Starting phenix.real_space_refine on Thu Jun 19 05:05:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.map" model { file = "/net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu6_21906/06_2025/6wu6_21906.cif" } resolution = 3.6 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= 0.099 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 6 5.49 5 S 183 5.16 5 Na 3 4.78 5 C 13935 2.51 5 N 3783 2.21 5 O 4029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21969 Number of models: 1 Model: "" Number of chains: 7 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: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 836 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 456 SG CYS B 55 31.260 67.146 83.685 1.00 26.52 S ATOM 493 SG CYS B 60 35.168 66.107 84.128 1.00 34.02 S ATOM 591 SG CYS B 75 28.122 64.110 80.931 1.00 51.12 S ATOM 1207 SG CYS B 152 36.471 66.545 73.838 1.00 45.97 S ATOM 1224 SG CYS B 155 41.547 67.041 68.097 1.00 52.57 S ATOM 1185 SG CYS B 149 42.733 69.350 74.019 1.00 38.74 S ATOM 1700 SG CYS B 216 36.947 71.735 69.810 1.00 51.94 S ATOM 1674 SG CYS B 212 40.341 69.545 62.515 1.00 53.33 S ATOM 1628 SG CYS B 206 46.713 69.206 58.702 1.00 58.18 S ATOM 1249 SG CYS B 159 43.877 65.005 61.045 1.00 55.83 S Restraints were copied for chains: F, J, H, L, E, I, G, K Time building chain proxies: 11.28, per 1000 atoms: 0.51 Number of scatterers: 21969 At special positions: 0 Unit cell: (130.68, 136.08, 137.16, 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 183 16.00 P 6 15.00 Na 3 11.00 O 4029 8.00 N 3783 7.00 C 13935 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 212 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 159 " pdb=" F3S F 303 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 212 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 159 " pdb=" F3S J 303 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 212 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 159 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 60 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 75 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 60 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 75 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 60 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 75 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 216 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 F 302 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 216 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 155 " pdb=" SF4 J 302 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 216 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 155 " Number of angles added : 72 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 21 sheets defined 50.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.769A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.782A pdb=" N ALA B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.960A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 4.489A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.915A pdb=" N ALA B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 96 Processing helix chain 'C' and resid 102 through 129 Processing helix chain 'D' and resid 12 through 39 Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 107 through 116 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 153 through 158 removed outlier: 3.770A pdb=" N THR F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 184 removed outlier: 3.783A pdb=" N ALA F 178 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 removed outlier: 3.961A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 200 " --> pdb=" O GLY F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 216 removed outlier: 4.490A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 238 removed outlier: 3.916A pdb=" N ALA F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA G 26 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU G 59 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 96 Processing helix chain 'G' and resid 102 through 129 Processing helix chain 'H' and resid 12 through 39 Processing helix chain 'H' and resid 44 through 53 Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'J' and resid 34 through 43 Processing helix chain 'J' and resid 107 through 116 Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 153 through 158 removed outlier: 3.769A pdb=" N THR J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 184 removed outlier: 3.782A pdb=" N ALA J 178 " --> pdb=" O GLY J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 200 removed outlier: 3.959A pdb=" N ARG J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA J 200 " --> pdb=" O GLY J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 216 removed outlier: 4.490A pdb=" N SER J 214 " --> pdb=" O MET J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.915A pdb=" N ALA J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 230 " --> pdb=" O ILE J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K 31 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL K 39 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU K 59 " --> pdb=" O PRO K 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 96 Processing helix chain 'K' and resid 102 through 129 Processing helix chain 'L' and resid 12 through 39 Processing helix chain 'L' and resid 44 through 53 Processing helix chain 'L' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 113 Processing helix chain 'A' and resid 17 through 30 removed outlier: 3.922A pdb=" N ARG A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 removed outlier: 5.707A pdb=" N HIS A 45 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 4.188A pdb=" N SER A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.672A pdb=" N ILE A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 30 removed outlier: 3.922A pdb=" N ARG E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 removed outlier: 5.708A pdb=" N HIS E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 140 through 156 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 448 removed outlier: 4.189A pdb=" N SER E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 removed outlier: 3.672A pdb=" N ILE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 Processing helix chain 'E' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP E 517 " --> pdb=" O CYS E 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR E 522 " --> pdb=" O ASN E 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA E 523 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 526 " --> pdb=" O THR E 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 30 removed outlier: 3.923A pdb=" N ARG I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 48 removed outlier: 5.707A pdb=" N HIS I 45 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR I 46 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER I 76 " --> pdb=" O THR I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 101 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 140 through 156 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY I 412 " --> pdb=" O LEU I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 426 " --> pdb=" O SER I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 448 removed outlier: 4.188A pdb=" N SER I 440 " --> pdb=" O ASP I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 removed outlier: 3.671A pdb=" N ILE I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 494 Processing helix chain 'I' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP I 517 " --> pdb=" O CYS I 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU I 521 " --> pdb=" O ASP I 517 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR I 522 " --> pdb=" O ASN I 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 523 " --> pdb=" O LEU I 519 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 526 " --> pdb=" O THR I 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'A' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL A 5 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 193 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU A 7 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 195 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 9 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 197 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL A 5 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 193 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU A 7 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 195 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 9 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 197 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 28.062A pdb=" N VAL A 378 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS A 194 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL A 380 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG A 196 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 382 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 198 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA A 368 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.512A pdb=" N GLN A 240 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL E 5 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE E 193 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU E 7 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA E 195 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP E 9 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 197 " --> pdb=" O ASP E 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL E 5 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE E 193 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU E 7 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA E 195 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP E 9 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 197 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 28.062A pdb=" N VAL E 378 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS E 194 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL E 380 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG E 196 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY E 382 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 198 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA E 368 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'E' and resid 239 through 242 removed outlier: 6.512A pdb=" N GLN E 240 " --> pdb=" O HIS E 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 556 through 560 Processing sheet with id=AB8, first strand: chain 'I' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL I 5 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE I 193 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU I 7 " --> pdb=" O PHE I 193 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA I 195 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP I 9 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA I 197 " --> pdb=" O ASP I 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL I 5 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE I 193 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU I 7 " --> pdb=" O PHE I 193 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA I 195 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP I 9 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA I 197 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 28.063A pdb=" N VAL I 378 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS I 194 " --> pdb=" O VAL I 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL I 380 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG I 196 " --> pdb=" O VAL I 380 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY I 382 " --> pdb=" O ARG I 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR I 198 " --> pdb=" O GLY I 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA I 368 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 116 through 117 Processing sheet with id=AC2, first strand: chain 'I' and resid 239 through 242 removed outlier: 6.513A pdb=" N GLN I 240 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 556 through 560 1041 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.48 Time building geometry restraints manager: 6.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 22140 1.76 - 2.30: 318 2.30 - 2.84: 6 2.84 - 3.38: 0 3.38 - 3.93: 9 Bond restraints: 22473 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.927 -1.694 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.927 -1.694 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.926 -1.693 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S2 F3S J 303 " pdb="FE3 F3S J 303 " ideal model delta sigma weight residual 2.300 3.925 -1.625 2.00e-02 2.50e+03 6.60e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.925 -1.625 2.00e-02 2.50e+03 6.60e+03 ... (remaining 22468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.17: 30516 10.17 - 20.34: 15 20.34 - 30.51: 9 30.51 - 40.68: 15 40.68 - 50.85: 6 Bond angle restraints: 30561 Sorted by residual: angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 63.90 50.85 3.00e+00 1.11e-01 2.87e+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 63.91 50.84 3.00e+00 1.11e-01 2.87e+02 angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 63.92 50.83 3.00e+00 1.11e-01 2.87e+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 64.06 48.53 3.00e+00 1.11e-01 2.62e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 64.07 48.52 3.00e+00 1.11e-01 2.62e+02 ... (remaining 30556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11618 17.61 - 35.21: 1288 35.21 - 52.81: 300 52.81 - 70.42: 42 70.42 - 88.02: 51 Dihedral angle restraints: 13299 sinusoidal: 5343 harmonic: 7956 Sorted by residual: dihedral pdb=" CA SER F 54 " pdb=" C SER F 54 " pdb=" N CYS F 55 " pdb=" CA CYS F 55 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER J 54 " pdb=" C SER J 54 " pdb=" N CYS J 55 " pdb=" CA CYS J 55 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N CYS B 55 " pdb=" CA CYS B 55 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 13296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.650: 3405 0.650 - 1.300: 0 1.300 - 1.949: 0 1.949 - 2.599: 0 2.599 - 3.249: 3 Chirality restraints: 3408 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 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 