Starting phenix.real_space_refine on Sat Dec 9 05:58:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/12_2023/6iww_9743_updated.pdb" } resolution = 3.9 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= -0.000 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6741 2.51 5 N 1653 2.21 5 O 1764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10227 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "B" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "D" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3054 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 397} Chain: "F" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 320 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.87, per 1000 atoms: 0.57 Number of scatterers: 10227 At special positions: 0 Unit cell: (104.304, 106.944, 85.8195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1764 8.00 N 1653 7.00 C 6741 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=0, symmetry=0 Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 0 sheets defined 73.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 18 through 36 removed outlier: 3.765A pdb=" N ILE A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.682A pdb=" N ASN A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 136 through 146 removed outlier: 3.682A pdb=" N PHE A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 162 through 182 removed outlier: 3.856A pdb=" N GLN A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 removed outlier: 3.934A pdb=" N ALA A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.217A pdb=" N TYR A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.705A pdb=" N LEU A 219 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 221 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 223 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 227 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 228 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N MET A 230 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 262 through 278 Proline residue: A 269 - end of helix Processing helix chain 'A' and resid 281 through 299 Proline residue: A 285 - end of helix removed outlier: 4.696A pdb=" N GLY A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 292 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 295 " --> pdb=" O PHE A 292 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET A 296 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 299 " --> pdb=" O MET A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 314 through 328 removed outlier: 5.055A pdb=" N ILE A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 337 through 364 removed outlier: 3.827A pdb=" N GLY A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.647A pdb=" N SER A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 430 removed outlier: 3.768A pdb=" N ALA A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 42 removed outlier: 3.915A pdb=" N ALA B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 36 removed outlier: 3.742A pdb=" N ILE C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 55 removed outlier: 3.570A pdb=" N LEU C 45 " --> pdb=" O PRO C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.724A pdb=" N ASN C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 103 through 115 Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'C' and resid 136 through 146 removed outlier: 3.700A pdb=" N PHE C 141 " --> pdb=" O PRO C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 157 through 182 removed outlier: 3.612A pdb=" N ALA C 165 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA C 166 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 169 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 172 " --> pdb=" O GLY C 169 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 179 " --> pdb=" O GLY C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.228A pdb=" N TYR C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 3.734A pdb=" N LEU C 219 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C 220 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 221 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 223 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C 227 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 233 through 244 Proline residue: C 238 - end of helix Processing helix chain 'C' and resid 247 through 250 No H-bonds generated for 'chain 'C' and resid 247 through 250' Processing helix chain 'C' and resid 262 through 278 Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 281 through 299 Proline residue: C 285 - end of helix removed outlier: 4.699A pdb=" N GLY C 288 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE C 292 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 295 " --> pdb=" O PHE C 292 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER C 299 " --> pdb=" O MET C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.717A pdb=" N GLN C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 328 removed outlier: 4.993A pdb=" N ILE C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 337 through 364 removed outlier: 3.812A pdb=" N GLY C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 355 " --> pdb=" O GLY C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 386 through 398 removed outlier: 3.580A pdb=" N SER C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 430 removed outlier: 3.739A pdb=" N ALA C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 42 removed outlier: 3.915A pdb=" N ALA D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 36 removed outlier: 3.689A pdb=" N ILE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 24 " --> pdb=" O GLN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.725A pdb=" N ASN E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.667A