Starting phenix.real_space_refine on Thu Mar 5 00:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kra_23003/03_2026/7kra_23003.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kra_23003/03_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_23003/03_2026/7kra_23003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kra_23003/03_2026/7kra_23003.map" model { file = "/net/cci-nas-00/data/ceres_data/7kra_23003/03_2026/7kra_23003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kra_23003/03_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-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.43, per 1000 atoms: 0.20 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: 1.62 Conformation dependent library (CDL) restraints added in 830.1 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: 0.44 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: 2.91 Time building geometry restraints manager: 2.10 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 - 23.74: 9895 23.74 - 47.48: 632 47.48 - 71.22: 57 71.22 - 94.96: 18 94.96 - 118.70: 4 Dihedral angle restraints: 10606 sinusoidal: 4267 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 10603 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: 9.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.640 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 15.475 118.697 6481 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 covalent geometry : bond 0.00497 (17664) covalent geometry : angle 0.82190 (23956) SS BOND : bond 0.00218 ( 5) SS BOND : angle 1.05552 ( 10) hydrogen bonds : bond 0.13278 ( 718) hydrogen bonds : angle 6.43751 ( 2082) link_NAG-ASN : bond 0.01403 ( 5) link_NAG-ASN : angle 6.67227 ( 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 : 0.744 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: 0.1453 time to fit residues: 50.9758 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 : 0.632 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3928 r_free = 0.3928 target = 0.121030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.080268 restraints weight = 36873.113| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.02 r_work: 0.3238 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 17674 Z= 0.300 Angle : 0.777 20.624 23981 Z= 0.399 Chirality : 0.050 0.595 2737 Planarity : 0.005 0.057 3007 Dihedral : 9.067 100.967 2429 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.06 % Allowed : 9.61 % Favored : 89.33 % 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: -1.78 (0.18), residues: 2061 helix: 0.22 (0.21), residues: 599 sheet: -0.29 (0.22), residues: 541 loop : -2.78 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 95 TYR 0.027 0.002 TYR J 160 PHE 0.017 0.002 PHE A 708 TRP 0.046 0.002 TRP A 35 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00719 (17664) covalent geometry : angle 0.74615 (23956) SS BOND : bond 0.01220 ( 5) SS BOND : angle 0.85469 ( 10) hydrogen bonds : bond 0.04783 ( 718) hydrogen bonds : angle 5.41279 ( 2082) link_NAG-ASN : bond 0.01143 ( 5) link_NAG-ASN : angle 8.68212 ( 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 224 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 14 MET cc_start: 0.7214 (ttm) cc_final: 0.6974 (mtt) REVERT: E 91 LYS cc_start: 0.8684 (mttm) cc_final: 0.8295 (mttt) REVERT: F 92 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8028 (mm-30) REVERT: G 86 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8183 (mt-10) REVERT: G 167 GLN cc_start: 0.9049 (tp40) cc_final: 0.8830 (tp40) REVERT: J 33 GLU cc_start: 0.8892 (mp0) cc_final: 0.8501 (mp0) REVERT: J 111 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: J 162 ARG cc_start: 0.8806 (tmm-80) cc_final: 0.8002 (tpm170) outliers start: 20 outliers final: 15 residues processed: 215 average time/residue: 0.1391 time to fit residues: 44.4514 Evaluate side-chains 199 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3967 r_free = 0.3967 target = 0.123659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083120 restraints weight = 37083.679| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.14 r_work: 0.3287 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17674 Z= 0.145 Angle : 0.665 17.620 23981 Z= 0.338 Chirality : 0.045 0.525 2737 Planarity : 0.004 0.047 3007 