Starting phenix.real_space_refine on Mon Aug 5 01:19:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbq_19034/08_2024/8rbq_19034.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.016 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: 6 Type Number sf(0) Gaussians Fe 18 7.16 5 P 4 5.49 5 S 96 5.16 5 C 7820 2.51 5 N 2012 2.21 5 O 2190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 88": "OE1" <-> "OE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3523 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 37, 'TRANS': 439} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1478 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 187} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 807 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 2 Chain: "D" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2320 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 282} Chain breaks: 1 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "B" 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: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 302 Unusual residues: {'LMT': 5, 'PTY': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 37.283 73.370 59.357 1.00 45.39 S ATOM 5726 SG CYS E 122 39.028 70.965 57.132 1.00 75.02 S ATOM 844 SG CYS A 113 41.347 74.017 54.715 1.00 51.48 S ATOM 5117 SG CYS E 39 40.026 77.348 56.316 1.00 71.75 S ATOM 4136 SG CYS C 376 42.148 90.594 96.617 1.00 33.81 S ATOM 4451 SG CYS C 419 37.986 92.158 96.996 1.00 10.84 S ATOM 4094 SG CYS C 370 38.758 90.272 90.582 1.00 10.19 S ATOM 4119 SG CYS C 373 41.448 95.623 93.319 1.00 21.56 S ATOM 4382 SG CYS C 409 44.294 81.309 102.702 1.00 8.31 S ATOM 4404 SG CYS C 412 45.896 86.890 105.913 1.00 13.57 S ATOM 4420 SG CYS C 415 43.140 87.210 100.674 1.00 27.24 S ATOM 4162 SG CYS C 380 48.681 86.177 100.503 1.00 26.58 S ATOM 8944 SG CYS B 119 30.378 43.473 108.328 1.00 82.60 S ATOM 9117 SG CYS B 145 24.857 44.427 108.411 1.00 80.07 S ATOM 9098 SG CYS B 142 28.973 45.573 103.259 1.00 66.64 S ATOM 9081 SG CYS B 139 27.627 49.973 107.492 1.00 27.27 S ATOM 8868 SG CYS B 109 22.343 40.394 118.183 1.00 84.64 S ATOM 8886 SG CYS B 112 22.377 35.360 113.998 1.00 89.96 S ATOM 8910 SG CYS B 115 26.384 40.027 113.855 1.00 72.60 S ATOM 9147 SG CYS B 149 19.627 39.516 112.504 1.00101.78 S Time building chain proxies: 6.68, per 1000 atoms: 0.55 Number of scatterers: 12140 At special positions: 0 Unit cell: (82.82, 143.5, 157.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 18 26.01 S 96 16.00 P 4 15.00 O 2190 8.00 N 2012 7.00 C 7820 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 - 3.50 Amino acid : False - 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 200 " pdb="FE1 FES A 200 " - pdb=" SG CYS A 25 " pdb="FE1 FES A 200 " - pdb=" SG CYS E 122 " pdb="FE2 FES A 200 " - pdb=" SG CYS E 39 " pdb="FE2 FES A 200 " - pdb=" SG CYS A 113 " pdb=" SF4 B 201 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb=" SF4 B 202 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb=" SF4 C 501 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 54.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.648A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 4.012A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.695A pdb=" N SER A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 94 removed outlier: 4.062A pdb=" N ALA A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.080A pdb=" N ILE A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 112' Processing helix chain 'A' and resid 113 through 125 Proline residue: A 119 - end of helix removed outlier: 3.527A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.045A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.609A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.615A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.508A pdb=" N ARG C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.623A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.576A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.500A pdb=" N ASP C 262 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.509A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.699A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.563A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'E' and resid 17 through 26 removed outlier: 4.147A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.542A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.877A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.778A pdb=" N VAL E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.642A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.404A pdb=" N ALA