Starting phenix.real_space_refine on Mon Jul 6 13:29:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.map" model { file = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9i_27965/07_2026/8e9i_27965.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 sd= 0.191 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 32 7.16 5 Zn 1 6.06 5 P 5 5.49 5 S 208 5.16 5 C 23016 2.51 5 N 6143 2.21 5 O 6066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35471 Number of models: 1 Model: "" Number of chains: 22 Chain: "O" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 878 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 112} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1304 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 168} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "A" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1623 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 21, 'TRANS': 197} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 2971 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 21, 'TRANS': 385} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 152 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 22, 'ASP:plan': 16, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 155 Chain: "E" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1564 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 22, 'TRANS': 209} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 13, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 5374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 5374 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 720} Unresolved non-hydrogen bonds: 411 Unresolved non-hydrogen angles: 513 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 32, 'ARG:plan': 11, 'ASN:plan1': 1, 'HIS:plan': 3, 'GLN:plan1': 5} Unresolved non-hydrogen planarities: 341 Chain: "F" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3105 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 403} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 18, 'GLU:plan': 19, 'GLN:plan1': 5, 'ARG:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "I" Number of atoms: 1183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1183 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 151} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 9, 'GLU:plan': 8, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 2847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2847 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 367} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6, 'PHE:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "J" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1585 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 9, 'TRANS': 220} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "K" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 736 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 3784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 3784 Classifications: {'peptide': 621} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 599} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 984 Unresolved non-hydrogen dihedrals: 614 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 14, 'PHE:plan': 10, 'GLU:plan': 16, 'GLN:plan1': 7, 'ASN:plan1': 3, 'TYR:plan': 3, 'HIS:plan': 7, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 357 Chain: "N" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3618 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 26, 'TRANS': 491} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 111 Chain: "M" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3712 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 28, 'TRANS': 489} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 16, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 135 Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'FES': 1, 'GTP': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' ZN': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'MQ9': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'XP2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1140 SG CYS B 38 54.290 82.395 100.338 1.00 43.29 S ATOM 1134 SG CYS B 37 59.931 79.643 100.843 1.00 44.17 S ATOM 1830 SG CYS B 132 56.957 78.994 95.334 1.00 41.56 S ATOM 1629 SG CYS B 103 54.290 76.053 99.138 1.00 40.62 S ATOM 8411 SG CYS E 107 76.385 59.519 29.284 1.00 62.62 S ATOM 8447 SG CYS E 112 79.382 60.191 27.556 1.00 63.29 S ATOM 8679 SG CYS E 148 79.125 55.300 31.441 1.00 59.80 S ATOM 8703 SG CYS E 152 81.933 55.561 29.397 1.00 63.58 S ATOM 9520 SG CYS G 48 69.343 48.294 60.603 1.00 43.38 S ATOM 9595 SG CYS G 59 70.579 51.813 61.509 1.00 43.50 S ATOM 9621 SG CYS G 62 74.394 47.573 63.921 1.00 48.17 S ATOM 9712 SG CYS G 76 72.092 45.452 62.293 1.00 47.45 S ATOM 9993 SG CYS G 114 63.308 66.956 67.538 1.00 40.22 S ATOM 10050 SG CYS G 123 62.558 60.191 67.564 1.00 39.37 S ATOM 10014 SG CYS G 117 57.984 63.170 65.898 1.00 41.29 S ATOM 10731 SG CYS G 213 58.974 55.417 62.281 1.00 42.07 S ATOM 10383 SG CYS G 166 63.250 51.760 60.561 1.00 43.68 S ATOM 10362 SG CYS G 163 61.370 56.423 56.395 1.00 42.56 S ATOM 10405 SG CYS G 169 57.912 51.112 57.414 1.00 44.59 S ATOM 10922 SG CYS G 239 42.599 43.334 73.128 1.00 45.20 S ATOM 10968 SG CYS G 246 47.758 39.704 72.061 1.00 45.29 S ATOM 11182 SG CYS G 274 43.807 42.589 67.144 1.00 45.56 S ATOM 10947 SG CYS G 242 42.128 38.001 70.230 1.00 47.15 S ATOM 16996 SG CYS F 334 86.795 72.543 38.577 1.00 62.45 S ATOM 17678 SG CYS F 426 85.465 75.271 37.515 1.00 64.30 S ATOM 17159 SG CYS F 354 74.348 52.315 52.811 1.00 46.62 S ATOM 17475 SG CYS F 397 76.565 49.047 47.632 1.00 52.01 S ATOM 17179 SG CYS F 357 75.060 55.429 48.523 1.00 47.41 S ATOM 17140 SG CYS F 351 70.494 50.508 47.903 1.00 50.63 S ATOM 18456 SG CYS I 99 53.608 80.211 87.873 1.00 38.92 S ATOM 18474 SG CYS I 102 59.534 77.163 87.334 1.00 40.43 S ATOM 18492 SG CYS I 105 57.136 79.064 82.419 1.00 40.93 S ATOM 18188 SG CYS I 64 54.967 74.152 86.156 1.00 39.26 S ATOM 18158 SG CYS I 60 54.241 75.252 77.847 1.00 40.31 S ATOM 18135 SG CYS I 57 56.552 73.004 72.552 1.00 40.38 S ATOM 18516 SG CYS I 109 57.707 78.679 73.967 1.00 42.53 S ATOM 18117 SG CYS I 54 51.339 76.977 72.437 1.00 42.56 S Time building chain proxies: 6.07, per 1000 atoms: 0.17 Number of scatterers: 35471 At special positions: 0 Unit cell: (112.12, 147.526, 279.709, 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) Zn 1 29.99 Fe 32 26.01 S 208 16.00 P 5 15.00 O 6066 8.00 N 6143 7.00 C 23016 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1000 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 112 " pdb="FE1 FES E1000 " - pdb=" SG CYS E 107 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 152 " pdb="FE2 FES E1000 " - pdb=" SG CYS E 148 " pdb=" FES G 801 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 59 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 62 " pdb="FE1 FES G 801 " - pdb=" SG CYS G 48 " pdb="FE2 FES G 801 " - pdb=" SG CYS G 76 " pdb=" SF4 B1000 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 132 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 38 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 103 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 37 " pdb=" SF4 F 503 " pdb="FE4 SF4 F 503 " - pdb=" SG CYS F 351 " pdb="FE2 SF4 F 503 " - pdb=" SG CYS F 397 " pdb="FE1 SF4 F 503 " - pdb=" SG CYS F 354 " pdb="FE3 SF4 F 503 " - pdb=" SG CYS F 357 " pdb=" SF4 G 803 " pdb="FE3 SF4 G 803 " - pdb=" NE2 HIS G 110 " pdb="FE1 SF4 G 803 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G 803 " - pdb=" SG CYS G 123 " pdb="FE4 SF4 G 803 " - pdb=" SG CYS G 117 " pdb=" SF4 G 804 " pdb="FE3 SF4 G 804 " - pdb=" SG CYS G 163 " pdb="FE2 SF4 G 804 " - pdb=" SG CYS G 166 " pdb="FE4 SF4 G 804 " - pdb=" SG CYS G 169 " pdb="FE1 SF4 G 804 " - pdb=" SG CYS G 213 " pdb=" SF4 G 805 " pdb="FE3 SF4 G 805 " - pdb=" SG CYS G 274 " pdb="FE4 SF4 G 805 " - pdb=" SG CYS G 242 " pdb="FE2 SF4 G 805 " - pdb=" SG CYS G 246 " pdb="FE1 SF4 G 805 " - pdb=" SG CYS G 239 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" NE2 HIS I 42 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 64 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 57 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 54 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 Zn2+ tetrahedral coordination pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 426 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 334 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 421 " 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9134 Finding SS restraints... Secondary structure from input PDB file: 230 helices and 31 sheets defined 62.0% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'O' and resid 15 through 26 Processing helix chain 'O' and resid 44 through 55 Processing helix chain 'O' and resid 70 through 82 Processing helix chain 'O' and resid 94 through 96 No H-bonds generated for 'chain 'O' and resid 94 through 96' Processing helix chain 'O' and resid 97 through 104 Processing helix chain 'O' and resid 115 through 127 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 36 through 47 Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'A' and resid 4 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.743A pdb=" N VAL A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 92 through 116 Processing helix chain 'C' and resid 31 through 34 removed outlier: 3.574A pdb=" N ASN C 34 " --> pdb=" O MET C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 62 through 75 removed outlier: 4.468A pdb=" N ALA C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 174 through 187 removed outlier: 4.210A pdb=" N HIS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 removed outlier: 4.234A pdb=" N HIS D 53 " --> pdb=" O PRO D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.830A pdb=" N PHE D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 159 through 182 removed outlier: 3.881A pdb=" N MET D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 226 Proline residue: D 215 - end of helix removed outlier: 3.740A pdb=" N LEU D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 288 through 313 removed outlier: 3.607A pdb=" N HIS D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 405 through 411 removed outlier: 3.717A pdb=" N THR D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 422 through 434 Processing helix chain 'D' and resid 436 through 442 Processing helix chain 'E' and resid 26 through 43 removed outlier: 3.948A pdb=" N GLN E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG E 43 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 49 Processing helix chain 'E' and resid 50 through 62 Processing helix chain 'E' and resid 66 through 78 Processing helix chain 'E' and resid 80 through 91 removed outlier: 3.777A pdb=" N TYR E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 116 through 129 Processing helix chain 'E' and resid 169 through 182 Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 216 through 230 removed outlier: 4.227A pdb=" N THR E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU E 221 " --> pdb=" O GLY E 217 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY E 223 " --> pdb=" O ALA E 219 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU E 224 " --> pdb=" O THR E 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 92 through 109 removed outlier: 4.744A pdb=" N ASN G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 205 through 213 removed outlier: 4.241A pdb=" N THR G 209 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL G 210 " --> pdb=" O SER G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 281 through 286 removed outlier: 3.986A pdb=" N ALA G 284 " --> pdb=" O PHE G 281 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 286 " --> pdb=" O TYR G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 321 Processing helix chain 'G' and resid 333 through 346 Processing helix chain 'G' and resid 361 through 371 Processing helix chain 'G' and resid 380 through 387 removed outlier: 3.555A pdb=" N ASN G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 416 removed outlier: 3.638A pdb=" N GLY G 416 " --> pdb=" O VAL G 412 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 444 through 451 Processing helix chain 'G' and resid 455 through 460 removed outlier: 3.553A pdb=" N ARG G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 474 Processing helix chain 'G' and resid 476 through 489 Processing helix chain 'G' and resid 499 through 507 removed outlier: 4.548A pdb=" N GLY G 503 " --> pdb=" O ALA G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 533 Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 567 through 571 Processing helix chain 'G' and resid 573 through 584 Processing helix chain 'G' and resid 595 through 601 Processing helix chain 'G' and resid 609 through 613 Processing helix chain 'G' and resid 637 through 650 Processing helix chain 'G' and resid 657 through 669 Processing helix chain 'G' and resid 706 through 710 Processing helix chain 'G' and resid 712 through 718 Processing helix chain 'G' and resid 727 through 734 Processing helix chain 'G' and resid 775 through 781 Processing helix chain 'F' and resid 8 through 12 removed outlier: 3.952A pdb=" N PHE F 11 " --> pdb=" O LEU F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 39 through 51 Processing helix chain 'F' and resid 61 through 68 Processing helix chain 'F' and resid 101 through 109 Processing helix chain 'F' and resid 110 through 125 Processing helix chain 'F' and resid 137 through 154 Processing helix chain 'F' and resid 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 179 through 183 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 209 through 213 Processing helix chain 'F' and resid 220 through 225 Processing helix chain 'F' and resid 225 through 240 removed outlier: 3.674A pdb=" N ILE F 229 " --> pdb=" O SER F 225 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL F 234 " --> pdb=" O MET F 230 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ASP F 235 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TRP F 236 " --> pdb=" O ASN F 232 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET F 240 " --> pdb=" O TRP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 279 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 310 through 316 Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 354 through 373 removed outlier: 3.744A pdb=" N TYR F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 392 removed outlier: 3.827A pdb=" N ILE F 381 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 421 removed outlier: 4.356A pdb=" N ASP F 401 " --> pdb=" O CYS F 397 " (cutoff:3.500A) Proline residue: F 406 - end of helix removed outlier: 7.070A pdb=" N ASP F 416 " --> pdb=" O LYS F 412 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU F 417 " --> pdb=" O HIS F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'F' and