Starting phenix.real_space_refine on Sun Sep 29 20:32:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jz2_22528/09_2024/7jz2_22528_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.172 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: 7 Type Number sf(0) Gaussians Fe 30 7.16 5 P 9 5.49 5 S 186 5.16 5 Na 3 4.78 5 C 14520 2.51 5 N 3921 2.21 5 O 4197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "C" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'HEM': 1, 'UQ2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4298 SG CYS B 75 79.724 104.845 57.102 1.00 25.54 S ATOM 4931 SG CYS B 155 76.201 91.973 66.627 1.00 22.51 S ATOM 5407 SG CYS B 216 71.860 97.703 66.077 1.00 23.12 S ATOM 4892 SG CYS B 149 73.317 91.509 61.104 1.00 26.11 S ATOM 4914 SG CYS B 152 78.004 96.628 62.112 1.00 22.99 S ATOM 4956 SG CYS B 159 78.230 89.297 74.675 1.00 23.87 S Restraints were copied for chains: E, I, F, J, G, K, H, L Time building chain proxies: 11.87, per 1000 atoms: 0.52 Number of scatterers: 22866 At special positions: 0 Unit cell: (131.76, 135, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 30 26.01 S 186 16.00 P 9 15.00 Na 3 11.00 O 4197 8.00 N 3921 7.00 C 14520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 159 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 212 " pdb=" F3S F 303 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 159 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 212 " pdb=" F3S J 303 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 159 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 212 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 75 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 55 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 60 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 75 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 55 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 60 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 75 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 55 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 60 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 216 " pdb=" SF4 F 302 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 216 " pdb=" SF4 J 302 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 155 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 216 " Number of angles added : 75 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 52.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 103 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 140 through 157 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.522A pdb=" N ALA B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'E' and resid 16 through 29 Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 140 through 157 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 220 through 230 Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.858A pdb=" N LEU E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 427 Processing helix chain 'E' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU E 444 " --> pdb=" O SER E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'E' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL E 511 " --> pdb=" O ASN E 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.891A pdb=" N LEU F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 117 removed outlier: 3.786A pdb=" N ILE F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 142 Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.684A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 66 Processing helix chain 'G' and resid 67 through 97 Processing helix chain 'G' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 40 Processing helix chain 'H' and resid 44 through 52 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'I' and resid 16 through 29 Processing helix chain 'I' and resid 44 through 49 Processing helix chain 'I' and resid 64 through 76 removed outlier: 4.276A pdb=" N HIS I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 103 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 140 through 157 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 220 through 230 Processing helix chain 'I' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU I 406 " --> pdb=" O GLY I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 427 Processing helix chain 'I' and resid 433 through 450 removed outlier: 3.970A pdb=" N VAL I 437 " --> pdb=" O SER I 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU I 444 " --> pdb=" O SER I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 Processing helix chain 'I' and resid 476 through 495 Processing helix chain 'I' and resid 507 through 533 removed outlier: 3.679A pdb=" N VAL I 511 " --> pdb=" O ASN I 507 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 44 Processing helix chain 'J' and resid 75 through 77 No H-bonds generated for 'chain 'J' and resid 75 through 77' Processing helix chain 'J' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU J 82 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 