E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.442A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 4.038A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 81 removed outlier: 3.886A pdb=" N LEU G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 80 " --> pdb=" O THR G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.582A pdb=" N ALA G 92 " --> pdb=" O ASN G 89 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 93' Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.232A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 removed outlier: 4.001A pdb=" N PHE G 173 " --> pdb=" O ILE G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.772A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 23 removed outlier: 3.688A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 removed outlier: 3.510A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix removed outlier: 3.513A pdb=" N PHE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 67 Processing helix chain 'D' and resid 69 through 75 removed outlier: 4.065A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.530A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.815A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 215 through 232 removed outlier: 3.558A pdb=" N GLU D 219 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 262 through 266 removed outlier: 3.672A pdb=" N GLY D 265 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU D 266 " --> pdb=" O ALA D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 266' Processing helix chain 'D' and resid 273 through 280 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 317 through 337 removed outlier: 4.626A pdb=" N PHE D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.526A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 228 through 233 removed outlier: 4.536A pdb=" N VAL C 164 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA6, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AA7, first strand: chain 'G' and resid 108 through 111 removed outlier: 6.489A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 14 through 18 Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101 612 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 4859 1.42 - 1.64: 7372 1.64 - 1.86: 120 1.86 - 2.07: 0 2.07 - 2.29: 52 Bond restraints: 12403 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C8 PTY D 403 " pdb=" O7 PTY D 403 " ideal model delta sigma weight residual 1.331 1.451 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C30 PTY D 403 " pdb=" O4 PTY D 403 " ideal model delta sigma weight residual 1.331 1.446 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" N CYS E 39 " pdb=" CA CYS E 39 " ideal model delta sigma weight residual 1.463 1.424 0.039 6.90e-03 2.10e+04 3.17e+01 bond pdb=" C CYS A 113 " pdb=" N ALA A 114 " ideal model delta sigma weight residual 1.333 1.263 0.069 1.38e-02 5.25e+03 2.52e+01 ... (remaining 12398 not shown) Histogram of bond angle deviations from ideal: 73.44 - 87.20: 50 87.20 - 100.95: 29 100.95 - 114.71: 7879 114.71 - 128.47: 8825 128.47 - 142.23: 98 Bond angle restraints: 16881 Sorted by residual: angle pdb=" N CYS A 25 " pdb=" CA CYS A 25 " pdb=" CB CYS A 25 " ideal model delta sigma weight residual 110.39 122.79 -12.40 9.50e-01 1.11e+00 1.71e+02 angle pdb=" CA PRO B 158 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 112.00 96.10 15.90 1.40e+00 5.10e-01 1.29e+02 angle pdb=" C CYS A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.28 107.39 11.89 1.10e+00 8.26e-01 1.17e+02 angle pdb=" CA PRO H 61 " pdb=" N PRO H 61 " pdb=" CD PRO H 61 " ideal model delta sigma weight residual 112.00 98.55 13.45 1.40e+00 5.10e-01 9.23e+01 angle pdb=" N CYS B 149 " pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sigma weight residual 110.32 96.92 13.40 1.48e+00 4.57e-01 8.20e+01 ... (remaining 16876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 6960 24.95 - 49.90: 565 49.90 - 74.85: 89 74.85 - 99.79: 32 99.79 - 124.74: 18 Dihedral angle restraints: 7664 sinusoidal: 3253 harmonic: 4411 Sorted by residual: dihedral pdb=" CA PHE C 3 " pdb=" C PHE C 3 " pdb=" N ASN C 4 " pdb=" CA ASN C 4 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE E 89 " pdb=" C ILE E 89 " pdb=" N ALA E 90 " pdb=" CA ALA E 90 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" N CYS B 149 " pdb=" C CYS B 149 " pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " ideal model delta harmonic sigma weight residual 122.80 109.20 13.60 0 2.50e+00 1.60e-01 2.96e+01 ... (remaining 7661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 2020 1.008 - 2.016: 0 2.016 - 3.024: 0 3.024 - 4.032: 0 4.032 - 5.040: 3 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.57 -5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.47 5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" C4' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" C5' FMN G 301 " pdb=" O4' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.45 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 2020 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.148 2.00e-02 2.50e+03 4.11e-02 8.03e+01 pdb=" C10 FMN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.000 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.004 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.020 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.038 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.010 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.027 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.005 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.001 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.004 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.062 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 60 " 0.117 5.00e-02 4.00e+02 1.65e-01 4.37e+01 pdb=" N PRO H 61 " -0.285 5.00e-02 4.00e+02 pdb=" CA PRO H 61 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO H 61 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 86 " 0.100 5.00e-02 4.00e+02 1.50e-01 3.62e+01 pdb=" N PRO C 87 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.077 5.00e-02 4.00e+02 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2147 2.77 - 3.31: 10984 3.31 - 3.84: 19985 3.84 - 4.37: 22185 4.37 - 4.90: 39444 Nonbonded interactions: 94745 Sorted by model distance: nonbonded pdb=" OD1 ASP D 284 " pdb=" O2' RBF D 404 " model vdw 2.242 3.040 nonbonded pdb=" O THR E 41 " pdb=" OG1 THR E 45 " model vdw 2.258 3.040 nonbonded pdb=" O ILE G 203 " pdb=" N ARG G 206 " model vdw 2.285 3.120 nonbonded pdb=" OG SER C 21 " pdb=" OG1 THR C 174 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR C 237 " pdb=" O CYS C 412 " model vdw 2.300 3.040 ... (remaining 94740 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.360 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.008 0.213 12403 Z= 0.540 Angle : 1.298 17.933 16881 Z= 0.669 Chirality : 0.203 5.040 2023 Planarity : 0.011 0.165 2066 Dihedral : 19.502 124.742 4838 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.39 % Favored : 94.09 % Rotamer: Outliers : 0.65 % Allowed : 24.55 % Favored : 74.80 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.20), residues: 1541 helix: -0.57 (0.17), residues: 775 sheet: -0.82 (0.55), residues: 105 loop : -1.47 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 96 HIS 0.007 0.001 HIS E 105 PHE 0.035 0.002 PHE A 70 TYR 0.044 0.002 TYR H 7 ARG 0.019 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8202 (ptt90) REVERT: E 110 VAL cc_start: 0.9025 (t) cc_final: 0.8754 (p) REVERT: G 88 ASN cc_start: 0.4531 (p0) cc_final: 0.4247 (p0) outliers start: 8 outliers final: 3 residues processed: 200 average time/residue: 0.2806 time to fit residues: 76.7753 Evaluate side-chains 144 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN G 39 GLN G 125 ASN G 152 HIS G 217 GLN H 31 GLN D 327 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12403 Z= 0.243 Angle : 0.703 10.199 16881 Z= 0.334 Chirality : 0.046 0.349 2023 Planarity : 0.006 0.087 2066 Dihedral : 12.935 103.259 2217 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 3.43 % Allowed : 22.19 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1541 helix: 1.03 (0.19), residues: 780 sheet: -0.98 (0.55), residues: 104 loop : -1.29 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.006 0.001 HIS C 224 PHE 0.010 0.001 PHE A 70 TYR 0.015 0.001 TYR C 237 ARG 0.008 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 88 ASN cc_start: 0.4790 (p0) cc_final: 0.4456 (p0) REVERT: H 63 LYS cc_start: 0.6814 (pptt) cc_final: 0.6561 (pptt) outliers start: 42 outliers final: 14 residues processed: 187 average time/residue: 0.2382 time to fit residues: 64.1654 Evaluate side-chains 147 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.8980 chunk 43 optimal weight: 0.0010 chunk 115 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 422 HIS E 181 HIS G 62 HIS ** G 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12403 Z= 0.255 Angle : 0.657 9.079 16881 Z= 0.317 Chirality : 0.045 0.361 2023 Planarity : 0.005 0.066 2066 Dihedral : 10.467 87.977 2210 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.84 % Favored : 93.90 % Rotamer: Outliers : 2.28 % Allowed : 24.39 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1541 helix: 1.45 (0.19), residues: 778 sheet: -0.87 (0.56), residues: 102 loop : -1.13 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.012 0.001 HIS G 62 