m-80) REVERT: E 69 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8619 (mm-30) REVERT: E 91 LYS cc_start: 0.8767 (mttm) cc_final: 0.8357 (mttt) REVERT: F 83 ASP cc_start: 0.8729 (m-30) cc_final: 0.8371 (m-30) REVERT: G 86 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8212 (mt-10) REVERT: G 105 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.6339 (mtt90) REVERT: I 166 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.5113 (m-10) REVERT: J 33 GLU cc_start: 0.8942 (mp0) cc_final: 0.8571 (mp0) REVERT: J 100 GLU cc_start: 0.8395 (mp0) cc_final: 0.7964 (mp0) REVERT: J 162 ARG cc_start: 0.8845 (tmm-80) cc_final: 0.8072 (tpm170) outliers start: 53 outliers final: 41 residues processed: 221 average time/residue: 0.1271 time to fit residues: 43.1625 Evaluate side-chains 223 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 166 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 162 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS H 67 ASN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.122166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081566 restraints weight = 36899.480| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 3.12 r_work: 0.3259 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17674 Z= 0.198 Angle : 0.684 18.358 23981 Z= 0.347 Chirality : 0.046 0.514 2737 Planarity : 0.004 0.093 3007 Dihedral : 5.943 38.942 2315 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.59 % Allowed : 17.74 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.11 (0.19), residues: 2061 helix: 0.96 (0.22), residues: 601 sheet: 0.09 (0.23), residues: 541 loop : -2.51 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 48 TYR 0.022 0.001 TYR E 24 PHE 0.016 0.001 PHE A 708 TRP 0.051 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (17664) covalent geometry : angle 0.65590 / 0.34 (23956) SS BOND : bond 0.00086 / 0.05 ( 5) SS BOND : angle 0.56236 / 0.28 ( 10) hydrogen bonds : bond 0.03961 / 2.64 ( 718) hydrogen bonds : angle 4.85581 / 3.36 ( 2082) link_NAG-ASN : bond 0.01371 / 0.81 ( 5) link_NAG-ASN : angle 7.83983 / 5.88 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7701 (tp30) cc_final: 0.7254 (pt0) REVERT: E 69 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8530 (mm-30) REVERT: E 91 LYS cc_start: 0.8789 (mttm) cc_final: 0.8378 (mttt) REVERT: F 83 ASP cc_start: 0.8717 (m-30) cc_final: 0.8345 (m-30) REVERT: G 86 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8222 (mt-10) REVERT: G 105 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6355 (mtt90) REVERT: I 166 TRP cc_start: 0.5758 (OUTLIER) cc_final: 0.5179 (m-10) REVERT: J 33 GLU cc_start: 0.8943 (mp0) cc_final: 0.8550 (mp0) REVERT: J 100 GLU cc_start: 0.8410 (mp0) cc_final: 0.7581 (mp0) REVERT: J 162 ARG cc_start: 0.8875 (tmm-80) cc_final: 0.8083 (tpm170) outliers start: 49 outliers final: 42 residues processed: 218 average time/residue: 0.1293 time to fit residues: 43.8946 Evaluate side-chains 223 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 166 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 26 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.123178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082717 restraints weight = 36915.838| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.12 r_work: 0.3281 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17674 Z= 0.156 Angle : 0.675 21.000 23981 Z= 0.340 Chirality : 0.044 0.392 2737 Planarity : 0.004 0.084 3007 Dihedral : 5.809 37.690 2315 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.64 % Allowed : 18.16 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.19), residues: 2061 helix: 1.02 (0.22), residues: 601 sheet: 0.16 (0.23), residues: 541 loop : -2.46 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 48 TYR 0.021 0.001 TYR J 160 PHE 0.014 0.001 PHE A 708 TRP 0.065 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (17664) covalent geometry : angle 0.64169 / 0.33 (23956) SS BOND : bond 0.00067 / 0.04 ( 5) SS BOND : angle 0.54258 / 0.28 ( 10) hydrogen bonds : bond 0.03761 / 2.52 ( 718) hydrogen bonds : angle 4.78487 / 3.30 ( 2082) link_NAG-ASN : bond 0.01389 / 0.84 ( 5) link_NAG-ASN : angle 8.45090 / 6.