Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 17:00:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/04_2023/6iww_9743_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/04_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_9743/04_2023/6iww_9743.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/04_2023/6iww_9743.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/04_2023/6iww_9743_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6iww_9743/04_2023/6iww_9743_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.75, per 1000 atoms: 0.56 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: 4.21 Conformation dependent library (CDL) restraints added in 1.5 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: 0.96 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: 2.91 Time building geometry restraints manager: 4.52 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 - 11.89: 5591 11.89 - 23.78: 489 23.78 - 35.67: 75 35.67 - 47.56: 19 47.56 - 59.45: 9 Dihedral angle restraints: 6183 sinusoidal: 2298 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 6180 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: 0.460 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: 0.000 Extract box with map and model: 2.690 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- 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 : 9.806 59.450 3699 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 % 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 *********************** 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 : 1.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.2500 time to fit residues: 138.3923 Evaluate side-chains 235 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7448 ------------------------------------------------------------------------------- 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: 0.8113 moved from start: 0.2523 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= 0.241 Angle : 0.655 6.803 14118 Z= 0.324 Chirality : 0.042 0.158 1779 Planarity : 0.006 0.050 1737 Dihedral : 6.869 57.437 1467 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.78 % 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: -1.94 (0.21), residues: 1374 helix: -1.03 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 336 *********************** 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 314 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 285 time to evaluate : 1.211 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 297 average time/residue: 0.2084 time to fit residues: 88.7986 Evaluate side-chains 258 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0961 time to fit residues: 5.2318 ------------------------------------------------------------------------------- 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: 0.9980 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 135 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 407 HIS E 77 GLN E 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 10401 Z= 0.187 Angle : 0.602 6.937 14118 Z= 0.295 Chirality : 0.041 0.149 1779 Planarity : 0.005 0.050 1737 Dihedral : 6.337 58.753 1467 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.05 % 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: -0.99 (0.22), residues: 1374 helix: -0.25 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : -1.51 (0.32), residues: 345 *********************** 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 280 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 269 time to evaluate : 1.260 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 275 average time/residue: 0.2348 time to fit residues: 92.8941 Evaluate side-chains 235 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0921 time to fit residues: 2.2529 ------------------------------------------------------------------------------- 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: 0.0870 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 407 HIS C 370 ASN C 407 HIS E 106 GLN E 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3389 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= 0.186 Angle : 0.611 11.579 14118 Z= 0.295 Chirality : 0.041 0.146 1779 Planarity : 0.005 0.051 1737 Dihedral : 6.035 58.664 1467 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.82 % 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: -0.39 (0.23), residues: 1374 helix: 0.20 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -1.24 (0.31), residues: 372 *********************** 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 276 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 1.174 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 263 average time/residue: 0.2113 time to fit residues: 79.3055 Evaluate side-chains 254 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 242 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0968 time to fit residues: 3.7574 ------------------------------------------------------------------------------- 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: 3.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10401 Z= 0.200 Angle : 0.595 8.881 14118 Z= 0.289 Chirality : 0.040 0.150 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.868 58.020 1467 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.34 % 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: 0.37 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 375 *********************** 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 277 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 1.213 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 270 average time/residue: 0.2249 time to fit residues: 86.2526 Evaluate side-chains 248 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0967 time to fit residues: 2.5419 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.5222 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10401 Z= 0.236 Angle : 0.620 7.291 14118 Z= 0.300 Chirality : 0.042 0.160 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.918 58.484 1467 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.82 % 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: -0.02 (0.23), residues: 1374 helix: 0.43 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -1.03 (0.31), residues: 366 *********************** 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 268 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 1.046 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 254 average time/residue: 0.2102 time to fit residues: 76.2023 Evaluate side-chains 245 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0934 time to fit residues: 3.1272 ------------------------------------------------------------------------------- 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: 0.0770 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10401 Z= 0.181 Angle : 0.618 10.995 14118 Z= 0.295 Chirality : 0.040 0.155 1779 Planarity : 0.005 0.049 1737 Dihedral : 5.721 59.707 1467 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.86 % 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: 0.31 (0.23), residues: 1374 helix: 0.63 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -0.72 (0.31), residues: 378 *********************** 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 278 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 269 time to evaluate : 1.232 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 272 average time/residue: 0.2106 time to fit residues: 81.6817 Evaluate side-chains 250 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 248 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1066 time to fit residues: 2.0490 ------------------------------------------------------------------------------- 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: 5.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10401 Z= 0.190 Angle : 0.631 10.861 14118 Z= 0.301 Chirality : 0.041 0.166 1779 Planarity : 0.005 0.049 1737 Dihedral : 5.595 59.850 1467 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.25 % 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: 0.42 (0.23), residues: 1374 helix: 0.73 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 378 *********************** 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 272 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 259 time to evaluate : 1.235 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 261 average time/residue: 0.2167 time to fit residues: 80.8329 Evaluate side-chains 248 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0991 time to fit residues: 2.8421 ------------------------------------------------------------------------------- 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: 9.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS C 407 HIS ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** 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: 0.8098 moved from start: 0.4246 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= 0.236 Angle : 0.677 12.140 14118 Z= 0.317 Chirality : 0.043 0.197 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.734 59.800 1467 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.67 % 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: 0.68 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -0.71 (0.32), residues: 378 *********************** 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 246 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 1.132 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 239 average time/residue: 0.2150 time to fit residues: 73.4480 Evaluate side-chains 231 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1008 time to fit residues: 2.0802 ------------------------------------------------------------------------------- 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: 0.7980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10401 Z= 0.269 Angle : 0.719 12.541 14118 Z= 0.333 Chirality : 0.044 0.194 1779 Planarity : 0.005 0.048 1737 Dihedral : 5.877 57.206 1467 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.57 % 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: 0.27 (0.23), residues: 1374 helix: 0.61 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 378 ********************** 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 235 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 229 time to evaluate : 1.051 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 230 average time/residue: 0.2151 time to fit residues: 70.8428 Evaluate side-chains 225 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 220 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0991 time to fit residues: 2.4580 ------------------------------------------------------------------------------- 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: 0.8980 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 96 optimal weight: 0.4980 chunk 6 optimal weight: 0.0270 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.121051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104012 restraints weight = 16454.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.106224 restraints weight = 9988.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.107637 restraints weight = 7230.887| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4548 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= 0.179 Angle : 0.681 11.862 14118 Z= 0.315 Chirality : 0.041 0.174 1779 Planarity : 0.005 0.052 1737 Dihedral : 5.546 50.219 1467 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.48 % 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: 0.53 (0.23), residues: 1374 helix: 0.82 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 384 =============================================================================== Job complete usr+sys time: 2152.70 seconds wall clock time: 39 minutes 43.68 seconds (2383.68 seconds total)