142 Processing helix chain 'J' and resid 155 through 158 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'J' and resid 171 through 184 Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 216 Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 54 removed outlier: 3.955A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 67 through 97 Processing helix chain 'K' and resid 102 through 129 removed outlier: 3.504A pdb=" N LEU K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 Processing helix chain 'L' and resid 44 through 52 Processing helix chain 'L' and resid 54 through 84 Processing helix chain 'L' and resid 86 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG A 6 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 177 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS A 171 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 179 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 169 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 181 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.910A pdb=" N THR A 159 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 10 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 36 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA A 368 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL A 233 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.623A pdb=" N GLN A 240 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE A 360 " --> pdb=" O CYS A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 25 Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG E 6 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 177 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS E 171 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY E 179 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU E 169 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 181 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR E 159 " --> pdb=" O CYS E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA E 10 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU E 36 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 12 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA E 368 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'E' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL E 233 " --> pdb=" O TYR E 559 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN E 240 " --> pdb=" O HIS E 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 360 through 361 removed outlier: 5.521A pdb=" N ILE E 360 " --> pdb=" O CYS E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 537 Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 25 Processing sheet with id=AB8, first strand: chain 'I' and resid 5 through 7 removed outlier: 6.298A pdb=" N ARG I 6 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 177 " --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS I 171 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY I 179 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU I 169 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR I 181 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR I 159 " --> pdb=" O CYS I 33 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA I 10 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 36 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL I 12 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA I 368 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'I' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL I 233 " --> pdb=" O TYR I 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN I 240 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE I 360 " --> pdb=" O CYS I 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'J' and resid 19 through 25 1221 hydrogen bonds defined for protein. 3519 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: 7.17 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 23046 1.74 - 2.29: 321 2.29 - 2.84: 9 2.84 - 3.40: 0 3.40 - 3.95: 9 Bond restraints: 23385 Sorted by residual: bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.951 -1.651 2.00e-02 2.50e+03 6.81e+03 bond pdb=" S2 F3S F 303 " pdb="FE3 F3S F 303 " ideal model delta sigma weight residual 2.300 3.950 -1.650 2.00e-02 2.50e+03 6.81e+03 ... (remaining 23380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.99: 31725 9.99 - 19.97: 15 19.97 - 29.96: 3 29.96 - 39.95: 21 39.95 - 49.93: 6 Bond angle restraints: 31770 Sorted by residual: angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.83 49.92 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S3 F3S J 303 " pdb="FE1 F3S J 303 " pdb=" S4 F3S J 303 " ideal model delta sigma weight residual 112.59 64.30 48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S3 F3S F 303 " pdb="FE1 F3S F 303 " pdb=" S4 F3S F 303 " ideal model delta sigma weight residual 112.59 64.31 48.28 3.00e+00 1.11e-01 2.59e+02 ... (remaining 31765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 12488 16.63 - 33.25: 972 33.25 - 49.88: 292 49.88 - 66.50: 90 66.50 - 83.13: 36 Dihedral angle