Starting phenix.real_space_refine on Wed Jun 11 16:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.map" model { file = "/net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sqb_40701/06_2025/8sqb_40701.cif" } resolution = 3.8 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= 0.004 sd= 0.049 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 36 5.16 5 C 8168 2.51 5 N 2230 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12991 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 6045 Classifications: {'peptide': 765} Link IDs: {'CIS': 2, 'PTRANS': 28, 'TRANS': 734} Chain breaks: 5 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2776 Classifications: {'peptide': 369} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 355} Chain breaks: 1 Chain: "C" Number of atoms: 1318 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 171, 1309 Classifications: {'peptide': 171} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 3 bond proxies already assigned to first conformer: 1319 Chain: "D" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1740 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "F" Number of atoms: 418 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 67, 410 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 67, 410 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 66} Chain breaks: 3 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 401 Time building chain proxies: 8.50, per 1000 atoms: 0.65 Number of scatterers: 12991 At special positions: 0 Unit cell: (114.48, 132.84, 130.68, 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 36 16.00 O 2557 8.00 N 2230 7.00 C 8168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS F1172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3068 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 22.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.670A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.775A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.797A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.785A pdb=" N SER C 122 " --> pdb=" O PRO C 118 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 207 removed outlier: 3.731A pdb=" N SER C 198 " --> pdb=" O MET C 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C 201 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE C 205 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 206 " --> pdb=" O MET C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 4.163A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 61 removed outlier: 4.230A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.818A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.500A pdb=" N ALA D 163 " --> pdb=" O TYR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.796A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.784A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 3.935A pdb=" N ARG A 76 " --> pdb=" O GLN A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 182 removed outlier: 3.654A pdb=" N ILE A 254 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 267 through 271 current: chain 'A' and resid 334 through 341 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.822A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.936A pdb=" N GLN A 445 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 459 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 470 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 486 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY A 510 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 509 " --> pdb=" O HIS A 533 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 528 " --> pdb=" O ASN A 573 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 564 through 574 current: chain 'A' and resid 592 through 600 removed outlier: 3.738A pdb=" N ASP A 614 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 596 " --> pdb=" O THR A 612 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 609 through 615 current: chain 'A' and resid 628 through 635 removed outlier: 3.572A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 630 " --> pdb=" O GLU A 717 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 632 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 716 " --> pdb=" O TRP A 739 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 771 " --> pdb=" O PHE A 738 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 784 " --> pdb=" O ASN A 805 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA8, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.796A pdb=" N ALA B 66 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 162 removed outlier: 4.136A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 209 removed outlier: 3.875A pdb=" N VAL B 209 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.787A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.621A pdb=" N ASP B 292 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.631A pdb=" N HIS B 347 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 142 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 142 current: chain 'C' and resid 158 through 164 removed outlier: 5.028A pdb=" N ARG C 158 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 182 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 32 through 34 current: chain 'E' and resid 73 through 80 Processing sheet with id=AB9, first strand: chain 'F' and resid 1265 through 1267 386 hydrogen bonds defined for protein. 