resid 429 through 433 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 8 through 18 removed outlier: 3.620A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 64 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 133 through 138 Processing helix chain 'I' and resid 157 through 163 Processing helix chain 'H' and resid 13 through 47 removed outlier: 3.749A pdb=" N LEU H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 59 Processing helix chain 'H' and resid 60 through 72 removed outlier: 4.730A pdb=" N LEU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 101 Proline residue: H 90 - end of helix Proline residue: H 96 - end of helix removed outlier: 3.830A pdb=" N PHE H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 126 through 149 removed outlier: 4.045A pdb=" N TYR H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 141 " --> pdb=" O ILE H 137 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE H 142 " --> pdb=" O GLY H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 184 removed outlier: 5.391A pdb=" N ILE H 170 " --> pdb=" O VAL H 166 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA H 171 " --> pdb=" O SER H 167 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 177 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA H 178 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 194 Processing helix chain 'H' and resid 199 through 204 removed outlier: 3.724A pdb=" N LEU H 203 " --> pdb=" O TRP H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 219 Processing helix chain 'H' and resid 229 through 234 Processing helix chain 'H' and resid 235 through 239 Processing helix chain 'H' and resid 242 through 269 removed outlier: 3.613A pdb=" N PHE H 246 " --> pdb=" O SER H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 3.993A pdb=" N LEU H 280 " --> pdb=" O PHE H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 312 Processing helix chain 'H' and resid 316 through 327 Processing helix chain 'H' and resid 327 through 348 Processing helix chain 'H' and resid 351 through 374 removed outlier: 3.528A pdb=" N TRP H 370 " --> pdb=" O VAL H 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 40 Processing helix chain 'J' and resid 42 through 64 Processing helix chain 'J' and resid 66 through 92 Processing helix chain 'J' and resid 106 through 127 Processing helix chain 'J' and resid 129 through 133 Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 144 through 154 Processing helix chain 'J' and resid 157 through 179 removed outlier: 3.903A pdb=" N SER J 165 " --> pdb=" O PHE J 161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 186 Processing helix chain 'J' and resid 189 through 195 removed outlier: 3.642A pdb=" N ILE J 195 " --> pdb=" O ARG J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 24 removed outlier: 4.154A pdb=" N LEU K 7 " --> pdb=" O PRO K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 53 Processing helix chain 'K' and resid 55 through 87 Processing helix chain 'L' and resid 8 through 25 removed outlier: 4.165A pdb=" N ILE L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) Proline residue: L 15 - end of helix Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 32 through 58 Processing helix chain 'L' and resid 87 through 112 removed outlier: 3.846A pdb=" N CYS L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE L 93 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 138 Processing helix chain 'L' and resid 140 through 161 Processing helix chain 'L' and resid 165 through 198 Processing helix chain 'L' and resid 201 through 209 Processing helix chain 'L' and resid 210 through 212 No H-bonds generated for 'chain 'L' and resid 210 through 212' Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 236 through 238 No H-bonds generated for 'chain 'L' and resid 236 through 238' Processing helix chain 'L' and resid 239 through 244 removed outlier: 4.453A pdb=" N ASP L 243 " --> pdb=" O SER L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 247 No H-bonds generated for 'chain 'L' and resid 245 through 247' Processing helix chain 'L' and resid 248 through 258 removed outlier: 3.547A pdb=" N ALA L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 271 removed outlier: 4.526A pdb=" N VAL L 265 " --> pdb=" O VAL L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 277 Processing helix chain 'L' and resid 278 through 301 Processing helix chain 'L' and resid 305 through 327 Processing helix chain 'L' and resid 328 through 360 removed outlier: 4.609A pdb=" N ALA L 333 " --> pdb=" O PRO L 329 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N PHE L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA L 347 " --> pdb=" O GLY L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 369 Processing helix chain 'L' and resid 371 through 375 Processing helix chain 'L' and resid 376 through 392 Processing helix chain 'L' and resid 396 through 412 removed outlier: 3.939A pdb=" N PHE L 400 " --> pdb=" O LEU L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 443 Processing helix chain 'L' and resid 459 through 475 Proline residue: L 465 - end of helix Processing helix chain 'L' and resid 477 through 482 Processing helix chain 'L' and resid 484 through 491 Processing helix chain 'L' and resid 504 through 528 removed outlier: 3.538A pdb=" N VAL L 508 " --> pdb=" O PRO L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 560 through 578 Processing helix chain 'L' and resid 578 through 599 removed outlier: 3.655A pdb=" N ALA L 583 " --> pdb=" O VAL L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 615 Processing helix chain 'L' and resid 615 through 625 removed outlier: 3.958A pdb=" N VAL L 619 " --> pdb=" O GLY L 615 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 31 Proline residue: N 13 - end of helix Processing helix chain 'N' and resid 32 through 62 removed outlier: 4.346A pdb=" N TYR N 37 " --> pdb=" O ARG N 33 " (cutoff:3.500A) Proline residue: N 38 - end of helix Processing helix chain 'N' and resid 79 through 100 Processing helix chain 'N' and resid 128 through 138 Processing helix chain 'N' and resid 143 through 161 Proline residue: N 159 - end of helix Processing helix chain 'N' and resid 163 through 182 Proline residue: N 177 - end of helix Processing helix chain 'N' and resid 188 through 222 Processing helix chain 'N' and resid 225 through 236 Processing helix chain 'N' and resid 239 through 259 Processing helix chain 'N' and resid 260 through 264 Processing helix chain 'N' and resid 265 through 274 removed outlier: 4.405A pdb=" N ASP N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 300 removed outlier: 3.623A pdb=" N ALA N 284 " --> pdb=" O ALA N 280 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 305 through 330 Proline residue: N 311 - end of helix removed outlier: 3.654A pdb=" N ALA N 328 " --> pdb=" O GLY N 324 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR N 330 " --> pdb=" O VAL N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 333 through 355 removed outlier: 3.665A pdb=" N GLY N 352 " --> pdb=" O PHE N 348 " (cutoff:3.500A) Processing helix chain 'N' and resid 357 through 384 Processing helix chain 'N' and resid 395 through 400 Processing helix chain 'N' and resid 401 through 406 Processing helix chain 'N' and resid 406 through 422 Processing helix chain 'N' and resid 426 through 442 removed outlier: 3.536A pdb=" N VAL N 430 " --> pdb=" O THR N 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 471 removed outlier: 4.033A pdb=" N