restraints: 13878 sinusoidal: 5664 harmonic: 8214 Sorted by residual: dihedral pdb=" C2D HEM K 201 " pdb=" C3D HEM K 201 " pdb=" CAD HEM K 201 " pdb=" CBD HEM K 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.81 -67.81 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.71 -67.71 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM G 201 " pdb=" C3D HEM G 201 " pdb=" CAD HEM G 201 " pdb=" CBD HEM G 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.70 -67.70 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.605: 3504 3.605 - 7.210: 0 7.210 - 10.816: 0 10.816 - 14.421: 0 14.421 - 18.026: 3 Chirality restraints: 3507 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.26 18.03 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S F 303 " pdb="FE1 F3S F 303 " pdb="FE3 F3S F 303 " pdb="FE4 F3S F 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S J 303 " pdb="FE1 F3S J 303 " pdb="FE3 F3S J 303 " pdb="FE4 F3S J 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 ... (remaining 3504 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 113 " 0.007 2.00e-02 2.50e+03 5.32e-03 7.07e-01 pdb=" CG TRP L 113 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP L 113 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 109 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C PHE D 109 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE D 109 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL D 110 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 109 " -0.004 2.00e-02 2.50e+03 8.36e-03 6.98e-01 pdb=" C PHE L 109 " 0.014 2.00e-02 2.50e+03 pdb=" O PHE L 109 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL L 110 " -0.005 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 395 2.64 - 3.20: 22686 3.20 - 3.77: 36860 3.77 - 4.33: 52080 4.33 - 4.90: 85072 Nonbonded interactions: 197093 Sorted by model distance: nonbonded pdb=" OD1 ASP J 46 " pdb=" OG SER J 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP F 46 " pdb=" OG SER F 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP B 46 " pdb=" OG SER B 48 " model vdw 2.070 3.040 nonbonded pdb=" NH1 ARG J 205 " pdb=" OD1 ASP L 82 " model vdw 2.114 3.120 nonbonded pdb=" OE1 GLU E 94 " pdb=" NH1 ARG E 413 " model vdw 2.115 3.120 ... (remaining 197088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'C' and resid 5 through 129) selection = (chain 'G' and resid 5 through 129) selection = (chain 'K' and resid 5 through 129) } ncs_group { reference = (chain 'D' and resid 3 through 115) selection = (chain 'H' and resid 3 through 115) selection = (chain 'L' and resid 3 through 115) } 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 51.050 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.033 1.702 23385 Z= 2.358 Angle : 1.281 49.935 31770 Z= 0.531 Chirality : 0.528 18.026 3507 Planarity : 0.002 0.019 4029 Dihedral : 14.261 83.128 8604 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 35.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.38 % Allowed : 2.39 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.14), residues: 2841 helix: 0.25 (0.13), residues: 1404 sheet: -3.15 (0.28), residues: 165 loop : -3.27 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 113 HIS 0.003 0.000 HIS E 147 PHE 0.010 0.001 PHE E 411 TYR 0.011 0.001 TYR B 8 ARG 0.002 0.000 ARG E 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 598 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6830 (mtp) cc_final: 0.6593 (mtp) REVERT: A 227 ILE cc_start: 0.7298 (mt) cc_final: 0.6841 (mt) REVERT: A 236 MET cc_start: 0.7449 (mmp) cc_final: 0.6907 (mmp) REVERT: A 443 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 1 MET cc_start: 0.5214 (ptt) cc_final: 0.4115 (mpp) REVERT: B 41 GLN cc_start: 0.6981 (tt0) cc_final: 0.6644 (mt0) REVERT: D 77 TRP cc_start: 0.7643 (t60) cc_final: 0.7348 (t-100) REVERT: E 209 TYR cc_start: 0.7159 (m-80) cc_final: 0.6879 (m-80) REVERT: E 227 ILE cc_start: 0.7479 (mt) cc_final: 0.7077 (mt) REVERT: E 568 ARG cc_start: 0.7382 (mtt180) cc_final: 0.7083 (mtt180) REVERT: F 9 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: F 232 MET cc_start: 0.7783 (mtp) cc_final: 0.7388 (mtp) REVERT: G 93 MET cc_start: 0.6906 (mtp) cc_final: 0.6495 (mtp) REVERT: H 56 PHE cc_start: 0.7072 (t80) cc_final: 0.5613 (m-80) REVERT: I 227 ILE cc_start: 0.7064 (mt) cc_final: 0.6598 (mt) REVERT: I 420 GLN cc_start: 0.6644 (tp40) cc_final: 0.6319 (tp40) REVERT: I 446 ARG cc_start: 0.7473 (tmm160) cc_final: 0.7234 (tmm160) REVERT: I 471 PHE cc_start: 0.6564 (m-80) cc_final: 0.6330 (m-80) REVERT: I 568 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: J 67 MET cc_start: 0.6782 (mtm) cc_final: 0.6422 (mtm) REVERT: J 235 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6774 (mm110) REVERT: L 45 TYR cc_start: 0.7261 (t80) cc_final: 0.7059 (t80) REVERT: L 56 PHE cc_start: 0.7054 (t80) cc_final: 0.5779 (m-80) outliers start: 33 outliers final: 7 residues processed: 626 average time/residue: 1.2371 time to fit residues: 888.2893 Evaluate side-chains 492 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 