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 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 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 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 ... (remaining 3405 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO F 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG J 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO J 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO J 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 93 " 0.040 5.00e-02 4.00e+02 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4197 2.76 - 3.30: 24231 3.30 - 3.83: 37134 3.83 - 4.37: 42216 4.37 - 4.90: 68711 Nonbonded interactions: 176489 Sorted by model distance: nonbonded pdb=" S1 F3S J 303 " pdb="FE1 F3S J 303 " model vdw 2.228 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.228 2.688 nonbonded pdb=" S1 F3S F 303 " pdb="FE1 F3S F 303 " model vdw 2.229 2.688 nonbonded pdb=" N LYS I 171 " pdb=" OD2 ASP I 436 " model vdw 2.233 3.120 nonbonded pdb=" N LYS E 171 " pdb=" OD2 ASP E 436 " model vdw 2.234 3.120 ... (remaining 176484 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: 0.26 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } 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 group one per residue 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: 0.240 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: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.110 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 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 : 0.038 1.694 22503 Z= 1.806 Angle : 2.180 54.185 30633 Z= 0.712 Chirality : 0.110 3.249 3408 Planarity : 0.006 0.073 3879 Dihedral : 16.337 88.025 8187 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 1.34 % Allowed : 10.77 % Favored : 87.89 % 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: -4.47 (0.13), residues: 2745 helix: -2.23 (0.12), residues: 1296 sheet: -3.30 (0.44), residues: 99 loop : -3.78 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 48 HIS 0.007 0.001 HIS H 71 PHE 0.026 0.002 PHE H 37 TYR 0.015 0.002 TYR L 29 ARG 0.005 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.14918 ( 1032) hydrogen bonds : angle 7.18997 ( 2988) metal coordination : bond 0.52386 ( 27) metal coordination : angle 32.58937 ( 72) covalent geometry : bond 0.03348 (22473) covalent geometry : angle 1.50448 (30561) Misc. bond : bond 0.43847 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 529 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.5720 (mmt) cc_final: 0.5419 (mmt) REVERT: F 1 MET cc_start: 0.3589 (ttt) cc_final: 0.3370 (ttt) REVERT: F 53 ARG cc_start: 0.6447 (pmt-80) cc_final: 0.6115 (ptt90) REVERT: J 223 THR cc_start: 0.7734 (m) cc_final: 0.7521 (m) REVERT: A 43 ARG cc_start: 0.8162 (mpt90) cc_final: 0.6979 (mmt180) REVERT: A 139 ASP cc_start: 0.5862 (t0) cc_final: 0.5605 (t0) REVERT: A 156 ASN cc_start: 0.6949 (t0) cc_final: 0.6204 (m-40) REVERT: A 356 MET cc_start: 0.6641 (ttp) cc_final: 0.6358 (ttp) REVERT: A 392 VAL cc_start: 0.6831 (p) cc_final: 0.5779 (t) REVERT: A 480 MET cc_start: 0.6056 (ttp) cc_final: 0.5736 (ttp) REVERT: E 43 ARG cc_start: 0.8111 (mpt90) cc_final: 0.6975 (mmt180) REVERT: E 53 ILE cc_start: 0.8174 (tp) cc_final: 0.7953 (tp) REVERT: E 156 ASN cc_start: 0.6987 (t0) cc_final: 0.6486 (m-40) REVERT: E 185 ILE cc_start: 0.6998 (tt) cc_final: 0.6760 (tt) REVERT: E 356 MET cc_start: 0.6223 (ttp) cc_final: 0.6017 (ttp) REVERT: E 392 VAL cc_start: 0.6742 (p) cc_final: 0.5650 (t) REVERT: E 454 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3895 (tp30) REVERT: E 461 LYS cc_start: 0.7562 (mmpt) cc_final: 0.7361 (tttp) REVERT: I 43 ARG cc_start: 0.8330 (mpt90) cc_final: 0.7059 (mmt180) REVERT: I 63 ASP cc_start: 0.5905 (p0) cc_final: 0.5298 (p0) REVERT: I 156 ASN cc_start: 0.6887 (t0) cc_final: 0.6363 (m-40) REVERT: I 356 MET cc_start: 0.6463 (ttp) cc_final: 0.6047 (ttp) REVERT: I 392 VAL cc_start: 0.6771 (p) cc_final: 0.5671 (t) REVERT: I 461 LYS cc_start: 0.7609 (mmpt) cc_final: 0.7356 (tttp) REVERT: I 475 ARG cc_start: 0.4393 (ptp-170) cc_final: 0.3213 (ptp-170) outliers start: 31 outliers final: 15 residues processed: 546 average time/residue: 0.3477 time to fit residues: 287.9244 Evaluate side-chains 459 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 443 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain I residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 3.9990 chunk 206 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN C 30 HIS F 113 GLN G 30 HIS J 113 GLN K 30 HIS A 25 GLN A 556 HIS E 25 GLN E 518 ASN E 556 HIS I 25 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 556 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.251124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.212968 restraints weight = 33424.