TYR N 460 " --> pdb=" O ALA N 456 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE N 461 " --> pdb=" O VAL N 457 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL N 465 " --> pdb=" O PHE N 461 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE N 466 " --> pdb=" O TYR N 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 485 through 505 removed outlier: 3.758A pdb=" N GLY N 503 " --> pdb=" O THR N 499 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 516 removed outlier: 6.284A pdb=" N LEU N 512 " --> pdb=" O PRO N 508 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 24 Proline residue: M 15 - end of helix Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 29 through 55 Processing helix chain 'M' and resid 72 through 75 Processing helix chain 'M' and resid 83 through 104 Proline residue: M 98 - end of helix Processing helix chain 'M' and resid 113 through 116 Processing helix chain 'M' and resid 117 through 139 Processing helix chain 'M' and resid 141 through 152 Processing helix chain 'M' and resid 152 through 162 removed outlier: 3.643A pdb=" N MET M 156 " --> pdb=" O MET M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 200 Processing helix chain 'M' and resid 209 through 220 Processing helix chain 'M' and resid 225 through 244 removed outlier: 3.566A pdb=" N ALA M 239 " --> pdb=" O GLY M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 250 Processing helix chain 'M' and resid 251 through 260 removed outlier: 4.575A pdb=" N ASP M 255 " --> pdb=" O ARG M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 270 Processing helix chain 'M' and resid 271 through 288 removed outlier: 3.714A pdb=" N VAL M 275 " --> pdb=" O VAL M 271 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR M 277 " --> pdb=" O ASP M 273 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS M 284 " --> pdb=" O MET M 280 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN M 286 " --> pdb=" O ARG M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 317 Proline residue: M 297 - end of helix Processing helix chain 'M' and resid 319 through 341 Processing helix chain 'M' and resid 343 through 375 Processing helix chain 'M' and resid 379 through 383 Processing helix chain 'M' and resid 385 through 390 removed outlier: 3.900A pdb=" N VAL M 389 " --> pdb=" O GLY M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 390 through 405 Processing helix chain 'M' and resid 410 through 425 removed outlier: 4.465A pdb=" N ILE M 414 " --> pdb=" O LEU M 410 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER M 415 " --> pdb=" O ALA M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 454 removed outlier: 4.301A pdb=" N ALA M 437 " --> pdb=" O PHE M 433 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU M 438 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL M 439 " --> pdb=" O ALA M 435 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR M 448 " --> pdb=" O TYR M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 492 Proline residue: M 481 - end of helix Processing helix chain 'M' and resid 493 through 511 Proline residue: M 502 - end of helix Processing sheet with id=AA1, first strand: chain 'O' and resid 37 through 42 removed outlier: 6.106A pdb=" N LEU O 7 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL O 40 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE O 9 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL O 42 " --> pdb=" O ILE O 9 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL O 11 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU O 59 " --> pdb=" O ARG O 8 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA O 60 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU O 91 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU O 62 " --> pdb=" O LEU O 91 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 88 " --> pdb=" O ALA O 108 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N VAL O 110 " --> pdb=" O ILE O 88 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL O 90 " --> pdb=" O VAL O 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.330A pdb=" N MET B 70 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET B 100 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 29 removed outlier: 3.757A pdb=" N ALA C 26 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 90 removed outlier: 5.132A pdb=" N LEU C 94 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA C 157 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 90 removed outlier: 5.132A pdb=" N LEU C 94 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA C 157 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AA7, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.825A pdb=" N ARG D 57 " --> pdb=" O CYS D 72 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N CYS D 72 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE D 59 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA D 70 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU D 61 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 190 through 191 Processing sheet with id=AB1, first strand: chain 'D' and resid 332 through 333 Processing sheet with id=AB2, first strand: chain 'D' and resid 373 through 381 Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 146 removed outlier: 6.498A pdb=" N TYR E 102 " --> pdb=" O THR E 142 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU E 144 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL E 104 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL E 146 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL E 106 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 23 through 28 removed outlier: 9.250A pdb=" N VAL G 86 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR G 19 " --> pdb=" O VAL G 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'G' and resid 182 through 185 Processing sheet with id=AB7, first strand: chain 'G' and resid 233 through 238 removed outlier: 5.387A pdb=" N ARG G 249 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG G 260 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP G 251 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 300 through 303 removed outlier: 6.374A pdb=" N VAL G 587 " --> pdb=" O VAL G 603 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE G 605 " --> pdb=" O VAL G 587 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER G 589 " --> pdb=" O PHE G 605 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G 561 " --> pdb=" O VAL G 588 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU G 590 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL G 563 " --> pdb=" O LEU G 590 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY G 325 " --> pdb=" O LEU G 562 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY G 564 " --> pdb=" O GLY G 325 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU G 327 " --> pdb=" O GLY G 564 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ASP G 354 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL G 326 " --> pdb=" O ASP G 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 436 through 437 removed outlier: 6.341A pdb=" N VAL G 390 " --> pdb=" O VAL G 420 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL G 422 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU G 392 " --> pdb=" O VAL G 422 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR G 389 " --> pdb=" O VAL G 464 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU G 466 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU G 391 " --> pdb=" O LEU G 466 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY G 468 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA G 393 " --> pdb=" O GLY G 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 615 through 618 Processing sheet with id=AC2, first strand: chain 'G' and resid 693 through 699 removed outlier: 4.033A pdb=" N TRP G 699 " --> pdb=" O LEU G 767 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA G 724 " --> pdb=" O ALA G 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 158 through 161 removed outlier: 5.796A pdb=" N PHE F 166 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 241 through 242 Processing sheet with id=AC5, first strand: chain 'F' and resid 261 through 266 removed outlier: 6.763A pdb=" N ILE F 328 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER F 254 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASP F 330 " --> pdb=" O SER F 254 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AC7, first strand: chain 'I' and resid 69 through 75 removed outlier: 6.471A pdb=" N ALA I 74 " --> pdb=" O GLY I 89 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY I 89 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 109 through 112 Processing sheet with id=AC9, first strand: chain 'L' and resid 65 through 66 Processing sheet with id=AD1, first strand: chain 'L' and resid 71 through 73 removed outlier: 3.732A pdb=" N VAL L 80 " --> pdb=" O VAL L 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 67 through 69 Processing sheet with id=AD3, first strand: chain 'N' and resid 385 through 386 Processing sheet with id=AD4, first strand: chain 'M' and resid 63 through 71 removed outlier: 5.242A pdb=" N PHE M 64 " --> pdb=" O VAL M 82 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL M 82 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP M 70 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR M 76 " --> pdb=" O TRP M 70 " (cutoff:3.500A) 2301 hydrogen bonds defined for protein. 6627 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: 8.69 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.40: 14371 1.40 - 1.62: 21590 1.62 - 1.84: 293 1.84 - 2.06: 0 2.06 - 2.29: 92 Bond restraints: 36346 Sorted by residual: bond pdb=" C50 XP2 L 701 " pdb=" O49 XP2 L 701 " ideal model delta sigma weight residual 1.344 1.442 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C39 XP2 L 701 " pdb=" O38 XP2 L 701 " ideal model delta sigma weight residual 1.348 1.440 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C28 XP2 L 701 " pdb=" C30 XP2 L 701 " ideal model delta sigma weight residual 1.561 1.484 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C58 XP2 L 701 " pdb=" C59 XP2 L 701 " ideal model delta sigma weight residual 1.526 1.603 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C14 XP2 L 701 " pdb=" O13 XP2 L 701 " ideal model delta sigma weight residual 1.361 1.436 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 36341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 49150 2.33 - 4.65: 731 4.65 - 6.98: 33 6.98 - 9.30: 8 9.30 - 11.63: 5 Bond angle restraints: 49927 Sorted by residual: angle pdb=" N GLY J 202 " pdb=" CA GLY J 202 " pdb=" C GLY J 202 " ideal model delta sigma weight residual 112.50 103.08 9.42 1.16e+00 7.43e-01 6.59e+01 angle pdb=" N PRO J 204 " pdb=" CA PRO J 204 " pdb=" CB PRO J 204 " ideal model delta sigma weight residual 103.25 96.55 6.70 1.05e+00 9.07e-01 4.08e+01 angle pdb=" N ILE L 200 " pdb=" CA ILE L 200 " pdb=" C ILE L 200 " ideal model delta sigma weight residual 113.47 109.06 4.41 1.01e+00 9.80e-01 1.91e+01 angle pdb=" C ARG F 73 " pdb=" CA ARG F 73 " pdb=" CB ARG F 73 " ideal model delta sigma weight residual 115.79 110.60 5.19 1.19e+00 7.06e-01 1.90e+01 angle pdb=" N PRO J 206 " pdb=" CA PRO J 206 " pdb=" C PRO J 206 " ideal model delta sigma weight residual 112.47 103.81 8.66 2.06e+00 2.36e-01 1.77e+01 ... (remaining 49922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 20937 35.46 - 70.92: 162 70.92 - 106.39: 21 106.39 - 141.85: 3 141.85 - 177.31: 2 Dihedral angle restraints: 21125 sinusoidal: 6812 harmonic: 14313 Sorted by residual: dihedral pdb=" C10 FMN F 501 " pdb=" C1' FMN F 501 " pdb=" N10 FMN F 501 " pdb=" C2' FMN F 501 " ideal model delta sinusoidal sigma weight residual 257.59 80.28 177.31 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP G 802 " pdb=" C1' GTP G 802 " pdb=" N9 GTP G 802 " pdb=" O4' GTP G 802 " ideal model delta sinusoidal sigma weight residual 104.59 -86.49 -168.92 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA ALA E 155 " pdb=" C ALA E 155 " pdb=" N PRO E 156 " pdb=" CA PRO E 156 " ideal model delta harmonic sigma weight residual 180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 21122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4767 0.048 - 0.096: 1033 0.096 - 0.144: 232 0.144 - 0.192: 7 0.192 - 0.240: 4 Chirality restraints: 6043 Sorted by residual: chirality pdb=" C73 XP2 L 701 " pdb=" C71 XP2 L 701 " pdb=" C74 XP2 L 701 " pdb=" O76 XP2 L 701 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C11 XP2 L 701 " pdb=" C12 XP2 L 701 " pdb=" C26 XP2 L 701 " pdb=" O10 XP2 L 701 " both_signs ideal model delta sigma weight residual False 2.38 2.60 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB THR G 137 " pdb=" CA THR G 137 " pdb=" OG1 THR G 137 " pdb=" CG2 THR G 137 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 6040 not shown) Planarity restraints: 6322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 MQ9 H 501 " -0.105 2.00e-02 2.50e+03 1.84e-01 1.19e+03 pdb=" C2 MQ9 H 501 " -0.021 2.00e-02 2.50e+03 pdb=" C3 MQ9 H 501 " -0.046 2.00e-02 2.50e+03 pdb=" C3A MQ9 H 501 " 0.037 2.00e-02 2.50e+03 pdb=" C3B MQ9 H 501 " 0.137 2.00e-02 2.50e+03 pdb=" C3C MQ9 H 501 " 0.159 2.00e-02 2.50e+03 pdb=" C3D MQ9 H 501 " 0.081 2.00e-02 2.50e+03 pdb=" C4 MQ9 H 501 " -0.150 2.00e-02 2.50e+03 pdb=" C5 MQ9 H 501 " 0.075 2.00e-02 2.50e+03 pdb=" C5M MQ9 H 501 " 0.380 2.00e-02 2.50e+03 pdb=" C6 MQ9 H 501 " 0.021 2.00e-02 2.50e+03 pdb=" C7 MQ9 H 501 " 0.095 2.00e-02 2.50e+03 pdb=" O1 MQ9 H 501 " -0.271 2.00e-02 2.50e+03 pdb=" O4 MQ9 H 501 " -0.394 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 MQ9 H 501 " 0.240 2.00e-02 2.50e+03 2.02e-01 5.10e+02 pdb=" C43 MQ9 H 501 " -0.334 2.00e-02 2.50e+03 pdb=" C44 MQ9 H 501 " -0.079 2.00e-02 2.50e+03 pdb=" C45 MQ9 H 501 " 0.002 2.00e-02 2.50e+03 pdb=" C46 MQ9 H 501 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 MQ9 H 501 " 0.012 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" C11 MQ9 H 501 " -0.145 2.00e-02 2.50e+03 pdb=" C7 MQ9 H 501 " -0.195 2.00e-02 2.50e+03 pdb=" C8 MQ9 H 501 " 0.266 2.00e-02 2.50e+03 pdb=" C9 MQ9 H 501 " 0.062 2.00e-02 2.50e+03 ... (remaining 6319 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 107 2.41 - 3.03: 25465 3.03 - 3.65: 58048 3.65 - 4.28: 88002 4.28 - 4.90: 146862 Nonbonded interactions: 318484 Sorted by model distance: nonbonded pdb=" OE2 GLU F 372 " pdb="ZN ZN F 502 " model vdw 1.787 2.230 nonbonded pdb=" OG SER K 49 " pdb=" O GLN K 54 " model vdw 1.896 3.040 nonbonded pdb=" OH TYR A 110 " pdb=" O TRP H 325 " model vdw 1.939 3.040 nonbonded pdb=" OG SER B 106 " pdb=" O LEU I 97 " model vdw 1.967 3.040 nonbonded pdb=" O PRO E 235 " pdb=" OG1 THR E 236 " model vdw 2.012 3.040 ... (remaining 318479 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.610 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: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 41.700 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 : 0.007 0.816 36387 Z= 0.503 Angle : 0.832 30.120 50020 Z= 0.395 Chirality : 0.042 0.240 6043 Planarity : 0.007 0.202 6322 Dihedral : 11.742 177.309 11991 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.46 % Favored : 94.34 % Rotamer: Outliers : 0.06 % Allowed : 0.10 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 5018 helix: 0.84 (0.10), residues: 2802 sheet: -0.28 (0.31), residues: 255 loop : -0.56 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 87 TYR 0.057 0.002 TYR N 367 PHE 0.023 0.002 PHE N 158 TRP 0.024 0.002 TRP A 121 HIS 0.008 0.001 HIS M 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.26 (36346) covalent geometry : angle 0.69669 / 0.39 (49927) hydrogen bonds : bond 0.13427 / 8.79 ( 2281) hydrogen bonds : angle 6.50371 / 4.76 ( 6627) metal coordination : bond 0.03513 / 2.61 ( 40) metal coordination : angle 10.55071 / 7.14 ( 93) Misc. bond : bond 0.81631 / 42.