Dihedral : 8.211 89.336 2429 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.48 % Allowed : 12.78 % Favored : 85.74 % 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: -1.47 (0.18), residues: 2061 helix: 0.58 (0.21), residues: 604 sheet: -0.15 (0.23), residues: 538 loop : -2.65 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 48 TYR 0.029 0.001 TYR E 24 PHE 0.015 0.001 PHE A 708 TRP 0.033 0.001 TRP B 166 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00328 (17664) covalent geometry : angle 0.63546 (23956) SS BOND : bond 0.00495 ( 5) SS BOND : angle 0.67679 ( 10) hydrogen bonds : bond 0.03918 ( 718) hydrogen bonds : angle 5.03075 ( 2082) link_NAG-ASN : bond 0.01394 ( 5) link_NAG-ASN : angle 7.90284 ( 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 223 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 721 MET cc_start: 0.6910 (ptt) cc_final: 0.6590 (ptt) REVERT: B 91 MET cc_start: 0.7951 (mtp) cc_final: 0.7537 (mtp) REVERT: B 108 TYR cc_start: 0.7826 (t80) cc_final: 0.7084 (t80) REVERT: B 227 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (tp) REVERT: C 133 MET cc_start: 0.8708 (mtp) cc_final: 0.8444 (mtp) REVERT: E 69 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8555 (mm-30) REVERT: E 91 LYS cc_start: 0.8778 (mttm) cc_final: 0.8385 (mttt) REVERT: G 86 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8224 (mt-10) REVERT: G 167 GLN cc_start: 0.9012 (tp40) cc_final: 0.8791 (tp40) REVERT: J 33 GLU cc_start: 0.8952 (mp0) cc_final: 0.8600 (mp0) REVERT: J 100 GLU cc_start: 0.8442 (mp0) cc_final: 0.8150 (mp0) REVERT: J 162 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.7991 (tpm170) outliers start: 28 outliers final: 18 residues processed: 211 average time/residue: 0.1369 time to fit residues: 43.4869 Evaluate side-chains 200 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 595 THR 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 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 36 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: 0.0870 chunk 150 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 chunk 210 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN B 71 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 ASN F 82 HIS ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.122869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082350 restraints weight = 37058.668| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.08 r_work: 0.3273 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17674 Z= 0.180 Angle : 0.673 20.640 23981 Z= 0.339 Chirality : 0.045 0.517 2737 Planarity : 0.004 0.048 3007 Dihedral : 7.743 77.111 2429 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.11 % Allowed : 14.99 % Favored : 82.89 % 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: -1.32 (0.18), residues: 2061 helix: 0.74 (0.21), residues: 605 sheet: -0.06 (0.23), residues: 538 loop : -2.60 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 48 TYR 0.023 0.001 TYR E 24 PHE 0.016 0.001 PHE A 708 TRP 0.034 0.001 TRP B 166 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00428 (17664) covalent geometry : angle 0.63902 (23956) SS BOND : bond 0.00095 ( 5) SS BOND : angle 0.53562 ( 10) hydrogen bonds : bond 0.03941 ( 718) hydrogen bonds : angle 4.91794 ( 2082) link_NAG-ASN : bond 0.01430 ( 5) link_NAG-ASN : angle 8.41615 ( 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 227 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.556 Fit side-chains REVERT: C 49 GLU cc_start: 0.7720 (tp30) cc_final: 0.7279 (pt0) REVERT: E 69 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8650 (mm-30) REVERT: E 91 LYS cc_start: 0.8744 (mttm) cc_final: 0.8349 (mttt) REVERT: F 78 GLN cc_start: 0.8288 (pm20) cc_final: 0.8057 (pm20) REVERT: F 83 ASP cc_start: 0.8631 (m-30) cc_final: 0.8282 (m-30) REVERT: G 86 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8197 (mt-10) REVERT: G 105 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.6284 (mtt90) REVERT: J 33 GLU cc_start: 0.8968 (mp0) cc_final: 0.8579 (mp0) REVERT: J 95 ARG cc_start: 0.8418 (ptp-110) cc_final: 0.8121 (ptp-110) REVERT: J 162 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8016 (tpm170) outliers start: 40 outliers final: 27 residues processed: 210 average time/residue: 