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.213498 restraints weight = 24465.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.215316 restraints weight = 17357.096| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 22503 Z= 0.248 Angle : 1.594 57.997 30633 Z= 0.511 Chirality : 0.085 2.472 3408 Planarity : 0.006 0.068 3879 Dihedral : 10.340 97.261 3220 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.11 % Allowed : 17.47 % Favored : 79.42 % 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: -2.91 (0.14), residues: 2745 helix: -0.70 (0.13), residues: 1323 sheet: -3.41 (0.43), residues: 105 loop : -3.21 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 163 HIS 0.014 0.002 HIS E 354 PHE 0.027 0.002 PHE H 51 TYR 0.035 0.002 TYR H 29 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 1032) hydrogen bonds : angle 5.33213 ( 2988) metal coordination : bond 0.02299 ( 27) metal coordination : angle 21.13247 ( 72) covalent geometry : bond 0.00522 (22473) covalent geometry : angle 1.22203 (30561) Misc. bond : bond 0.08153 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 476 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.6167 (mmt) cc_final: 0.5891 (mmt) REVERT: B 23 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4428 (m-10) REVERT: F 53 ARG cc_start: 0.6126 (pmt-80) cc_final: 0.5832 (ptt90) REVERT: H 29 TYR cc_start: 0.8058 (t80) cc_final: 0.7501 (t80) REVERT: H 83 TYR cc_start: 0.8002 (m-10) cc_final: 0.7650 (m-10) REVERT: J 9 ARG cc_start: 0.5428 (ttp80) cc_final: 0.5077 (mtp180) REVERT: J 23 TYR cc_start: 0.4789 (OUTLIER) cc_final: 0.4228 (m-10) REVERT: K 28 ILE cc_start: 0.7251 (mm) cc_final: 0.6950 (mt) REVERT: A 43 ARG cc_start: 0.8274 (mpt90) cc_final: 0.7210 (mmt180) REVERT: A 139 ASP cc_start: 0.5906 (t70) cc_final: 0.5674 (t0) REVERT: A 392 VAL cc_start: 0.6884 (p) cc_final: 0.6000 (t) REVERT: A 461 LYS cc_start: 0.7629 (mmpt) cc_final: 0.7209 (tttp) REVERT: A 475 ARG cc_start: 0.4175 (ptp-170) cc_final: 0.2404 (ptp-170) REVERT: E 43 ARG cc_start: 0.8218 (mpt90) cc_final: 0.6753 (mmt180) REVERT: E 86 GLU cc_start: 0.7487 (tp30) cc_final: 0.7185 (tp30) REVERT: E 155 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7835 (tmmt) REVERT: E 235 ASP cc_start: 0.7066 (t0) cc_final: 0.6702 (t70) REVERT: E 377 ASP cc_start: 0.8286 (m-30) cc_final: 0.8082 (t0) REVERT: E 392 VAL cc_start: 0.6808 (p) cc_final: 0.5871 (t) REVERT: E 461 LYS cc_start: 0.7543 (mmpt) cc_final: 0.7220 (tttp) REVERT: E 465 GLU cc_start: 0.6472 (tp30) cc_final: 0.6190 (tp30) REVERT: E 475 ARG cc_start: 0.3899 (ptp-170) cc_final: 0.2659 (ptp-170) REVERT: E 499 LEU cc_start: 0.6672 (tp) cc_final: 0.6403 (tt) REVERT: I 43 ARG cc_start: 0.8389 (mpt90) cc_final: 0.7117 (mmt180) REVERT: I 63 ASP cc_start: 0.6605 (p0) cc_final: 0.6060 (p0) REVERT: I 392 VAL cc_start: 0.6784 (p) cc_final: 0.5791 (t) REVERT: I 461 LYS cc_start: 0.7793 (mmpt) cc_final: 0.7479 (tttp) REVERT: I 465 GLU cc_start: 0.6648 (tp30) cc_final: 0.6154 (tp30) REVERT: I 475 ARG cc_start: 0.3771 (ptp-170) cc_final: 0.2570 (ptp-170) REVERT: I 494 LEU cc_start: 0.6653 (pp) cc_final: 0.6198 (tt) outliers start: 72 outliers final: 46 residues processed: 510 average time/residue: 0.3461 time to fit residues: 271.5513 Evaluate side-chains 490 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 442 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 389 ILE Chi-restraints excluded: chain I residue 520 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 216 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 157 optimal weight: 0.5980 chunk 261 optimal weight: 30.0000 chunk 218 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 GLN L 94 GLN A 25 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.249863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.210660 restraints weight = 33441.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.212068 restraints weight = 25016.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.213623 restraints weight = 16845.068| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 22503 Z= 0.198 Angle : 1.454 84.656 30633 Z= 0.491 Chirality : 0.057 1.292 3408 Planarity : 0.005 0.067 3879 Dihedral : 9.591 88.995 3205 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.29 % Allowed : 20.88 % Favored : 75.83 % 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: -2.43 (0.15), residues: 2745 helix: -0.24 (0.13), residues: 1323 sheet: -3.35 (0.42), residues: 105 loop : -3.03 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 163 HIS 0.010 0.002 HIS E 354 PHE 0.019 0.002 PHE I 506 TYR 0.022 0.002 TYR H 29 ARG 0.006 0.000 ARG I 108 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 1032) hydrogen bonds : angle 5.07460 ( 2988) metal coordination : bond 0.00960 ( 27) metal coordination : angle 17.04850 ( 72) covalent geometry : bond 0.00447 (22473) covalent geometry : angle 1.19798 (30561) Misc. bond : bond 0.10472 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 440 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.3910 (m-10) REVERT: F 20 MET cc_start: 0.4949 (mmt) cc_final: 0.4410 (mmp) REVERT: G 74 MET cc_start: 0.8136 (mmt) cc_final: 0.7864 (mmm) REVERT: H 29 TYR cc_start: 0.8122 (t80) cc_final: 0.7582 (t80) REVERT: J 9 ARG cc_start: 0.5388 (ttp80) cc_final: 0.5111 (mtp180) REVERT: J 23 TYR cc_start: 0.4444 (OUTLIER) cc_final: 0.3934 (m-10) REVERT: J 210 MET cc_start: 0.4723 (mtt) cc_final: 0.4384 (mmt) REVERT: A 20 MET cc_start: 0.7455 (mmt) cc_final: 0.7069 (mmt) REVERT: A 43 ARG cc_start: 0.8336 (mpt90) cc_final: 0.6969 (mmt180) REVERT: A 139 ASP cc_start: 0.5989 (t70) cc_final: 0.5692 (t0) REVERT: A 155 LYS cc_start: 0.8189 (tmmt) cc_final: 0.7606 (tmmt) REVERT: A 356 MET cc_start: 0.6426 (ttp) cc_final: 0.5733 (ttp) REVERT: A 392 VAL cc_start: 0.6840 (p) cc_final: 0.5921 (t) REVERT: A 461 LYS cc_start: 0.7630 (mmpt) cc_final: 0.7310 (tttp) REVERT: E 69 MET cc_start: 0.6670 (mtt) cc_final: 0.6232 (mtt) REVERT: E 86 GLU cc_start: 0.7508 (tp30) cc_final: 0.7296 (tp30) REVERT: E 235 ASP cc_start: 0.7064 (t0) cc_final: 0.6706 (t70) REVERT: E 236 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5648 (mmt) REVERT: E 377 ASP cc_start: 0.8315 (m-30) cc_final: 0.8083 (t0) REVERT: E 392 VAL cc_start: 0.6895 (p) cc_final: 0.6002 (t) REVERT: E 461 LYS cc_start: 0.7606 (mmpt) cc_final: 0.7318 (tttp) REVERT: E 465 GLU cc_start: 0.6522 (tp30) cc_final: 0.6262 (tp30) REVERT: E 475 ARG cc_start: 0.3936 (ptp-170) cc_final: 0.2513 (ptp-170) REVERT: E 499 LEU cc_start: 0.6638 (tp) cc_final: 0.6312 (tt) REVERT: I 20 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6955 (mmt) REVERT: I 43 ARG cc_start: 0.8449 (mpt90) cc_final: 0.7389 (mmt180) REVERT: I 63 ASP cc_start: 0.6607 (p0) cc_final: 0.6153 (p0) REVERT: I 69 MET cc_start: 0.6951 (mtt) cc_final: 0.6585 (mtt) REVERT: I 236 MET cc_start: 0.5723 (mmm) cc_final: 0.5344 (mpp) REVERT: I 392 VAL cc_start: 0.6782 (p) cc_final: 0.5866 (t) REVERT: I 461 LYS cc_start: 0.7815 (mmpt) cc_final: 0.7412 (tttp) REVERT: I 465 GLU cc_start: 0.6666 (tp30) cc_final: 0.6179 (tp30) REVERT: I 475 ARG cc_start: 0.3861 (ptp-170) cc_final: 0.2690 (ptp-170) outliers start: 76 outliers final: 57 residues processed: 484 average time/residue: 0.3286 time to fit residues: 247.9751 Evaluate side-chains 488 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 427 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 520 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.5767 > 50: distance: 32 - 54: 18.845 distance: 37 - 62: 36.519 distance: 46 - 69: 35.679 distance: 49 - 54: 15.980 distance: 50 - 77: 33.378 distance: 54 - 55: 30.257 distance: 55 - 56: 24.021 distance: 55 - 58: 29.636 distance: 56 - 57: 21.961 distance: 56 - 62: 19.778 distance: 58 - 59: 43.961 distance: 59 - 60: 31.940 distance: 59 - 61: 20.774 distance: 62 - 63: 40.439 distance: 63 - 64: 35.087 distance: 63 - 66: 39.795 distance: 64 - 65: 39.331 distance: 64 - 69: 40.623 distance: 66 - 68: 52.634 distance: 69 - 70: 5.658 distance: 70 - 71: 43.945 distance: 70 - 73: 30.303 distance: 71 - 72: 40.551 distance: 71 - 77: 21.214 distance: 73 - 74: 20.348 distance: 74 - 75: 5.654 distance: 74 - 76: 20.211 distance: 77 - 78: 40.704 distance: 78 - 79: 33.566 distance: 78 - 81: 39.823 distance: 79 - 80: 47.020 distance: 79 - 89: 7.124 distance: 81 - 82: 24.577 distance: 82 - 83: 22.929 distance: 83 - 85: 17.948 distance: 84 - 86: 20.550 distance: 85 - 87: 20.604 distance: 86 - 87: 39.976 distance: 87 - 88: 49.046 distance: 89 - 90: 42.323 distance: 90 - 91: 15.929 distance: 90 - 93: 13.598 distance: 91 - 92: 56.734 distance: 91 - 96: 16.767 distance: 96 - 97: 22.969 distance: 97 - 98: 40.783 distance: 97 - 100: 39.594 distance: 98 - 99: 5.720 distance: 98 - 105: 16.742 distance: 100 - 101: 56.293 distance: 101 - 102: 5.328 distance: 102 - 103: 27.519 distance: 103 - 104: 49.934 distance: 105 - 106: 23.954 distance: 105 - 111: 31.990 distance: 106 - 107: 69.278 distance: 107 - 108: 29.488 distance: 107 - 112: 41.257 distance: 108 - 133: 22.766 distance: 109 - 110: 47.912 distance: 110 - 111: 40.131 distance: 112 - 113: 31.661 distance: 113 - 114: 20.452 distance: 113 - 116: 18.726 distance: 114 - 115: 23.714 distance: 115 - 144: 34.653 distance: 117 - 118: 11.237 distance: 120 - 121: 20.009 distance: 121 - 122: 9.708 distance: 121 - 124: 32.022 distance: 122 - 123: 8.757 distance: 122 - 125: 10.163 distance: 123 - 151: 34.448 distance: 125 - 126: 39.582 distance: 126 - 127: 21.543 distance: 126 - 129: 6.836 distance: 127 - 128: 31.000 distance: 127 - 133: 21.509 distance: 128 - 155: 36.358 distance: 129 - 130: 3.614 distance: 130 - 131: 14.317 distance: 130 - 132: 34.650