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.278 Fit side-chains REVERT: D 354 MET cc_start: 0.8051 (tpt) cc_final: 0.7818 (tpt) REVERT: G 185 MET cc_start: 0.8092 (mtt) cc_final: 0.7861 (mtt) REVERT: K 80 MET cc_start: 0.8324 (mmm) cc_final: 0.8062 (mmm) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.6827 time to fit residues: 128.5789 Evaluate side-chains 149 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.037320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.031947 restraints weight = 293551.368| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.42 r_work: 0.3026 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 36387 Z= 0.208 Angle : 0.791 29.129 50020 Z= 0.326 Chirality : 0.043 0.195 6043 Planarity : 0.005 0.122 6322 Dihedral : 7.479 168.882 5581 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.13 % Rotamer: Outliers : 0.48 % Allowed : 3.61 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.12), residues: 5018 helix: 1.36 (0.10), residues: 2837 sheet: -0.17 (0.30), residues: 272 loop : -0.37 (0.15), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 87 TYR 0.029 0.002 TYR N 367 PHE 0.028 0.002 PHE L 345 TRP 0.019 0.001 TRP L 148 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (36346) covalent geometry : angle 0.63653 / 0.32 (49927) hydrogen bonds : bond 0.04808 / 3.28 ( 2281) hydrogen bonds : angle 5.14335 / 3.77 ( 6627) metal coordination : bond 0.02540 / 1.72 ( 40) metal coordination : angle 10.91758 / 7.51 ( 93) Misc. bond : bond 0.00243 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 1.360 Fit side-chains REVERT: A 99 MET cc_start: 0.9239 (tpp) cc_final: 0.8783 (tpp) REVERT: C 144 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8557 (ttm) REVERT: G 185 MET cc_start: 0.8814 (mtt) cc_final: 0.8460 (mtt) REVERT: H 186 MET cc_start: 0.8769 (mtp) cc_final: 0.8567 (ttm) REVERT: J 176 MET cc_start: 0.9266 (mmm) cc_final: 0.9046 (mmm) outliers start: 15 outliers final: 3 residues processed: 156 average time/residue: 0.6901 time to fit residues: 132.5504 Evaluate side-chains 154 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 342 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 412 optimal weight: 0.9990 chunk 442 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 419 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 380 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 GLN ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 415 ASN F 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.037302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.031907 restraints weight = 294707.371| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.45 r_work: 0.3032 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 36387 Z= 0.165 Angle : 0.743 28.216 50020 Z= 0.296 Chirality : 0.042 0.211 6043 Planarity : 0.005 0.124 6322 Dihedral : 6.864 172.940 5581 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.43 % Favored : 96.43 % Rotamer: Outliers : 0.89 % Allowed : 5.34 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 5018 helix: 1.58 (0.10), residues: 2844 sheet: -0.19 (0.32), residues: 248 loop : -0.29 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.027 0.001 TYR M 444 PHE 0.027 0.001 PHE L 345 TRP 0.021 0.001 TRP L 148 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (36346) covalent geometry : angle 0.58226 / 0.29 (49927) hydrogen bonds : bond 0.04135 / 2.84 ( 2281) hydrogen bonds : angle 4.77165 / 3.49 ( 6627) metal coordination : bond 0.01978 / 1.36 ( 40) metal coordination : angle 10.71408 / 7.48 ( 93) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.226 Fit side-chains REVERT: C 144 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8534 (ttm) REVERT: D 300 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8712 (mtt) REVERT: G 185 MET cc_start: 0.8841 (mtt) cc_final: 0.8558 (mmm) REVERT: J 176 MET cc_start: 0.9229 (mmm) cc_final: 0.8979 (mmm) outliers start: 28 outliers final: 7 residues processed: 166 average time/residue: 0.6425 time to fit residues: 132.9585 Evaluate side-chains 159 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 59 optimal weight: 7.9990 chunk 483 optimal weight: 4.9990 chunk 412 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 386 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 376 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 260 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.037139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.031733 restraints weight = 293503.536| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.44 r_work: 0.3029 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 36387 Z= 0.163 Angle : 0.724 26.863 50020 Z= 0.286 Chirality : 0.041 0.193 6043 Planarity : 0.005 0.128 6322 Dihedral : 6.582 176.524 5581 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 1.41 % Allowed : 6.55 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.12), residues: 5018 helix: 1.68 (0.10), residues: 2847 sheet: -0.12 (0.32), residues: 255 loop : -0.26 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 168 TYR 0.025 0.001 TYR M 444 PHE 0.027 0.001 PHE L 345 TRP 0.018 0.001 TRP L 148 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (36346) covalent geometry : angle 0.56726 / 0.28 (49927) hydrogen bonds : bond 0.03927 / 2.69 ( 2281) hydrogen bonds : angle 4.64012 / 3.40 ( 6627) metal coordination : bond 0.02059 / 1.41 ( 40) metal coordination : angle 10.45676 / 7.28 ( 93) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 1.385 Fit side-chains REVERT: C 144 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8613 (ttm) REVERT: D 300 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8718 (mtt) REVERT: E 65 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (mm) REVERT: G 185 MET cc_start: 0.8829 (mtt) cc_final: 0.8615 (mmm) REVERT: J 176 MET cc_start: 0.9230 (mmm) cc_final: 0.8922 (mmm) REVERT: N 155 MET cc_start: 0.8753 (mtm) cc_final: 0.8373 (ptp) REVERT: M 452 MET cc_start: 0.9033 (mtt) cc_final: 0.8694 (mmt) outliers start: 44 outliers final: 13 residues processed: 177 average time/residue: 0.6214 time to fit residues: 137.4330 Evaluate side-chains 166 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 110 optimal weight: 0.6980 chunk 413 optimal weight: 10.0000 chunk 386 optimal weight: 0.8980 chunk 418 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 445 optimal weight: 0.8980 chunk 414 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 GLN L 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.036716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.031287 