485 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 352 THR Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 173 GLN A 214 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 450 ASN A 452 ASN A 531 ASN B 71 ASN B 123 ASN B 133 HIS B 207 HIS B 211 ASN B 237 ASN C 91 HIS D 14 HIS D 94 GLN E 50 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 173 GLN E 214 ASN E 450 ASN E 452 ASN E 496 ASN E 518 ASN E 531 ASN F 71 ASN F 207 HIS F 211 ASN F 228 HIS F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS H 14 HIS ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 143 HIS I 214 ASN I 367 GLN ** I 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN I 452 ASN I 518 ASN I 531 ASN J 71 ASN J 123 ASN J 133 HIS J 207 HIS J 228 HIS J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS L 14 HIS L 94 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.186 23385 Z= 0.413 Angle : 1.279 67.553 31770 Z= 0.497 Chirality : 0.062 1.508 3507 Planarity : 0.005 0.047 4029 Dihedral : 9.274 77.243 3437 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.40 % Allowed : 13.02 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2841 helix: 1.17 (0.13), residues: 1434 sheet: -2.79 (0.28), residues: 189 loop : -2.55 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 113 HIS 0.006 0.002 HIS H 14 PHE 0.025 0.002 PHE D 60 TYR 0.024 0.002 TYR B 8 ARG 0.005 0.001 ARG I 578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 531 time to evaluate : 2.424 Fit side-chains REVERT: A 225 MET cc_start: 0.6773 (mtp) cc_final: 0.6547 (mtp) REVERT: A 471 PHE cc_start: 0.7129 (m-80) cc_final: 0.6648 (m-80) REVERT: A 490 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 568 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6981 (mtt180) REVERT: B 1 MET cc_start: 0.5485 (ptt) cc_final: 0.5061 (ptt) REVERT: B 2 ARG cc_start: 0.6619 (ptm160) cc_final: 0.6317 (ptm160) REVERT: B 33 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6254 (ptt) REVERT: C 101 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6896 (mt-10) REVERT: D 77 TRP cc_start: 0.7713 (t60) cc_final: 0.7353 (t-100) REVERT: E 31 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6552 (mp10) REVERT: E 227 ILE cc_start: 0.7535 (mt) cc_final: 0.7273 (mt) REVERT: E 352 THR cc_start: 0.7881 (t) cc_final: 0.7539 (m) REVERT: E 449 ASN cc_start: 0.6485 (m-40) cc_final: 0.6112 (m-40) REVERT: F 33 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5882 (ptt) REVERT: F 102 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7267 (t70) REVERT: G 123 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7418 (mp) REVERT: H 56 PHE cc_start: 0.7287 (t80) cc_final: 0.5757 (m-80) REVERT: I 3 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7685 (mp) REVERT: I 227 ILE cc_start: 0.7341 (mt) cc_final: 0.7076 (mt) REVERT: I 517 ASP cc_start: 0.6933 (m-30) cc_final: 0.6707 (m-30) REVERT: I 520 MET cc_start: 0.8467 (tpt) cc_final: 0.8061 (tpt) REVERT: J 67 MET cc_start: 0.6975 (mtm) cc_final: 0.6701 (mtm) REVERT: J 102 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7201 (t70) REVERT: J 235 GLN cc_start: 0.7075 (mm-40) cc_final: 0.6837 (mm110) REVERT: K 101 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: L 56 PHE cc_start: 0.7288 (t80) cc_final: 0.5892 (m-80) REVERT: L 77 TRP cc_start: 0.7594 (t60) cc_final: 0.7285 (t-100) outliers start: 105 outliers final: 37 residues processed: 574 average time/residue: 1.2039 time to fit residues: 796.7901 Evaluate side-chains 535 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 489 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN A 218 ASN A 452 ASN A 518 ASN B 71 ASN B 237 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 452 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 173 GLN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN J 71 ASN J 109 GLN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 23385 Z= 0.238 Angle : 1.108 85.725 31770 Z= 0.431 Chirality : 0.058 1.467 3507 Planarity : 0.005 0.049 4029 Dihedral : 8.286 77.307 3433 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.56 % Allowed : 16.42 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2841 helix: 1.62 (0.13), residues: 1434 sheet: -2.27 (0.31), residues: 189 loop : -2.15 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 113 HIS 0.005 0.001 HIS E 143 PHE 0.016 0.001 PHE D 60 TYR 0.027 0.002 TYR H 45 ARG 0.010 0.001 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 521 time to evaluate : 2.316 Fit side-chains REVERT: A 471 PHE cc_start: 0.7028 (m-80) cc_final: 0.6609 (m-80) REVERT: A 490 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7160 (mp) REVERT: B 1 MET cc_start: 0.5459 (ptt) cc_final: 0.5157 (ptt) REVERT: B 2 ARG cc_start: 0.6556 (ptm160) cc_final: 0.6354 (ttt90) REVERT: C 123 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7415 (mp) REVERT: D 27 THR cc_start: 0.6204 (p) cc_final: 0.5783 (m) REVERT: E 210 GLN cc_start: 0.6608 (tt0) cc_final: 0.6169 (mt0) REVERT: E 227 ILE cc_start: 0.7480 (mt) cc_final: 0.7240 (mt) REVERT: E 352 THR cc_start: 