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7704 (tp30) cc_final: 0.7262 (pt0) REVERT: E 54 TYR cc_start: 0.8242 (m-80) cc_final: 0.7891 (m-80) REVERT: E 69 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8557 (mm-30) REVERT: E 91 LYS cc_start: 0.8794 (mttm) cc_final: 0.8387 (mttt) REVERT: F 83 ASP cc_start: 0.8722 (m-30) cc_final: 0.8343 (m-30) REVERT: G 86 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8049 (mt-10) REVERT: G 105 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6332 (mtt90) REVERT: I 166 TRP cc_start: 0.5798 (OUTLIER) cc_final: 0.5182 (m-10) REVERT: J 33 GLU cc_start: 0.8938 (mp0) cc_final: 0.8542 (mp0) REVERT: J 100 GLU cc_start: 0.8408 (mp0) cc_final: 0.7805 (mp0) REVERT: J 162 ARG cc_start: 0.8860 (tmm-80) cc_final: 0.8097 (tpm170) outliers start: 50 outliers final: 42 residues processed: 214 average time/residue: 0.1237 time to fit residues: 41.4508 Evaluate side-chains 222 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 9 TRP Chi-restraints excluded: chain I residue 160 GLU Chi-restraints excluded: chain I residue 166 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 88 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 158 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.124100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083766 restraints weight = 36740.878| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.13 r_work: 0.3299 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17674 Z= 0.136 Angle : 0.659 20.835 23981 Z= 0.330 Chirality : 0.044 0.364 2737 Planarity : 0.004 0.079 3007 Dihedral : 5.637 35.640 2315 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.38 % Allowed : 18.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.92 (0.19), residues: 2061 helix: 1.10 (0.22), residues: 600 sheet: 0.25 (0.23), residues: 543 loop : -2.42 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 48 TYR 0.017 0.001 TYR E 24 PHE 0.013 0.001 PHE A 708 TRP 0.052 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17664) covalent geometry : angle 0.62497 / 0.32 (23956) SS BOND : bond 0.00063 / 0.04 ( 5) SS BOND : angle 0.46023 / 0.24 ( 10) hydrogen bonds : bond 0.03582 / 2.40 ( 718) hydrogen bonds : angle 4.70530 / 3.24 ( 2082) link_NAG-ASN : bond 0.01382 / 0.84 ( 5) link_NAG-ASN : angle 8.33071 / 6.48 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8345 (t60) cc_final: 0.8128 (t60) REVERT: A 102 MET cc_start: 0.8865 (mmm) cc_final: 0.8617 (tpp) REVERT: C 49 GLU cc_start: 0.7715 (tp30) cc_final: 0.7279 (pt0) REVERT: E 69 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8539 (mm-30) REVERT: E 91 LYS cc_start: 0.8786 (mttm) cc_final: 0.8383 (mttt) REVERT: E 92 GLU cc_start: 0.8830 (mp0) cc_final: 0.8609 (mp0) REVERT: F 83 ASP cc_start: 0.8706 (m-30) cc_final: 0.8325 (m-30) REVERT: G 86 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8008 (mt-10) REVERT: I 166 TRP cc_start: 0.5786 (OUTLIER) cc_final: 0.5132 (m-10) REVERT: J 33 GLU cc_start: 0.8933 (mp0) cc_final: 0.8534 (mp0) REVERT: J 100 GLU cc_start: 0.8395 (mp0) cc_final: 0.7875 (mp0) REVERT: J 162 ARG cc_start: 0.8829 (tmm-80) cc_final: 0.8063 (tpm170) outliers start: 45 outliers final: 41 residues processed: 218 average time/residue: 0.1297 time to fit residues: 43.7807 Evaluate side-chains 220 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 105 ARG Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 166 TRP Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 126 ILE Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 154 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.124359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.084007 restraints weight = 36786.201| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 3.14 r_work: 0.3303 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17674 Z= 0.139 Angle : 0.656 20.723 23981 Z= 0.329 Chirality : 0.044 0.374 2737 Planarity : 0.004 0.076 3007 Dihedral : 5.555 35.543 2315 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.48 % Allowed : 18.53 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: -0.85 (0.19), residues: 2061 helix: 1.13 (0.22), residues: 600 sheet: 0.31 (0.23), residues: 544 loop : -2.38 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 48 TYR 0.016 0.001 TYR E 24 PHE 0.014 0.001 PHE A 708 TRP 0.043 0.001 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17664) covalent geometry : angle 0.62310 / 0.32 (23956) SS BOND : bond 0.00071 / 0.04 ( 5) SS BOND : angle 0.46053 / 0.24 ( 10) hydrogen bonds : bond 0.03567 / 2.39 ( 718) hydrogen bonds : angle 4.67028 / 3.22 ( 2082) link_NAG-ASN : bond 0.01432 / 0.88 ( 5) link_NAG-ASN : angle 8.22996 / 6.42 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.39 seconds wall clock time: 77 minutes 14.79 seconds (4634.79 seconds total)