restraints weight = 296074.701| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.44 r_work: 0.3008 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 36387 Z= 0.217 Angle : 0.749 27.064 50020 Z= 0.298 Chirality : 0.042 0.188 6043 Planarity : 0.005 0.118 6322 Dihedral : 6.485 176.835 5581 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 1.37 % Allowed : 7.80 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.12), residues: 5018 helix: 1.67 (0.10), residues: 2855 sheet: -0.13 (0.32), residues: 271 loop : -0.28 (0.16), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 168 TYR 0.022 0.002 TYR M 444 PHE 0.026 0.001 PHE L 345 TRP 0.015 0.001 TRP L 148 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (36346) covalent geometry : angle 0.59117 / 0.30 (49927) hydrogen bonds : bond 0.04036 / 2.76 ( 2281) hydrogen bonds : angle 4.65018 / 3.40 ( 6627) metal coordination : bond 0.02665 / 1.84 ( 40) metal coordination : angle 10.69824 / 7.49 ( 93) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.345 Fit side-chains REVERT: D 300 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8743 (mtt) REVERT: G 185 MET cc_start: 0.8915 (mtt) cc_final: 0.8627 (mmm) REVERT: J 176 MET cc_start: 0.9231 (mmm) cc_final: 0.8931 (mmm) REVERT: L 280 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8434 (t) REVERT: N 264 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8749 (p-80) outliers start: 43 outliers final: 17 residues processed: 177 average time/residue: 0.5780 time to fit residues: 127.9269 Evaluate side-chains 170 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain J residue 205 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 264 HIS Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 70 optimal weight: 0.8980 chunk 121 optimal weight: 0.0570 chunk 161 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 404 optimal weight: 0.9990 chunk 430 optimal weight: 2.9990 chunk 435 optimal weight: 9.9990 chunk 245 optimal weight: 0.8980 chunk 349 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 chunk 464 optimal weight: 0.7980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.037480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.032125 restraints weight = 292091.266| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.45 r_work: 0.3049 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 36387 Z= 0.115 Angle : 0.703 27.839 50020 Z= 0.272 Chirality : 0.040 0.226 6043 Planarity : 0.004 0.134 6322 Dihedral : 6.332 175.553 5581 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 1.25 % Allowed : 8.31 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 5018 helix: 1.80 (0.10), residues: 2856 sheet: -0.13 (0.32), residues: 268 loop : -0.29 (0.16), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 95 TYR 0.024 0.001 TYR M 444 PHE 0.028 0.001 PHE L 345 TRP 0.018 0.001 TRP L 148 HIS 0.005 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (36346) covalent geometry : angle 0.54219 / 0.27 (49927) hydrogen bonds : bond 0.03656 / 2.50 ( 2281) hydrogen bonds : angle 4.48027 / 3.28 ( 6627) metal coordination : bond 0.01236 / 0.83 ( 40) metal coordination : angle 10.39525 / 7.29 ( 93) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: D 300 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8664 (mtt) REVERT: E 65 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9029 (mm) REVERT: E 128 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8872 (mp) REVERT: G 185 MET cc_start: 0.8748 (mtt) cc_final: 0.8503 (mmm) REVERT: G 701 MET cc_start: 0.9166 (mmt) cc_final: 0.8902 (mmt) REVERT: J 176 MET cc_start: 0.9239 (mmm) cc_final: 0.8938 (mmm) REVERT: L 280 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (t) outliers start: 39 outliers final: 15 residues processed: 175 average time/residue: 0.6325 time to fit residues: 139.2140 Evaluate side-chains 169 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain J residue 205 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 348 optimal weight: 20.0000 chunk 458 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 433 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 438 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 350 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.036566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.031131 restraints weight = 296076.343| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.44 r_work: 0.3003 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 36387 Z= 0.233 Angle : 0.761 25.985 50020 Z= 0.303 Chirality : 0.042 0.180 6043 Planarity : 0.005 0.122 6322 Dihedral : 6.398 177.348 5581 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.85 % Favored : 96.07 % Rotamer: Outliers : 1.34 % Allowed : 8.60 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 5018 helix: 1.79 (0.10), residues: 2846 sheet: 0.01 (0.33), residues: 261 loop : -0.28 (0.15), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 168 TYR 0.020 0.002 TYR M 444 PHE 0.025 0.001 PHE L 345 TRP 0.013 0.001 TRP L 148 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (36346) covalent geometry : angle 0.60924 / 0.30 (49927) hydrogen bonds : bond 0.04006 / 2.75 ( 2281) hydrogen bonds : angle 4.58108 / 3.35 ( 6627) metal coordination : bond 0.02847 / 1.99 ( 40) metal coordination : angle 10.58553 / 7.40 ( 93) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: C 144 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (ttm) REVERT: D 300 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: E 128 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8907 (mp) REVERT: G 185 MET cc_start: 0.8909 (mtt) cc_final: 0.8689 (mmm) REVERT: J 41 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7408 (mtm-85) REVERT: J 176 MET cc_start: 0.9234 (mmm) cc_final: 0.8946 (mmm) REVERT: L 245 MET cc_start: 0.7851 (mmm) cc_final: 0.7532 (mmm) REVERT: L 280 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8478 (t) outliers start: 42 outliers final: 24 residues processed: 177 average time/residue: 0.6463 time to fit residues: 143.3321 Evaluate side-chains 179 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain J residue 205 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 7 optimal weight: 2.9990 chunk 409 optimal weight: 10.0000 chunk 283 optimal weight: 0.7980 chunk 358 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 391 optimal weight: 20.0000 chunk 251 optimal weight: 1.9990 chunk 448 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.037015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.031623 restraints weight = 294888.135| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.46 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 36387 Z= 0.147 Angle : 0.719 27.078 50020 Z= 0.279 Chirality : 0.040 0.166 6043 Planarity : 0.004 0.115 6322 Dihedral : 6.301 176.450 5581 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 1.28 % Allowed : 9.11 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5018 helix: 1.84 (0.10), residues: 2847 sheet: -0.10 (0.32), residues: 269 loop : -0.27 (0.16), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 95 TYR 0.023 0.001 TYR M 444 PHE 0.027 0.001 PHE L 345 TRP 0.015 0.001 TRP L 148 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (36346) covalent geometry : angle 0.56025 / 0.28 (49927) hydrogen bonds : bond 0.03726 / 2.55 ( 2281) hydrogen bonds : angle 4.48737 / 3.29 ( 6627) metal coordination : bond 0.01770 / 1.21 ( 40) metal coordination : angle 10.45517 / 7.34 ( 93) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: C 144 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8647 (ttm) REVERT: D 300 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8705 (mtt) REVERT: E 128 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8860 (mp) REVERT: G 137 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8812 (p) REVERT: G 185 MET cc_start: 0.8818 (mtt) cc_final: 0.8521 (mmm) REVERT: J 41 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7345 (mtm-85) REVERT: J 176 MET cc_start: 0.9266 (mmm) cc_final: 0.8958 (mmm) REVERT: L 280 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8532 (t) REVERT: N 155 MET cc_start: 0.8588 (mtm) cc_final: 0.8253 (mtp) outliers start: 40 outliers final: 19 residues processed: 180 average time/residue: 0.6406 time to fit residues: 145.0149 Evaluate side-chains 175 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 383 optimal weight: 40.0000 chunk 59 optimal weight: 5.9990 chunk 351 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 475 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.036559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.031137 restraints weight = 295368.104| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.44 r_work: 0.3005 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 36387 Z= 0.227 Angle : 0.761 26.112 50020 Z= 0.302 Chirality : 0.042 0.217 6043 Planarity : 0.005 0.112 6322 Dihedral : 6.351 177.506 5581 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.89 % Favored : 96.03 % Rotamer: Outliers : 1.31 % Allowed : 9.08 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.12), residues: 5018 helix: 1.79 (0.10), residues: 2855 sheet: -0.17 (0.32), residues: 272 loop : -0.27 (0.16), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 168 TYR 0.020 0.002 TYR M 444 PHE 0.026 0.001 PHE L 345 TRP 0.013 0.001 TRP N 309 HIS 0.007 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 (36346) covalent geometry : angle 0.60955 / 0.30 (49927) hydrogen bonds : bond 0.03925 / 2.69 ( 2281) hydrogen bonds : angle 4.54920 / 3.33 ( 6627) metal coordination : bond 0.02713 / 1.88 ( 40) metal coordination : angle 10.59883 / 7.42 ( 93) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: C 144 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8787 (ttm) REVERT: D 300 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8850 (mtt) REVERT: E 128 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8895 (mp) REVERT: G 185 MET cc_start: 0.9004 (mtt) cc_final: 0.8778 (mmm) REVERT: J 41 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7417 (mtm-85) REVERT: J 90 MET cc_start: 0.9444 (ttt) cc_final: 0.9239 (ttm) REVERT: J 176 MET cc_start: 0.9352 (mmm) cc_final: 0.9091 (mmm) REVERT: L 280 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8519 (t) REVERT: N 155 MET cc_start: 0.8983 (mtm) cc_final: 0.8618 (mtp) outliers start: 41 outliers final: 24 residues processed: 181 average time/residue: 0.6274 time to fit residues: 142.0368 Evaluate side-chains 179 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 117 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 320 VAL Chi-restraints excluded: chain M residue 354 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 291 optimal weight: 9.9990 chunk 260 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 357 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 220 optimal weight: 0.0570 chunk 398 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.037466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.032112 restraints weight = 293459.596| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.46 r_work: 0.3053 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36387 Z= 0.116 Angle : 0.714 27.329 50020 Z= 0.276 Chirality : 0.040 0.229 6043 Planarity : 0.005 0.143 6322 Dihedral : 6.185 175.777 5581 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.29 % Favored : 96.61 % Rotamer: Outliers : 0.93 % Allowed : 9.68 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.12), residues: 5018 helix: 1.88 (0.10), residues: 2857 sheet: -0.12 (0.32), residues: 271 loop : -0.27 (0.16), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 383 TYR 0.025 0.001 TYR M 444 PHE 0.028 0.001 PHE L 345 TRP 0.019 0.001 TRP L 148 HIS 0.004 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (36346) covalent geometry : angle 0.55756 / 0.27 (49927) hydrogen bonds : bond 0.03537 / 2.42 ( 2281) hydrogen bonds : angle 4.40897 / 3.23 ( 6627) metal coordination : bond 0.01193 / 0.80 ( 40) metal coordination : angle 10.36757 / 7.27 ( 93) Misc. bond : bond 0.00005 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10036 Ramachandran restraints generated. 5018 Oldfield, 0 Emsley, 5018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.379 Fit side-chains REVERT: C 144 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8737 (ttp) REVERT: D 300 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8669 (mtt) REVERT: E 128 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8929 (mp) REVERT: G 701 MET cc_start: 0.9158 (mmt) cc_final: 0.8914 (mmt) REVERT: J 41 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7250 (mtm-85) REVERT: J 176 MET cc_start: 0.9271 (mmm) cc_final: 0.9009 (mmm) REVERT: L 280 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8538 (t) REVERT: N 155 MET cc_start: 0.8944 (mtm) cc_final: 0.8543 (mtp) outliers start: 29 outliers final: 17 residues processed: 172 average time/residue: 0.6359 time to fit residues: 136.8937 Evaluate side-chains 172 residues out of total 3930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain G residue 441 VAL Chi-restraints excluded: chain G residue 703 LEU Chi-restraints excluded: chain G residue 744 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 182 TYR Chi-restraints excluded: chain J residue 41 ARG Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain N residue 294 MET Chi-restraints excluded: chain N residue 452 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 272 optimal weight: 0.8980 chunk 352 optimal weight: 0.9990 chunk 400 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 482 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 chunk 331 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.036805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.031371 restraints weight = 293942.992| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.44 r_work: 0.3020 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 36387 Z= 0.193 Angle : 0.740 25.641 50020 Z= 0.291 Chirality : 0.041 0.153 6043 Planarity : 0.004 0.097 6322 Dihedral : 6.242 177.217 5581 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 0.89 % Allowed : 9.78 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 0.00 % Twisted Proline : 0.64 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 5018 helix: 1.87 (0.10), residues: 2872 sheet: -0.04 (0.33), residues: 269 loop : -0.25 (0.16), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 168 TYR 0.021 0.001 TYR M 444 PHE 0.026 0.001 PHE L 345 TRP 0.013 0.001 TRP L 148 HIS 0.006 0.001 HIS I 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (36346) covalent geometry : angle 0.58873 / 0.29 (49927) hydrogen bonds : bond 0.03757 / 2.58 ( 2281) hydrogen bonds : angle 4.46521 / 3.27 ( 6627) metal coordination : bond 0.02320 / 1.62 ( 40) metal coordination : angle 10.42545 / 7.30 ( 93) Misc. bond : bond 0.00020 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8974.06 seconds wall clock time: 154 minutes 40.13 seconds (9280.13 seconds total)