pdb=" N PHE E 141 " --> pdb=" O PRO E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 154 No H-bonds generated for 'chain 'E' and resid 151 through 154' Processing helix chain 'E' and resid 157 through 160 Processing helix chain 'E' and resid 162 through 182 removed outlier: 3.819A pdb=" N GLN E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY E 169 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE E 170 " --> pdb=" O ALA E 166 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.547A pdb=" N ALA E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ILE E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY E 200 " --> pdb=" O ILE E 196 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 213 removed outlier: 4.292A pdb=" N TYR E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.738A pdb=" N LEU E 219 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY E 220 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 221 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA E 223 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 227 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 231 No H-bonds generated for 'chain 'E' and resid 229 through 231' Processing helix chain 'E' and resid 233 through 244 Proline residue: E 238 - end of helix Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 262 through 278 Proline residue: E 269 - end of helix Processing helix chain 'E' and resid 281 through 299 Proline residue: E 285 - end of helix removed outlier: 4.689A pdb=" N GLY E 288 " --> pdb=" O PRO E 285 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE E 292 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU E 295 " --> pdb=" O PHE E 292 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET E 296 " --> pdb=" O GLY E 293 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER E 299 " --> pdb=" O MET E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 314 through 328 removed outlier: 5.044A pdb=" N ILE E 319 " --> pdb=" O ASN E 315 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 334 No H-bonds generated for 'chain 'E' and resid 331 through 334' Processing helix chain 'E' and resid 337 through 364 removed outlier: 3.776A pdb=" N GLY E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE E 348 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 355 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 removed outlier: 3.538A pdb=" N GLY E 380 " --> pdb=" O GLY E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 386 through 398 removed outlier: 3.584A pdb=" N SER E 398 " --> pdb=" O VAL E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 430 removed outlier: 3.760A pdb=" N ALA E 420 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 42 removed outlier: 3.914A pdb=" N ALA F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1542 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: 2.88 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3146 1.34 - 1.46: 1606 1.46 - 1.57: 5520 1.57 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 10401 Sorted by residual: bond pdb=" C6' LMT E1000 " pdb=" O6' LMT E1000 " ideal model delta sigma weight residual 1.407 1.364 0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C8 LMT E1000 " pdb=" C9 LMT E1000 " ideal model delta sigma weight residual 1.531 1.490 0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C6' LMT C1000 " pdb=" O6' LMT C1000 " ideal model delta sigma weight residual 1.407 1.367 0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C8 LMT A1000 " pdb=" C9 LMT A1000 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.04e+00 bond pdb=" C8 LMT C1000 " pdb=" C9 LMT C1000 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.02e+00 ... (remaining 10396 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.29: 292 105.29 - 112.45: 5438 112.45 - 119.60: 3581 119.60 - 126.76: 4723 126.76 - 133.91: 84 Bond angle restraints: 14118 Sorted by residual: angle pdb=" N PRO E 238 " pdb=" CA PRO E 238 " pdb=" C PRO E 238 " ideal model delta sigma weight residual 110.70 115.58 -4.88 1.22e+00 6.72e-01 1.60e+01 angle pdb=" N PRO A 238 " pdb=" CA PRO A 238 " pdb=" C PRO A 238 " ideal model delta sigma weight residual 110.70 115.49 -4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N PRO C 238 " pdb=" CA PRO C 238 " pdb=" C PRO C 238 " ideal model delta sigma weight residual 110.70 115.32 -4.62 1.22e+00 6.72e-01 1.43e+01 angle pdb=" CA PRO E 238 " pdb=" C PRO E 238 " pdb=" N PRO E 239 " ideal model delta sigma weight residual 117.93 122.31 -4.38 1.20e+00 6.94e-01 1.33e+01 angle pdb=" CA PRO A 238 " pdb=" C PRO A 238 " pdb=" N PRO A 239 " ideal model delta sigma weight residual 117.93 122.30 -4.37 1.20e+00 6.94e-01 1.33e+01 ... (remaining 14113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 6138 22.11 - 44.22: 147 44.22 - 66.33: 24 66.33 - 88.44: 1 88.44 - 110.55: 23 Dihedral angle restraints: 6333 sinusoidal: 2448 harmonic: 3885 Sorted by residual: dihedral pdb=" CA ALA A 130 " pdb=" C ALA A 130 " pdb=" N ILE A 131 " pdb=" CA ILE A 131 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ALA C 130 " pdb=" C ALA C 130 " pdb=" N ILE C 131 " pdb=" CA ILE C 131 " ideal model delta harmonic sigma weight residual 180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ALA A 231 " pdb=" C ALA A 231 " pdb=" N LEU A 232 " pdb=" CA LEU A 232 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 6330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1202 0.055 - 0.109: 451 0.109 - 0.164: 99 0.164 - 0.219: 16 0.219 - 0.273: 11 Chirality restraints: 1779 Sorted by residual: chirality pdb=" CB ILE C 131 " pdb=" CA ILE C 131 " pdb=" CG1 ILE C 131 " pdb=" CG2 ILE C 131 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE A 131 " pdb=" CA ILE A 131 " pdb=" CG1 ILE A 131 " pdb=" CG2 ILE A 131 