0.1255 time to fit residues: 40.2675 Evaluate side-chains 208 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 559 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 623 MET 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 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 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 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: 0.0020 chunk 158 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS I 5 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 218 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084155 restraints weight = 36652.447| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.14 r_work: 0.3305 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1748 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= 0.130 Angle : 0.642 18.719 23981 Z= 0.322 Chirality : 0.044 0.499 2737 Planarity : 0.004 0.045 3007 Dihedral : 7.291 76.109 2429 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % 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: -1.12 (0.19), residues: 2061 helix: 0.93 (0.22), residues: 599 sheet: 0.07 (0.23), residues: 538 loop : -2.49 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 48 TYR 0.021 0.001 TYR B 108 PHE 0.013 0.001 PHE A 708 TRP 0.041 0.001 TRP B 166 HIS 0.005 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00292 (17664) covalent geometry : angle 0.61184 (23956) SS BOND : bond 0.00096 ( 5) SS BOND : angle 0.51415 ( 10) hydrogen bonds : bond 0.03564 ( 718) hydrogen bonds : angle 4.74574 ( 2082) link_NAG-ASN : bond 0.01507 ( 5) link_NAG-ASN : angle 7.81966 ( 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 229 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8913 (mmm) cc_final: 0.8682 (tpp) REVERT: C 49 GLU cc_start: 0.7662 (tp30) cc_final: 0.7281 (pt0) REVERT: E 69 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8588 (mm-30) REVERT: E 91 LYS cc_start: 0.8765 (mttm) cc_final: 0.8361 (mttt) REVERT: F 78 GLN cc_start: 0.8246 (pm20) cc_final: 0.7938 (pm20) REVERT: F 83 ASP cc_start: 0.8662 (m-30) cc_final: 0.8288 (m-30) REVERT: G 86 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8244 (mt-10) REVERT: G 167 GLN cc_start: 0.8998 (tp40) cc_final: 0.8794 (tp40) REVERT: I 166 TRP cc_start: 0.5774 (OUTLIER) cc_final: 0.4869 (m-10) REVERT: J 33 GLU cc_start: 0.8936 (mp0) cc_final: 0.8546 (mp0) REVERT: J 95 ARG cc_start: 0.8402 (ptp-110) cc_final: 0.8177 (ptp-110) REVERT: J 98 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8258 (mtm110) REVERT: J 162 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8026 (tpm170) outliers start: 41 outliers final: 28 residues processed: 211 average time/residue: 0.1233 time to fit residues: 40.0749 Evaluate side-chains 210 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 560 VAL Chi-restraints excluded: chain A residue 613 THR 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 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 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 I residue 166 TRP Chi-restraints excluded: chain J residue 71 LEU 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: 1.9990 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 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: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.123176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.082665 restraints weight = 36871.516| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.13 r_work: 0.3280 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17674 Z= 0.172 Angle : 0.656 18.511 23981 Z= 0.331 Chirality : 0.045 0.518 2737 Planarity : 0.004 0.046 3007 Dihedral : 7.206 80.118 2429 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.38 % Allowed : 16.68 % 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: -1.07 (0.19), residues: 2061 helix: 1.01 (0.22), residues: 600 sheet: 0.12 (0.23), residues: 538 loop : -2.50 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 48 TYR 0.020 0.001 TYR E 24 PHE 0.015 0.001 PHE A 708 TRP 0.052 0.002 TRP A 35 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00407 (17664) covalent geometry : angle 0.62725 (23956) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.54300 ( 10) hydrogen bonds : bond 0.03755 ( 718) hydrogen bonds : angle 