1029 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: 4.00 Time building geometry restraints manager: 4.20 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: 4365 1.34 - 1.46: 2851 1.46 - 1.57: 5970 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 13255 Sorted by residual: bond pdb=" C ASP D 136 " pdb=" N PRO D 137 " ideal model delta sigma weight residual 1.332 1.310 0.023 8.20e-03 1.49e+04 7.56e+00 bond pdb=" CB TRP D 191 " pdb=" CG TRP D 191 " ideal model delta sigma weight residual 1.498 1.426 0.072 3.10e-02 1.04e+03 5.41e+00 bond pdb=" C THR B 386 " pdb=" N VAL B 387 " ideal model delta sigma weight residual 1.329 1.286 0.043 2.19e-02 2.09e+03 3.86e+00 bond pdb=" CB TRP A 449 " pdb=" CG TRP A 449 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.46e+00 ... (remaining 13250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 17691 2.53 - 5.06: 285 5.06 - 7.59: 24 7.59 - 10.12: 2 10.12 - 12.65: 4 Bond angle restraints: 18006 Sorted by residual: angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.21 107.00 6.21 1.15e+00 7.56e-01 2.91e+01 angle pdb=" C GLY C 169 " pdb=" N TYR C 170 " pdb=" CA TYR C 170 " ideal model delta sigma weight residual 121.70 130.09 -8.39 1.80e+00 3.09e-01 2.17e+01 angle pdb=" N ILE C 82 " pdb=" CA ILE C 82 " pdb=" C ILE C 82 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N GLY B 354 " pdb=" CA GLY B 354 " pdb=" C GLY B 354 " ideal model delta sigma weight residual 113.30 102.53 10.77 2.90e+00 1.19e-01 1.38e+01 angle pdb=" CA TRP B 228 " pdb=" CB TRP B 228 " pdb=" CG TRP B 228 " ideal model delta sigma weight residual 113.60 120.62 -7.02 1.90e+00 2.77e-01 1.36e+01 ... (remaining 18001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7007 17.96 - 35.92: 687 35.92 - 53.88: 110 53.88 - 71.83: 19 71.83 - 89.79: 16 Dihedral angle restraints: 7839 sinusoidal: 3026 harmonic: 4813 Sorted by residual: dihedral pdb=" CA ILE B 227 " pdb=" C ILE B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta harmonic sigma weight residual 180.00 129.11 50.89 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA ASP B 300 " pdb=" C ASP B 300 " pdb=" N GLN B 301 " pdb=" CA GLN B 301 " ideal model delta harmonic sigma weight residual 180.00 151.98 28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ARG A 346 " pdb=" C ARG A 346 " pdb=" N PHE A 347 " pdb=" CA PHE A 347 " ideal model delta harmonic sigma weight residual 180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 7836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1266 0.038 - 0.077: 508 0.077 - 0.115: 169 0.115 - 0.153: 29 0.153 - 0.192: 6 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CB ILE D 35 " pdb=" CA ILE D 35 " pdb=" CG1 ILE D 35 " pdb=" CG2 ILE D 35 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA THR B 37 " pdb=" N THR B 37 " pdb=" C THR B 37 " pdb=" CB THR B 37 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA TYR C 170 " pdb=" N TYR C 170 " pdb=" C TYR C 170 " pdb=" CB TYR C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1975 not shown) Planarity restraints: 2374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 60 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C VAL C 60 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL C 60 " -0.012 2.00e-02 2.50e+03 pdb=" N THR C 61 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 437 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY A 437 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 437 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 438 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 104 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.90e+00 pdb=" CG PHE B 104 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 104 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 104 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 104 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 104 " 0.004 2.00e-02 2.50e+03 ... (remaining 2371 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 325 2.53 - 3.12: 12262 3.12 - 3.71: 21776 3.71 - 4.31: 28364 4.31 - 4.90: 44270 Nonbonded interactions: 106997 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" O VAL B 286 " model vdw 1.936 3.040 nonbonded pdb=" OG1 THR A 505 " pdb=" O SER A 537 " model vdw 1.990 3.040 nonbonded pdb=" O ASN E 41 " pdb=" OG SER E 44 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR B 309 " pdb=" OD1 ASP B 311 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR E 92 " pdb=" OD2 ASP E 105 " model vdw 2.088 3.040 ... (remaining 106992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 0.072 13256 Z= 0.387 Angle : 0.840 12.652 18008 Z= 0.464 Chirality : 0.046 0.192 1978 Planarity : 0.004 0.040 2374 Dihedral : 14.861 89.793 4768 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 33.