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE E 131 " pdb=" CA ILE E 131 " pdb=" CG1 ILE E 131 " pdb=" CG2 ILE E 131 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1776 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 151 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 152 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 151 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO E 152 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 152 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 152 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 151 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO C 152 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " -0.033 5.00e-02 4.00e+02 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3060 2.82 - 3.34: 10144 3.34 - 3.86: 17112 3.86 - 4.38: 20349 4.38 - 4.90: 33713 Nonbonded interactions: 84378 Sorted by model distance: nonbonded pdb=" O GLY C 201 " pdb=" OG SER C 382 " model vdw 2.301 2.440 nonbonded pdb=" O VAL A 144 " pdb=" OG1 THR A 148 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR A 229 " pdb=" O LEU A 343 " model vdw 2.317 2.440 nonbonded pdb=" O GLY A 201 " pdb=" OG SER A 382 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR E 229 " pdb=" O LEU E 343 " model vdw 2.321 2.440 ... (remaining 84373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 2.330 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.580 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 0.064 10401 Z= 0.525 Angle : 1.088 9.417 14118 Z= 0.547 Chirality : 0.060 0.273 1779 Planarity : 0.009 0.061 1737 Dihedral : 13.483 110.551 3849 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.17), residues: 1374 helix: -2.71 (0.12), residues: 1038 sheet: None (None), residues: 0 loop : -2.14 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 32 HIS 0.009 0.002 HIS C 72 PHE 0.025 0.003 PHE A 141 TYR 0.015 0.003 TYR E 118 ARG 0.002 0.000 ARG C 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.2124 time to fit residues: 115.4310 Evaluate side-chains 235 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 72 HIS A 77 GLN A 106 GLN A 237 GLN C 72 HIS C 106 GLN C 192 GLN E 20 GLN E 72 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10401 Z= 0.247 Angle : 0.674 6.685 14118 Z= 0.330 Chirality : 0.042 0.157 1779 Planarity : 0.006 0.049 1737 Dihedral : 8.485 58.611 1617 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.68 % Allowed : 10.15 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.97 (0.21), residues: 1374 helix: -1.04 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -1.59 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP E 32 HIS 0.004 0.001 HIS A 72 PHE 0.014 0.001 PHE A 268 TYR 0.021 0.002 TYR A 182 ARG 0.003 0.000 ARG C 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 1.094 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 297 average time/residue: 0.1990 time to fit residues: 85.2399 Evaluate side-chains 259 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 239 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1032 time to fit residues: 5.5105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 167 GLN A 407 HIS ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10401 Z= 0.246 Angle : 0.632 7.002 14118 Z= 0.309 Chirality : 0.042 0.154 1779 Planarity : 0.006 0.049 1737 Dihedral : 7.096 52.870 1617 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.05 % Allowed : 13.79 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.07 (0.22), residues: 1374 helix: -0.33 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.48 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 32 HIS 0.009 0.001 HIS A 407 PHE 0.013 0.001 PHE A 268 TYR 0.016 0.003 TYR E 127 ARG 0.004 0.001 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 256 time to evaluate : 1.189 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 262 average time/residue: 0.2051 time to fit residues: 77.1781 Evaluate side-chains 240 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 1.123 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0945 time to fit residues: 2.5826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 0.0270 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 407 HIS C 407 HIS E 77 GLN E 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10401 Z= 0.200 Angle : 0.617 11.396 14118 Z= 0.299 Chirality : 0.041 0.149 1779 Planarity : 0.005 0.049 1737 Dihedral : 6.525 50.463 1617 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.63 % Allowed : 15.42 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.23), residues: 1374 helix: 0.11 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -0.94 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 32 HIS 0.006 0.001 HIS A 407 PHE 0.014 0.001 PHE A 268 TYR 0.019 0.002 TYR E 127 ARG 0.005 0.001 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 260 time to evaluate : 1.216 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 266 average time/residue: 0.2092 time to fit residues: 79.8879 Evaluate side-chains 245 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0988 time to fit residues: 3.5577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10401 Z= 0.249 Angle : 0.623 9.049 14118 Z= 0.303 Chirality : 0.042 0.188 1779 Planarity : 0.005 0.049 1737 Dihedral : 6.450 48.861 1617 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.63 % Allowed : 17.72 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.34 (0.23), residues: 1374 helix: 0.22 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.26 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.003 0.001 HIS C 407 PHE 0.014 0.001 PHE A 39 TYR 0.019 0.002 TYR E 127 ARG 0.006 0.001 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 249 time to evaluate : 1.110 Fit side-chains outliers