4.76169 ( 2082) link_NAG-ASN : bond 0.01449 ( 5) link_NAG-ASN : angle 7.64551 ( 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 232 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7720 (tp30) cc_final: 0.7307 (pt0) REVERT: C 133 MET cc_start: 0.8576 (mtp) cc_final: 0.8331 (mtp) REVERT: E 50 MET cc_start: 0.7536 (mtp) cc_final: 0.6957 (mtm) REVERT: E 69 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8669 (mm-30) REVERT: E 91 LYS cc_start: 0.8795 (mttm) cc_final: 0.8404 (mttt) REVERT: F 78 GLN cc_start: 0.8304 (pm20) cc_final: 0.7955 (pm20) REVERT: F 83 ASP cc_start: 0.8730 (m-30) cc_final: 0.8355 (m-30) REVERT: G 86 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8256 (mt-10) REVERT: G 105 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.6340 (mtt90) REVERT: I 166 TRP cc_start: 0.5698 (OUTLIER) cc_final: 0.4958 (m-10) REVERT: J 33 GLU cc_start: 0.8950 (mp0) cc_final: 0.8558 (mp0) REVERT: J 95 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8179 (ptp-110) REVERT: J 162 ARG cc_start: 0.8857 (tmm-80) cc_final: 0.8076 (tpm170) outliers start: 45 outliers final: 35 residues processed: 216 average time/residue: 0.1282 time to fit residues: 42.7177 Evaluate side-chains 219 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 139 THR 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 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 160 GLU Chi-restraints excluded: chain I residue 166 TRP 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: 0.0980 chunk 130 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.124300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084082 restraints weight = 36975.928| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.08 r_work: 0.3305 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17674 Z= 0.137 Angle : 0.640 17.773 23981 Z= 0.322 Chirality : 0.044 0.503 2737 Planarity : 0.004 0.045 3007 Dihedral : 7.112 83.068 2429 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.53 % Allowed : 17.74 % Favored : 79.73 % 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: -0.96 (0.19), residues: 2061 helix: 1.09 (0.22), residues: 600 sheet: 0.21 (0.23), residues: 541 loop : -2.45 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 48 TYR 0.021 0.001 TYR J 160 PHE 0.014 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 covalent geometry : bond 0.00314 (17664) covalent geometry : angle 0.61351 (23956) SS BOND : bond 0.00417 ( 5) SS BOND : angle 0.58629 ( 10) hydrogen bonds : bond 0.03536 ( 718) hydrogen bonds : angle 4.67244 ( 2082) link_NAG-ASN : bond 0.01446 ( 5) link_NAG-ASN : angle 7.27434 ( 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 240 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8903 (mmm) cc_final: 0.8671 (tpp) REVERT: C 49 GLU cc_start: 0.7720 (tp30) cc_final: 0.7300 (pt0) REVERT: E 69 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8596 (mm-30) REVERT: E 91 LYS cc_start: 0.8798 (mttm) cc_final: 0.8389 (mttt) REVERT: F 78 GLN cc_start: 0.8243 (pm20) cc_final: 0.7860 (pm20) REVERT: F 83 ASP cc_start: 0.8693 (m-30) cc_final: 0.8316 (m-30) REVERT: G 86 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8260 (mt-10) REVERT: G 105 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.6226 (mtt90) REVERT: G 167 GLN cc_start: 0.8976 (tp40) cc_final: 0.8755 (tp40) REVERT: J 33 GLU cc_start: 0.8922 (mp0) cc_final: 0.8540 (mp0) REVERT: J 95 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.8157 (ptp-110) REVERT: J 162 ARG cc_start: 0.8827 (tmm-80) cc_final: 0.8058 (tpm170) outliers start: 48 outliers final: 38 residues processed: 225 average time/residue: 0.1271 time to fit residues: 44.1471 Evaluate side-chains 226 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 84 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3964 r_free = 0.3964 target = 0.123434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082950 restraints weight = 36834.602| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.14 r_work: 0.3282 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17674 Z= 0.168 Angle : 0.656 17.702 23981 Z= 0.332 Chirality : 0.045 0.518 2737 Planarity : 0.004 0.045 3007 Dihedral : 7.140 84.528 2429 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 2.75 % Allowed : 17.58 % Favored : 