PHE 0.027 0.001 PHE G 121 TYR 0.014 0.001 TYR C 237 ARG 0.005 0.000 ARG E 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6927 (tmm) cc_final: 0.6679 (tmm) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 0.2728 time to fit residues: 63.1432 Evaluate side-chains 154 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain H residue 2 ARG Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12403 Z= 0.299 Angle : 0.653 7.356 16881 Z= 0.317 Chirality : 0.045 0.345 2023 Planarity : 0.005 0.058 2066 Dihedral : 9.627 83.650 2210 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.10 % Favored : 93.71 % Rotamer: Outliers : 3.59 % Allowed : 23.41 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1541 helix: 1.61 (0.19), residues: 779 sheet: -0.99 (0.55), residues: 102 loop : -1.03 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.004 0.001 HIS G 62 PHE 0.012 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 138 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6933 (tmm) cc_final: 0.6671 (tmm) REVERT: C 449 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8948 (tt) outliers start: 44 outliers final: 24 residues processed: 167 average time/residue: 0.2482 time to fit residues: 59.6553 Evaluate side-chains 151 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN G 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12403 Z= 0.233 Angle : 0.638 13.476 16881 Z= 0.308 Chirality : 0.044 0.297 2023 Planarity : 0.005 0.056 2066 Dihedral : 9.062 74.974 2210 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.97 % Favored : 93.84 % Rotamer: Outliers : 3.10 % Allowed : 24.23 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1541 helix: 1.74 (0.19), residues: 780 sheet: -0.95 (0.54), residues: 104 loop : -0.94 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.010 0.001 HIS G 62 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.008 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6923 (tmm) cc_final: 0.6657 (tmm) REVERT: G 225 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: D 317 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7562 (tm-30) outliers start: 38 outliers final: 24 residues processed: 175 average time/residue: 0.2416 time to fit residues: 60.7508 Evaluate side-chains 153 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 0.0030 chunk 142 optimal weight: 0.7980 overall best weight: 2.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12403 Z= 0.296 Angle : 0.651 11.932 16881 Z= 0.316 Chirality : 0.044 0.251 2023 Planarity : 0.005 0.056 2066 Dihedral : 8.735 68.327 2210 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.29 % Favored : 93.51 % Rotamer: Outliers : 3.51 % Allowed : 25.12 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1541 helix: 1.77 (0.19), residues: 774 sheet: -0.90 (0.55), residues: 102 loop : -0.92 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.009 0.001 HIS G 62 PHE 0.011 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6923 (tmm) cc_final: 0.6657 (tmm) REVERT: C 449 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8957 (tt) REVERT: G 225 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: H 71 TYR cc_start: 0.6477 (OUTLIER) cc_final: 0.4908 (p90) REVERT: D 317 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 43 outliers final: 33 residues processed: 167 average time/residue: 0.2451 time to fit residues: 58.3016 Evaluate side-chains 167 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 92 optimal weight: 40.0000 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN ** G 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12403 Z= 0.268 Angle : 0.655 14.399 16881 Z= 0.317 Chirality : 0.044 0.208 2023 Planarity : 0.005 0.056 2066 Dihedral : 8.523 63.282 2210 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.10 % Favored : 93.71 % Rotamer: Outliers : 3.92 % Allowed : 24.55 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.23), residues: 1541 helix: 1.88 (0.19), residues: 767 sheet: -1.05 (0.56), residues: 100 loop : -0.90 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.009 0.001 HIS G 62 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6925 (tmm) cc_final: 0.6661 (tmm) REVERT: C 449 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8951 (tt) REVERT: H 71 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.5061 (p90) outliers start: 48 outliers final: 37 residues processed: 164 average time/residue: 0.2350 time to fit residues: 55.8814 Evaluate side-chains 168 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 129 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 110 ARG Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 125 ASN G 225 GLN H 