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.27 % Favored : 80.61 % Rotamer: Outliers : 1.02 % Allowed : 12.37 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -5.64 (0.16), residues: 1643 helix: -2.42 (0.22), residues: 334 sheet: -4.20 (0.20), residues: 410 loop : -4.17 (0.16), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 228 HIS 0.007 0.001 HIS A 677 PHE 0.029 0.002 PHE B 104 TYR 0.018 0.002 TYR A 757 ARG 0.010 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.22303 ( 386) hydrogen bonds : angle 9.06043 ( 1029) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.38200 ( 2) covalent geometry : bond 0.00793 (13255) covalent geometry : angle 0.83985 (18006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 203 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8677 (m-10) cc_final: 0.8270 (m-80) REVERT: A 147 TYR cc_start: 0.8563 (m-80) cc_final: 0.8354 (m-80) REVERT: A 325 MET cc_start: 0.7521 (ptp) cc_final: 0.6478 (ppp) REVERT: A 396 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 801 GLN cc_start: 0.7478 (mt0) cc_final: 0.6817 (mt0) REVERT: B 42 PHE cc_start: 0.3713 (OUTLIER) cc_final: 0.3171 (m-10) REVERT: B 127 GLU cc_start: 0.8053 (tp30) cc_final: 0.7804 (tp30) REVERT: B 221 MET cc_start: 0.8661 (mtp) cc_final: 0.8454 (mtt) REVERT: B 278 MET cc_start: 0.5808 (mmt) cc_final: 0.5419 (tpp) REVERT: B 289 PHE cc_start: 0.7745 (p90) cc_final: 0.7444 (p90) REVERT: C 127 LYS cc_start: 0.6591 (mmtt) cc_final: 0.6293 (mppt) REVERT: C 202 MET cc_start: 0.6865 (mmt) cc_final: 0.6557 (mmt) REVERT: D 176 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7364 (ttmm) REVERT: D 191 TRP cc_start: 0.8730 (m-10) cc_final: 0.8238 (m-10) REVERT: D 199 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6943 (tm-30) REVERT: E 87 THR cc_start: 0.8200 (t) cc_final: 0.7918 (p) REVERT: E 104 ILE cc_start: 0.7731 (pt) cc_final: 0.7502 (mp) outliers start: 10 outliers final: 7 residues processed: 211 average time/residue: 0.2625 time to fit residues: 78.7670 Evaluate side-chains 144 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 GLN A 678 GLN ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089676 restraints weight = 93393.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091047 restraints weight = 50844.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092844 restraints weight = 30356.290| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13256 Z= 0.178 Angle : 0.716 8.349 18008 Z= 0.374 Chirality : 0.046 0.226 1978 Planarity : 0.004 0.044 2374 Dihedral : 6.469 53.184 1839 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 3.71 % Allowed : 14.77 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.41 (0.18), residues: 1643 helix: -0.78 (0.25), residues: 351 sheet: -3.62 (0.22), residues: 372 loop : -3.64 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 228 HIS 0.005 0.001 HIS A 533 PHE 0.024 0.002 PHE B 104 TYR 0.021 0.002 TYR A 454 ARG 0.006 0.001 ARG A 120 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 386) hydrogen bonds : angle 6.12769 ( 1029) SS BOND : bond 0.00057 ( 1) SS BOND : angle 0.69338 ( 2) covalent geometry : bond 0.00387 (13255) covalent geometry : angle 0.71625 (18006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) REVERT: A 663 PHE cc_start: 0.8299 (m-80) cc_final: 0.7990 (m-80) REVERT: A 801 GLN cc_start: 0.8057 (mt0) cc_final: 0.7839 (mp10) REVERT: B 32 MET cc_start: 0.7175 (pmm) cc_final: 0.6565 (pmm) REVERT: B 76 ASP cc_start: 0.8572 (p0) cc_final: 0.8132 (p0) REVERT: B 296 ILE cc_start: 0.8073 (mp) cc_final: 0.7842 (tt) REVERT: C 202 MET cc_start: 0.6631 (mmt) cc_final: 0.5910 (mmt) REVERT: D 52 ILE cc_start: 0.8327 (mt) cc_final: 0.7910 (mt) REVERT: D 53 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8842 (t) REVERT: E 33 ASN cc_start: 0.8084 (p0) cc_final: 0.7693 (p0) outliers start: 47 outliers final: 25 residues processed: 213 average time/residue: 0.2210 time to fit residues: 70.4298 Evaluate side-chains 173 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 301 GLN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 100 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 142 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 0.0570 chunk 14 optimal weight: 10.0000 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.117567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092117 restraints weight = 78912.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093390 restraints weight = 39362.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094895 restraints weight = 26976.974| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13256 Z= 0.137 Angle : 0.657 7.707 18008 Z= 0.341 Chirality : 0.045 0.168 1978 Planarity : 0.004 0.040 2374 Dihedral : 5.956 56.235 1835 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 3.06 % Allowed : 18.27 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.71 (0.19), residues: 1643 helix: 0.17 (0.27), residues: 354 sheet: -3.34 (0.22), residues: 388 loop : -3.26 (0.18), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 228 HIS 0.004 0.001 HIS A 533 PHE 0.019 0.001 PHE A 478 TYR 0.019 0.001 TYR A 504 ARG 0.006 0.001 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 386) hydrogen bonds : angle 5.30563 ( 1029) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.37722 ( 2) covalent geometry : bond 0.00288 (13255) covalent geometry : angle 0.65685 (18006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8024 (m-80) cc_final: 0.7414 (m-80) REVERT: A 546 TRP cc_start: 0.7302 (m100) cc_final: 0.6728 (m-10) REVERT: A 663 PHE cc_start: 0.8327 (m-80) cc_final: 0.8098 (m-80) REVERT: A 801 GLN cc_start: 0.8011 (mt0) cc_final: 0.7806 (mp10) REVERT: B 76 ASP cc_start: 0.8220 (p0) cc_final: 0.7938 (p0) REVERT: C 78 LYS cc_start: 0.8834 (mmmm) cc_final: 0.8349 (mmtt) REVERT: C 202 MET cc_start: 0.6747 (mmt) cc_final: 0.6153 (mmt) REVERT: D 199 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 33 ASN cc_start: 0.8127 (p0) cc_final: 0.7763 (p0) outliers start: 38 outliers final: 25 residues processed: 211 average time/residue: 0.2101 time to fit residues: 68.1478 Evaluate side-chains 180 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 139 optimal weight: 0.1980 chunk 119 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.120440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094198 restraints weight = 81204.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.095364 restraints weight = 37412.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097459 restraints weight = 23022.429| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13256 Z= 0.151 Angle : 0.653 7.897 18008 Z= 0.339 Chirality : 0.044 0.153 1978 Planarity : 0.004 0.038 2374 Dihedral : 5.899 59.878 1834 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 4.51 % Allowed : 19.36 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.48 (0.19), residues: 1643 helix: 0.33 (0.27), residues: 360 sheet: -3.14 (0.22), residues: 402 loop : -3.13 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 191 HIS 0.004 0.001 HIS A 533 PHE 0.017 0.001 PHE B 104 TYR 0.028 0.002 TYR C 157 ARG 0.005 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 386) hydrogen bonds : angle 5.04095 ( 1029) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.41031 ( 2) covalent geometry : bond 0.00334 (13255) covalent geometry : angle 0.65343 (18006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3286 Ramachandran restraints generated. 1643 Oldfield, 0 Emsley, 1643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8287 (m-10) cc_final: 0.7762 (m-80) REVERT: A 191 ASP cc_start: 0.8565 (p0) cc_final: 0.7864 (t0) REVERT: A 368 GLU cc_start: 0.7536 (tt0) cc_final: 0.7184 (mm-30) REVERT: A 552 MET cc_start: 0.8790 (mtp) cc_final: 0.8386 (mtp) REVERT: A 663 PHE cc_start: 0.8476 (m-80) cc_final: 0.8246 (m-80) REVERT: A 801 GLN cc_start: 0.8178 (mt0) cc_final: 0.7865 (mp10) REVERT: B 76 ASP cc_start: 0.8341 (p0) cc_final: 0.7953 (p0) REVERT: B 324 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7579 (t-170) REVERT: C 78 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8577 (mmmm) REVERT: C 202 MET cc_start: 0.6775 (mmt) cc_final: 0.6301 (mmt) REVERT: E 67 PRO cc_start: 0.8838 (Cg_endo) cc_final: 0.8556 (Cg_exo) outliers start: 58 outliers final: 45 residues processed: 215 average time/residue: 0.2104 time to fit residues: 69.4570 Evaluate side-chains 189 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 143 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 95 PHE Chi-restraints excluded: chain F residue 1274 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.9812 > 50: distance: 97 - 101: 7.505 distance: 101 - 102: 11.401 distance: 102 - 103: 8.774 distance: 102 - 105: 15.950 distance: 103 - 104: 12.805 distance: 103 - 109: 11.262 distance: 105 - 106: 14.214 distance: 106 - 107: 11.858 distance: 106 - 108: 5.450 distance: 109 - 110: 30.044 distance: 110 - 111: 41.692 distance: 110 - 113: 17.586 distance: 111 - 112: 33.245 distance: 111 - 115: 25.562 distance: 113 - 114: 38.454 distance: 115 - 116: 7.893 distance: 116 - 117: 6.631 distance: 116 - 119: 26.884 distance: 117 - 118: 7.211 distance: 117 - 123: 13.606 distance: 119 - 120: 31.205 distance: 120 - 121: 16.708 distance: 120 - 122: 41.461 distance: 123 - 124: 18.209 distance: 124 - 125: 10.397 distance: 124 - 127: 9.667 distance: 125 - 126: 24.292 distance: 125 - 134: 23.661 distance: 127 - 128: 10.016 distance: 128 - 129: 7.482 distance: 129 - 130: 11.008 distance: 130 - 131: 5.351 distance: 131 - 132: 3.403 distance: 131 - 133: 5.631 distance: 134 - 135: 21.880 distance: 135 - 136: 4.598 distance: 136 - 137: 10.824 distance: 136 - 138: 8.047 distance: 138 - 139: 8.448 distance: 139 - 140: 14.002 distance: 139 - 142: 15.795 distance: 140 - 141: 17.149 distance: 140 - 147: 12.182 distance: 142 - 143: 15.307 distance: 143 - 144: 7.366 distance: 144 - 145: 4.400 distance: 144 - 146: 3.831 distance: 148 - 149: 19.194 distance: 148 - 151: 9.391 distance: 149 - 150: 24.950 distance: 149 - 153: 14.784 distance: 151 - 152: 11.014 distance: 153 - 154: 6.365 distance: 154 - 155: 22.205 distance: 154 - 157: 24.203 distance: 155 - 156: 14.435 distance: 155 - 158: 20.259 distance: 158 - 159: 24.080 distance: 158 - 164: 23.829 distance: 159 - 160: 18.035 distance: 159 - 162: 22.505 distance: 160 - 161: 9.741 distance: 160 - 165: 8.286 distance: 162 - 163: 12.957 distance: 163 - 164: 9.498 distance: 165 - 166: 15.411 distance: 166 - 167: 12.792 distance: 166 - 169: 10.743 distance: 167 - 168: 14.340 distance: 167 - 172: 7.863 distance: 169 - 170: 17.286 distance: 169 - 171: 19.117