79.67 % 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: -0.96 (0.19), residues: 2061 helix: 1.11 (0.22), residues: 601 sheet: 0.20 (0.23), residues: 541 loop : -2.46 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 48 TYR 0.025 0.001 TYR E 24 PHE 0.015 0.001 PHE A 708 TRP 0.049 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00395 (17664) covalent geometry : angle 0.63038 (23956) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.51356 ( 10) hydrogen bonds : bond 0.03675 ( 718) hydrogen bonds : angle 4.70012 ( 2082) link_NAG-ASN : bond 0.01415 ( 5) link_NAG-ASN : angle 7.26591 ( 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 244 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 49 GLU cc_start: 0.7734 (tp30) cc_final: 0.7266 (pt0) REVERT: C 52 TYR cc_start: 0.8210 (m-80) cc_final: 0.7986 (m-80) REVERT: E 54 TYR cc_start: 0.8228 (m-80) cc_final: 0.7866 (m-80) REVERT: E 69 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8566 (mm-30) REVERT: E 91 LYS cc_start: 0.8763 (mttm) cc_final: 0.8356 (mttt) REVERT: F 78 GLN cc_start: 0.8294 (pm20) cc_final: 0.7855 (pm20) REVERT: F 83 ASP cc_start: 0.8721 (m-30) cc_final: 0.8325 (m-30) REVERT: G 86 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8262 (mt-10) REVERT: G 105 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.6316 (mtt90) REVERT: J 33 GLU cc_start: 0.8914 (mp0) cc_final: 0.8510 (mp0) REVERT: J 95 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8171 (ptp-110) REVERT: J 162 ARG cc_start: 0.8841 (tmm-80) cc_final: 0.8081 (tpm170) outliers start: 52 outliers final: 44 residues processed: 228 average time/residue: 0.1248 time to fit residues: 43.7274 Evaluate side-chains 234 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 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 C residue 55 TRP 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 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 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 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: 2.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 171 optimal weight: 0.0870 chunk 145 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.084329 restraints weight = 36865.490| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 3.14 r_work: 0.3307 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17674 Z= 0.130 Angle : 0.640 17.257 23981 Z= 0.322 Chirality : 0.044 0.496 2737 Planarity : 0.004 0.044 3007 Dihedral : 7.053 85.128 2429 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.38 % Allowed : 18.11 % Favored : 79.51 % 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: -0.87 (0.19), residues: 2061 helix: 1.16 (0.22), residues: 600 sheet: 0.29 (0.23), residues: 543 loop : -2.42 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 48 TYR 0.019 0.001 TYR J 160 PHE 0.013 0.001 PHE A 708 TRP 0.058 0.002 TRP B 166 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00293 (17664) covalent geometry : angle 0.61506 (23956) SS BOND : bond 0.00090 ( 5) SS BOND : angle 0.48608 ( 10) hydrogen bonds : bond 0.03456 ( 718) hydrogen bonds : angle 4.61791 ( 2082) link_NAG-ASN : bond 0.01419 ( 5) link_NAG-ASN : angle 7.06082 ( 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 240 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8866 (mmm) cc_final: 0.8624 (tpp) REVERT: C 49 GLU cc_start: 0.7721 (tp30) cc_final: 0.7259 (pt0) REVERT: E 24 TYR cc_start: 0.8795 (t80) cc_final: 0.8554 (t80) REVERT: E 69 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 91 LYS cc_start: 0.8755 (mttm) cc_final: 0.8337 (mttt) REVERT: F 78 GLN cc_start: 0.8247 (pm20) cc_final: 0.7818 (pm20) REVERT: F 83 ASP cc_start: 0.8692 (m-30) cc_final: 0.8313 (m-30) REVERT: G 86 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8008 (mt-10) REVERT: J 33 GLU cc_start: 0.8909 (mp0) cc_final: 0.8498 (mp0) REVERT: J 95 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8137 (ptp-110) REVERT: J 162 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8070 (tpm170) outliers start: 45 outliers final: 39 residues processed: 224 average time/residue: 0.1314 time to fit residues: 45.1912 Evaluate side-chains 224 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 607 MET 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 65 