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12403 Z= 0.341 Angle : 0.697 15.264 16881 Z= 0.336 Chirality : 0.045 0.203 2023 Planarity : 0.005 0.056 2066 Dihedral : 8.394 60.258 2210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 4.00 % Allowed : 25.04 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1541 helix: 1.84 (0.19), residues: 768 sheet: -1.22 (0.54), residues: 104 loop : -0.89 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.007 0.001 HIS G 62 PHE 0.012 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.008 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6822 (tmm) cc_final: 0.6569 (tmm) REVERT: C 449 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8990 (tt) REVERT: E 19 GLN cc_start: 0.8611 (pp30) cc_final: 0.8299 (pp30) REVERT: G 35 MET cc_start: 0.6724 (tpt) cc_final: 0.6373 (tpt) REVERT: G 225 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: H 71 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.4965 (p90) outliers start: 49 outliers final: 33 residues processed: 167 average time/residue: 0.2506 time to fit residues: 59.7265 Evaluate side-chains 164 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 471 LYS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN G 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12403 Z= 0.196 Angle : 0.669 15.064 16881 Z= 0.324 Chirality : 0.043 0.201 2023 Planarity : 0.005 0.053 2066 Dihedral : 8.125 59.595 2210 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.96 % Rotamer: Outliers : 2.77 % Allowed : 25.86 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1541 helix: 1.86 (0.19), residues: 781 sheet: -1.11 (0.55), residues: 102 loop : -0.89 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 96 HIS 0.008 0.001 HIS G 62 PHE 0.014 0.001 PHE A 143 TYR 0.016 0.001 TYR C 237 ARG 0.007 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 449 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8954 (tt) REVERT: E 19 GLN cc_start: 0.8561 (pp30) cc_final: 0.8258 (pp30) REVERT: G 35 MET cc_start: 0.6719 (tpt) cc_final: 0.6376 (tpt) REVERT: H 71 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.5079 (p90) outliers start: 34 outliers final: 24 residues processed: 161 average time/residue: 0.2416 time to fit residues: 56.2660 Evaluate side-chains 153 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 ASN G 125 ASN H 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12403 Z= 0.222 Angle : 0.681 14.273 16881 Z= 0.330 Chirality : 0.043 0.199 2023 Planarity : 0.005 0.054 2066 Dihedral : 7.993 59.410 2210 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.29 % Favored : 93.51 % Rotamer: Outliers : 2.69 % Allowed : 25.69 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1541 helix: 1.87 (0.19), residues: 782 sheet: -1.10 (0.55), residues: 104 loop : -0.85 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.008 0.001 HIS G 62 PHE 0.019 0.001 PHE G 198 TYR 0.016 0.001 TYR C 237 ARG 0.009 0.000 ARG G 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7507 (ttm) REVERT: C 449 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8953 (tt) REVERT: E 19 GLN cc_start: 0.8557 (pp30) cc_final: 0.8259 (pp30) REVERT: G 35 MET cc_start: 0.6647 (tpt) cc_final: 0.6308 (tpt) REVERT: H 71 TYR cc_start: 0.6589 (OUTLIER) cc_final: 0.5009 (p90) outliers start: 33 outliers final: 26 residues processed: 157 average time/residue: 0.2513 time to fit residues: 56.3846 Evaluate side-chains 159 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 38 TYR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 125 ASN Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 71 TYR Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0030 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 121 optimal weight: 0.0050 chunk 50 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.094978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063472 restraints weight = 33644.568| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.94 r_work: 0.2945 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12403 Z= 0.210 Angle : 0.684 13.748 16881 Z= 0.332 Chirality : 0.043 0.198 2023 Planarity : 0.005 0.054 2066 Dihedral : 7.874 59.700 2210 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.45 % Favored : 94.35 % Rotamer: Outliers : 2.37 % Allowed : 26.10 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1541 helix: 1.93 (0.19), residues: 777 sheet: -1.02 (0.56), residues: 102 loop : -0.86 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 96 HIS 0.008 0.001 HIS G 62 PHE 0.016 0.001 PHE G 198 TYR 0.016 0.001 TYR C 237 ARG 0.009 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2600.34 seconds wall clock time: 47 minutes 9.86 seconds (2829.86 seconds total)