0.7836 (t) cc_final: 0.7469 (m) REVERT: F 33 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5842 (ptt) REVERT: G 123 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7346 (mp) REVERT: I 227 ILE cc_start: 0.7348 (mt) cc_final: 0.7111 (mt) REVERT: I 520 MET cc_start: 0.8397 (tpt) cc_final: 0.7950 (tpt) REVERT: I 568 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.7028 (mtt-85) REVERT: J 67 MET cc_start: 0.6994 (mtm) cc_final: 0.6748 (mtm) REVERT: J 235 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6845 (mm110) REVERT: K 101 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: L 56 PHE cc_start: 0.7249 (t80) cc_final: 0.5858 (m-80) outliers start: 85 outliers final: 29 residues processed: 558 average time/residue: 1.2107 time to fit residues: 779.9299 Evaluate side-chains 525 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 491 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 4.9990 chunk 272 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN B 71 ASN B 211 ASN B 237 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 211 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN I 367 GLN I 452 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 23385 Z= 0.329 Angle : 1.136 84.354 31770 Z= 0.451 Chirality : 0.060 1.410 3507 Planarity : 0.005 0.049 4029 Dihedral : 8.091 78.236 3433 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.36 % Allowed : 18.09 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2841 helix: 1.57 (0.13), residues: 1434 sheet: -2.11 (0.32), residues: 189 loop : -2.14 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 113 HIS 0.007 0.002 HIS A 143 PHE 0.021 0.002 PHE L 60 TYR 0.040 0.002 TYR L 45 ARG 0.007 0.001 ARG I 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 509 time to evaluate : 2.514 Fit side-chains REVERT: A 490 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 568 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6995 (mtt180) REVERT: B 1 MET cc_start: 0.5210 (ptt) cc_final: 0.4929 (ptt) REVERT: B 2 ARG cc_start: 0.6517 (ptm160) cc_final: 0.6171 (ptm160) REVERT: B 9 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: C 101 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: C 123 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7430 (mp) REVERT: D 27 THR cc_start: 0.6363 (p) cc_final: 0.5978 (m) REVERT: E 50 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: E 210 GLN cc_start: 0.6646 (tt0) cc_final: 0.6190 (mt0) REVERT: E 227 ILE cc_start: 0.7470 (mt) cc_final: 0.7258 (mt) REVERT: F 33 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.5940 (ptt) REVERT: F 168 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7741 (mttt) REVERT: G 53 SER cc_start: 0.7531 (t) cc_final: 0.7246 (p) REVERT: G 119 VAL cc_start: 0.7752 (t) cc_final: 0.7550 (t) REVERT: G 123 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7374 (mp) REVERT: H 56 PHE cc_start: 0.7187 (t80) cc_final: 0.5709 (m-80) REVERT: I 227 ILE cc_start: 0.7381 (mt) cc_final: 0.7178 (mt) REVERT: I 480 MET cc_start: 0.7146 (mtm) cc_final: 0.6940 (mtt) REVERT: I 517 ASP cc_start: 0.7067 (m-30) cc_final: 0.6845 (m-30) REVERT: I 520 MET cc_start: 0.8413 (tpt) cc_final: 0.8058 (tpt) REVERT: J 2 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6403 (ptm-80) REVERT: K 101 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6741 (mt-10) REVERT: L 56 PHE cc_start: 0.7268 (t80) cc_final: 0.5867 (m-80) outliers start: 104 outliers final: 43 residues processed: 560 average time/residue: 1.2132 time to fit residues: 786.5365 Evaluate side-chains 540 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 488 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 0.0670 chunk 232 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 overall best weight: 4.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 71 ASN B 237 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 496 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 367 GLN I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 23385 Z= 0.336 Angle : 1.155 84.500 31770 Z= 0.458 Chirality : 0.060 1.410 3507 Planarity : 0.005 0.055 4029 Dihedral : 8.120 77.455 3432 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.36 % Allowed : 20.23 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2841 helix: 1.53 (0.13), residues: 1434 sheet: -2.01 (0.31), residues: 219 loop : -2.13 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 113 HIS 0.007 0.002 HIS A 143 PHE 0.028 0.002 PHE L 52 TYR 0.032 0.002 TYR L 45 ARG 0.008 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 487 time to evaluate : 2.470 Fit side-chains REVERT: A 490 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 568 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7031 (mtt180) REVERT: B 1 MET cc_start: 0.5234 (ptt) cc_final: 0.4928 (ptt) REVERT: B 2 ARG cc_start: 0.6471 (ptm160) cc_final: 0.6113 (ptm160) REVERT: B 9 ARG cc_start: 0.7492 (mmm-85) cc_final: 0.7263 (mmm-85) REVERT: C 101 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: C 123 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7454 (mp) REVERT: D 27 THR cc_start: 0.6453 (p) cc_final: 0.6122 (m) REVERT: E 50 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: E 210 GLN cc_start: 0.6694 (tt0) cc_final: 0.6261 (mt0) REVERT: E 398 ASN cc_start: 0.7202 (OUTLIER) cc_final: 0.6938 (t0) REVERT: E 449 ASN cc_start: 0.6166 (m-40) cc_final: 0.5829 (m-40) REVERT: E 574 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6830 (pp20) REVERT: F 33 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5973 (ptt) REVERT: F 168 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7784 (mtmt) REVERT: G 123 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7283 (mp) REVERT: H 56 PHE cc_start: 0.7214 (t80) cc_final: 0.5707 (m-80) REVERT: I 517 ASP cc_start: 0.7050 (m-30) cc_final: 0.6833 (m-30) REVERT: I 520 MET cc_start: 0.8373 (tpt) cc_final: 0.8080 (tpt) REVERT: I 568 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7226 (mtt-85) REVERT: I 574 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6703 (pp20) REVERT: J 2 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6332 (ttt90) REVERT: J 9 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7219 (mmm-85) REVERT: J 102 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7046 (t70) REVERT: J 235 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6478 (mm-40) REVERT: K 101 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: L 56 PHE cc_start: 0.7245 (t80) cc_final: 0.5865 (m-80) outliers start: 104 outliers final: 50 residues processed: 540 average time/residue: 1.2055 time to fit residues: 754.2142 Evaluate side-chains 537 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 472 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN B 71 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 367 GLN I 452 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23385 Z= 0.213 Angle : 1.110 84.441 31770 Z= 0.428 Chirality : 0.058 1.417 3507 Planarity : 0.004 0.053 4029 Dihedral : 7.539 80.003 3431 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.52 % Allowed : 21.86 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2841 helix: 1.91 (0.14), residues: 1434 sheet: -1.90 (0.32), residues: 225 loop : -1.93 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 113 HIS 0.004 0.001 HIS A 143 PHE 0.017 0.001 PHE L 52 TYR 0.031 0.001 TYR L 45 ARG 0.007 0.001 ARG I 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 509 time to evaluate : 2.332 Fit side-chains REVERT: A 196 ARG cc_start: 0.6688 (mtp180) cc_final: 0.6420 (mtp180) REVERT: A 568 ARG cc_start: 0.7245 (mtt180) cc_final: 0.6921 (mtt180) REVERT: B 2 ARG cc_start: 0.6344 (ptm160) cc_final: 0.6083 (ptm160) REVERT: B 9 ARG cc_start: 0.7432 (mmm-85) cc_final: 0.7166 (mmm-85) REVERT: B 142 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6288 (mppt) REVERT: C 93 MET cc_start: 0.6521 (mtp) cc_final: 0.6292 (mtt) REVERT: D 27 THR cc_start: 0.6289 (p) cc_final: 0.5973 (m) REVERT: E 50 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7685 (mt0) REVERT: E 210 GLN cc_start: 0.6573 (tt0) cc_final: 0.6247 (mt0) REVERT: E 405 LEU cc_start: 0.6905 (mm) cc_final: 0.6603 (mt) REVERT: E 545 PHE cc_start: 0.6318 (m-10) cc_final: 0.6098 (m-10) REVERT: E 574 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6782 (pp20) REVERT: F 33 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5963 (ptt) REVERT: F 168 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7640 (mttt) REVERT: G 31 ARG cc_start: 0.6927 (ttm170) cc_final: 0.6623 (ttm-80) REVERT: I 520 MET cc_start: 0.8345 (tpt) cc_final: 0.8071 (tpt) REVERT: I 568 ARG cc_start: 0.7564 (mtt180) cc_final: 0.7140 (mtt180) REVERT: I 574 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: J 2 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.6211 (ttt90) REVERT: J 9 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7207 (mmm-85) REVERT: J 235 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6425 (mm-40) REVERT: L 56 PHE cc_start: 0.7167 (t80) cc_final: 0.5798 (m-80) outliers start: 84 outliers final: 34 residues processed: 553 average time/residue: 1.2185 time to fit residues: 776.4130 Evaluate side-chains 529 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 486 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 228 HIS B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 23385 Z= 0.370 Angle : 1.181 84.836 31770 Z= 0.470 Chirality : 0.061 1.390 3507 Planarity : 0.005 0.064 4029 Dihedral : 7.928 78.946 3426 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.85 % Allowed : 22.86 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2841 helix: 1.54 (0.13), residues: 1440 sheet: -1.70 (0.32), residues: 219 loop : -2.03 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 113 HIS 0.007 0.002 HIS E 45 PHE 0.027 0.002 PHE L 52 TYR 0.037 0.003 TYR L 45 ARG 0.010 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 492 time to evaluate : 2.634 Fit side-chains REVERT: A 196 ARG cc_start: 0.6705 (mtp180) cc_final: 0.6416 (mtp180) REVERT: A 490 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 568 ARG cc_start: 0.7375 (mtt180) cc_final: 0.7029 (mtt-85) REVERT: B 2 ARG cc_start: 0.6412 (ptm160) cc_final: 0.6064 (ptm160) REVERT: C 101 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: D 27 THR cc_start: 0.6383 (p) cc_final: 0.6093 (m) REVERT: E 50 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: E 210 GLN cc_start: 0.6755 (tt0) cc_final: 0.6342 (mt0) REVERT: E 398 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6979 (t0) REVERT: E 449 ASN cc_start: 0.6102 (m-40) cc_final: 0.5833 (m-40) REVERT: E 574 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: F 142 LYS cc_start: 0.6864 (mppt) cc_final: 0.6619 (mttp) REVERT: F 168 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7797 (mtmt) REVERT: G 46 TRP cc_start: 0.7040 (t60) cc_final: 0.6800 (t60) REVERT: G 123 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7307 (mp) REVERT: H 56 PHE cc_start: 0.7188 (t80) cc_final: 0.5678 (m-80) REVERT: I 196 ARG cc_start: 0.6924 (mtp85) cc_final: 0.6667 (mtp85) REVERT: I 520 MET cc_start: 0.8371 (tpt) cc_final: 0.8088 (tpt) REVERT: I 568 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7324 (mtt-85) REVERT: I 584 LYS cc_start: 0.6744 (mtpp) cc_final: 0.6448 (mmmm) REVERT: J 9 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7148 (mmm-85) REVERT: J 102 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.6856 (t70) REVERT: K 101 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6850 (mt-10) REVERT: L 56 PHE cc_start: 0.7234 (t80) cc_final: 0.5846 (m-80) outliers start: 92 outliers final: 55 residues processed: 539 average time/residue: 1.1923 time to fit residues: 746.6479 Evaluate side-chains 551 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 486 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 71 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23385 Z= 0.246 Angle : 1.140 84.679 31770 Z= 0.446 Chirality : 0.059 1.406 3507 Planarity : 0.005 0.059 4029 Dihedral : 7.625 80.476 3426 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.10 % Allowed : 23.79 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2841 helix: 1.77 (0.14), residues: 1440 sheet: -1.77 (0.32), residues: 225 loop : -1.90 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 113 HIS 0.005 0.001 HIS A 68 PHE 0.022 0.002 PHE L 60 TYR 0.037 0.002 TYR L 45 ARG 0.013 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 499 time to evaluate : 2.585 Fit side-chains REVERT: A 196 ARG cc_start: 0.6706 (mtp180) cc_final: 0.6498 (mtp180) REVERT: A 490 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7203 (mp) REVERT: B 2 ARG cc_start: 0.6355 (ptm160) cc_final: 0.6073 (ptm160) REVERT: B 9 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: C 101 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: D 27 THR cc_start: 0.6327 (p) cc_final: 0.6048 (m) REVERT: E 50 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: E 210 GLN cc_start: 0.6618 (tt0) cc_final: 0.6274 (mt0) REVERT: E 405 LEU cc_start: 0.6783 (mm) cc_final: 0.6503 (mt) REVERT: E 449 ASN cc_start: 0.5984 (m-40) cc_final: 0.5620 (m-40) REVERT: E 490 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7413 (mp) REVERT: E 568 ARG cc_start: 0.7287 (mtt180) cc_final: 0.7086 (mtt-85) REVERT: E 574 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: F 168 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7679 (mttt) REVERT: G 46 TRP cc_start: 0.7006 (t60) cc_final: 0.6776 (t60) REVERT: H 56 PHE cc_start: 0.7198 (t80) cc_final: 0.5701 (m-80) REVERT: I 196 ARG cc_start: 0.6873 (mtp85) cc_final: 0.6641 (mtp85) REVERT: I 520 MET cc_start: 0.8337 (tpt) cc_final: 0.7969 (tpt) REVERT: I 531 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: I 568 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7266 (mtt180) REVERT: I 574 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: I 584 LYS cc_start: 0.6768 (mtpp) cc_final: 0.6455 (mmmm) REVERT: J 9 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7245 (mmm-85) REVERT: K 101 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6668 (mt-10) REVERT: L 56 PHE cc_start: 0.7178 (t80) cc_final: 0.5820 (m-80) outliers start: 74 outliers final: 46 residues processed: 538 average time/residue: 1.2009 time to fit residues: 747.1576 Evaluate side-chains 532 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 476 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 240 GLN Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 9.9990 chunk 260 optimal weight: 0.1980 chunk 237 optimal weight: 0.0770 chunk 253 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 198 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 228 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 252 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN E 64 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 218 ASN I 470 ASN I 531 ASN J 71 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23385 Z= 0.206 Angle : 1.118 84.626 31770 Z= 0.435 Chirality : 0.058 1.416 3507 Planarity : 0.005 0.055 4029 Dihedral : 7.192 82.944 3426 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.22 % Allowed : 24.92 