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 GLU 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 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 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: 0.7980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 158 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 126 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.124838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.084642 restraints weight = 36718.568| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.15 r_work: 0.3314 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17674 Z= 0.133 Angle : 0.650 21.125 23981 Z= 0.326 Chirality : 0.044 0.402 2737 Planarity : 0.004 0.044 3007 Dihedral : 7.020 85.332 2429 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.27 % Allowed : 18.27 % Favored : 79.46 % 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: -0.84 (0.19), residues: 2061 helix: 1.19 (0.22), residues: 595 sheet: 0.32 (0.23), residues: 544 loop : -2.40 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 48 TYR 0.016 0.001 TYR B 108 PHE 0.013 0.001 PHE A 708 TRP 0.052 0.002 TRP A 35 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00303 (17664) covalent geometry : angle 0.61945 (23956) SS BOND : bond 0.00087 ( 5) SS BOND : angle 0.48378 ( 10) hydrogen bonds : bond 0.03445 ( 718) hydrogen bonds : angle 4.60337 ( 2082) link_NAG-ASN : bond 0.01375 ( 5) link_NAG-ASN : angle 7.90078 ( 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 225 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8848 (mmm) cc_final: 0.8609 (tpp) REVERT: C 49 GLU cc_start: 0.7764 (tp30) cc_final: 0.7288 (pt0) REVERT: E 69 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8521 (mm-30) REVERT: E 91 LYS cc_start: 0.8753 (mttm) cc_final: 0.8334 (mttt) REVERT: E 92 GLU cc_start: 0.8834 (mp0) cc_final: 0.8606 (mp0) REVERT: F 78 GLN cc_start: 0.8266 (pm20) cc_final: 0.7842 (pm20) REVERT: F 83 ASP cc_start: 0.8678 (m-30) cc_final: 0.8298 (m-30) REVERT: G 86 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8050 (mt-10) REVERT: J 33 GLU cc_start: 0.8907 (mp0) cc_final: 0.8483 (mp0) REVERT: J 95 ARG cc_start: 0.8400 (ptp-110) cc_final: 0.8157 (ptp-110) REVERT: J 162 ARG cc_start: 0.8825 (tmm-80) cc_final: 0.8064 (tpm170) outliers start: 43 outliers final: 41 residues processed: 212 average time/residue: 0.1234 time to fit residues: 40.5961 Evaluate side-chains 223 residues out of total 1910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 148 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 ILE 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 622 VAL 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 55 TRP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 77 GLU 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 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 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 62 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 203 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3981 r_free = 0.3981 target = 0.124697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084463 restraints weight = 36764.143| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.14 r_work: 0.3310 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17674 Z= 0.140 Angle : 0.654 20.625 23981 Z= 0.327 Chirality : 0.044 0.358 2737 Planarity : 0.004 0.046 3007 Dihedral : 7.018 85.003 2429 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.53 % Allowed : 18.22 % Favored : 79.25 % 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: -0.81 (0.19), residues: 2061 helix: 1.17 (0.22), residues: 601 sheet: 0.38 (0.23), residues: 544 loop : -2.39 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 48 TYR 0.023 0.001 TYR E 24 PHE 0.014 0.001 PHE A 708 TRP 0.055 0.002 TRP A 35 HIS 0.006 0.001 HIS F 82 Details of bonding type rmsd covalent geometry : bond 0.00323 (17664) covalent geometry : angle 0.62377 (23956) SS BOND : bond 0.00103 ( 5) SS BOND : angle 0.45514 ( 10) hydrogen bonds : bond 0.03461 ( 718) hydrogen bonds : angle 4.60402 ( 2082) link_NAG-ASN : bond 0.01445 ( 5) link_NAG-ASN : angle 7.94200 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.82 seconds wall clock time: 83 minutes 46.68 seconds (5026.68 seconds total)