start: 17 outliers final: 5 residues processed: 257 average time/residue: 0.2083 time to fit residues: 77.1633 Evaluate side-chains 230 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 225 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0974 time to fit residues: 2.3638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 407 HIS C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10401 Z= 0.246 Angle : 0.641 12.362 14118 Z= 0.306 Chirality : 0.042 0.168 1779 Planarity : 0.005 0.046 1737 Dihedral : 6.382 47.961 1617 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.92 % Allowed : 19.44 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.04 (0.23), residues: 1374 helix: 0.40 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.005 0.001 HIS C 407 PHE 0.013 0.001 PHE A 39 TYR 0.018 0.002 TYR C 429 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 249 time to evaluate : 1.170 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 257 average time/residue: 0.2096 time to fit residues: 76.4154 Evaluate side-chains 237 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0916 time to fit residues: 3.2813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS C 370 ASN C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10401 Z= 0.223 Angle : 0.639 13.173 14118 Z= 0.304 Chirality : 0.042 0.170 1779 Planarity : 0.005 0.047 1737 Dihedral : 6.273 47.206 1617 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.34 % Allowed : 20.88 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.03 (0.23), residues: 1374 helix: 0.43 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -0.84 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.004 0.001 HIS C 407 PHE 0.012 0.001 PHE D 43 TYR 0.021 0.003 TYR C 429 ARG 0.004 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 1.165 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 252 average time/residue: 0.2144 time to fit residues: 77.5113 Evaluate side-chains 232 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0932 time to fit residues: 2.0644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 407 HIS C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10401 Z= 0.205 Angle : 0.630 13.123 14118 Z= 0.300 Chirality : 0.041 0.172 1779 Planarity : 0.005 0.047 1737 Dihedral : 6.121 47.357 1617 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.86 % Allowed : 22.13 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1374 helix: 0.49 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -0.81 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 32 HIS 0.004 0.001 HIS C 407 PHE 0.012 0.001 PHE A 49 TYR 0.022 0.002 TYR A 429 ARG 0.004 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 1.234 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 256 average time/residue: 0.2234 time to fit residues: 82.3178 Evaluate side-chains 240 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1021 time to fit residues: 2.2160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS C 370 ASN C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10401 Z= 0.195 Angle : 0.643 12.210 14118 Z= 0.302 Chirality : 0.041 0.184 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.984 46.609 1617 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.96 % Allowed : 22.51 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.20 (0.23), residues: 1374 helix: 0.57 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -0.87 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.004 0.001 HIS C 407 PHE 0.011 0.001 PHE A 49 TYR 0.023 0.002 TYR C 429 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 249 time to evaluate : 1.143 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 253 average time/residue: 0.2040 time to fit residues: 74.3502 Evaluate side-chains 242 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0963 time to fit residues: 2.5484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10401 Z= 0.237 Angle : 0.666 11.866 14118 Z= 0.313 Chirality : 0.042 0.188 1779 Planarity : 0.005 0.048 1737 Dihedral : 6.003 45.744 1617 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.77 % Allowed : 24.04 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.17 (0.23), residues: 1374 helix: 0.54 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.004 0.001 HIS A 407 PHE 0.011 0.001 PHE A 49 TYR 0.025 0.002 TYR C 429 ARG 0.004 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 242 time to evaluate : 1.023 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 243 average time/residue: 0.2123 time to fit residues: 74.5098 Evaluate side-chains 242 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 238 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1010 time to fit residues: 2.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN C 370 ASN C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 ASN ** E 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.114376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.097928 restraints weight = 16522.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099659 restraints weight = 10578.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.100936 restraints weight = 7995.551| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10401 Z= 0.264 Angle : 0.686 11.387 14118 Z= 0.323 Chirality : 0.043 0.189 1779 Planarity : 0.005 0.048 1737 Dihedral : 6.136 47.191 1617 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.48 % Allowed : 24.14 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.23), residues: 1374 helix: 0.49 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -0.78 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 49 TYR 0.025 0.002 TYR C 429 ARG 0.009 0.001 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.23 seconds wall clock time: 40 minutes 14.54 seconds (2414.54 seconds total)