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.16), residues: 2841 helix: 2.00 (0.14), residues: 1440 sheet: -1.62 (0.32), residues: 225 loop : -1.80 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 113 HIS 0.006 0.001 HIS A 68 PHE 0.020 0.001 PHE E 471 TYR 0.038 0.001 TYR L 45 ARG 0.009 0.001 ARG I 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 499 time to evaluate : 2.636 Fit side-chains REVERT: A 196 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6489 (mtp180) REVERT: B 9 ARG cc_start: 0.7396 (mmm-85) cc_final: 0.7128 (mmm-85) REVERT: B 41 GLN cc_start: 0.7169 (tt0) cc_final: 0.6647 (mt0) REVERT: C 93 MET cc_start: 0.6497 (mtp) cc_final: 0.6293 (mtt) REVERT: C 101 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: D 27 THR cc_start: 0.6241 (p) cc_final: 0.5924 (m) REVERT: D 77 TRP cc_start: 0.7675 (t60) cc_final: 0.7203 (t-100) REVERT: E 28 GLN cc_start: 0.6408 (tm-30) cc_final: 0.6175 (tm-30) REVERT: E 210 GLN cc_start: 0.6387 (tt0) cc_final: 0.6109 (mt0) REVERT: E 568 ARG cc_start: 0.7277 (mtt180) cc_final: 0.7068 (mtt-85) REVERT: E 574 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: I 196 ARG cc_start: 0.6857 (mtp85) cc_final: 0.6623 (mtp85) REVERT: I 520 MET cc_start: 0.8330 (tpt) cc_final: 0.8091 (tpt) REVERT: I 568 ARG cc_start: 0.7569 (mtt180) cc_final: 0.7167 (mtt180) REVERT: I 574 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6744 (pp20) REVERT: J 235 GLN cc_start: 0.6530 (OUTLIER) cc_final: 0.6297 (mm110) REVERT: L 56 PHE cc_start: 0.7169 (t80) cc_final: 0.5775 (m-80) outliers start: 53 outliers final: 32 residues processed: 529 average time/residue: 1.1299 time to fit residues: 695.5496 Evaluate side-chains 515 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 479 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 280 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 71 ASN B 237 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN F 71 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 23385 Z= 0.220 Angle : 1.129 84.719 31770 Z= 0.441 Chirality : 0.058 1.413 3507 Planarity : 0.005 0.054 4029 Dihedral : 7.104 83.762 3426 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 25.75 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2841 helix: 2.02 (0.14), residues: 1440 sheet: -1.47 (0.33), residues: 225 loop : -1.75 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 113 HIS 0.006 0.001 HIS A 68 PHE 0.020 0.001 PHE E 471 TYR 0.041 0.002 TYR L 45 ARG 0.010 0.001 ARG I 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 487 time to evaluate : 2.374 Fit side-chains REVERT: A 196 ARG cc_start: 0.6646 (mtp180) cc_final: 0.6428 (mtp180) REVERT: B 9 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.7123 (mmm160) REVERT: C 93 MET cc_start: 0.6501 (mtp) cc_final: 0.6295 (mtt) REVERT: D 27 THR cc_start: 0.6243 (p) cc_final: 0.5923 (m) REVERT: D 77 TRP cc_start: 0.7621 (t60) cc_final: 0.7198 (t-100) REVERT: E 210 GLN cc_start: 0.6341 (tt0) cc_final: 0.6091 (mt0) REVERT: E 568 ARG cc_start: 0.7289 (mtt180) cc_final: 0.7058 (mtt-85) REVERT: E 574 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6770 (pp20) REVERT: I 130 GLN cc_start: 0.6323 (mm-40) cc_final: 0.5867 (tp-100) REVERT: I 520 MET cc_start: 0.8295 (tpt) cc_final: 0.7954 (tpt) REVERT: I 568 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7169 (mtt180) REVERT: I 574 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6745 (pp20) REVERT: J 235 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6421 (mm110) REVERT: L 56 PHE cc_start: 0.7161 (t80) cc_final: 0.5772 (m-80) outliers start: 47 outliers final: 30 residues processed: 509 average time/residue: 1.1819 time to fit residues: 700.4876 Evaluate side-chains 508 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 475 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 514 LEU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 455 ASP Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 20.0000 chunk 238 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 230 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 237 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN F 135 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.147546 restraints weight = 29967.789| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.11 r_work: 0.3702 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 23385 Z= 0.225 Angle : 1.134 84.736 31770 Z= 0.442 Chirality : 0.058 1.411 3507 Planarity : 0.004 0.054 4029 Dihedral : 7.076 83.912 3426 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.76 % Allowed : 26.26 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2841 helix: 2.02 (0.14), residues: 1440 sheet: -1.44 (0.33), residues: 225 loop : -1.72 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 113 HIS 0.006 0.001 HIS A 68 PHE 0.020 0.001 PHE E 471 TYR 0.043 0.002 TYR L 45 ARG 0.010 0.001 ARG I 578 =============================================================================== Job complete usr+sys time: 10893.74 seconds wall clock time: 189 minutes 51.52 seconds (11391.52 seconds total)