Starting phenix.real_space_refine on Fri Dec 8 08:59:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wha_21669/12_2023/6wha_21669_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 44 5.16 5 C 5016 2.51 5 N 1355 2.21 5 O 1473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 355": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7888 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1679 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 8, 'TRANS': 235} Chain breaks: 5 Unresolved non-hydrogen bonds: 265 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1650 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2471 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1712 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'U0G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.92, per 1000 atoms: 0.62 Number of scatterers: 7888 At special positions: 0 Unit cell: (97.1394, 113.329, 121.85, 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 44 16.00 O 1473 8.00 N 1355 7.00 C 5016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 14 sheets defined 32.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 110 through 136 removed outlier: 3.599A pdb=" N MET A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 146 through 178 removed outlier: 4.377A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 191 through 216 Proline residue: A 209 - end of helix removed outlier: 4.366A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 232 through 243 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.802A pdb=" N LYS A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 355 through 381 Proline residue: A 377 - end of helix removed outlier: 3.726A pdb=" N TYR A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 392 Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.589A pdb=" N GLU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.813A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'C' and resid 4 through 22 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing sheet with id= A, first strand: chain 'B' and resid 36 through 39 removed outlier: 7.053A pdb=" N ALA B 105 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE B 107 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 138 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N PHE B 108 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 140 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 110 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE B 142 " --> pdb=" O VAL B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.713A pdb=" N ASP B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 72 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 83 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.842A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 111 through 115 removed outlier: 3.705A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.984A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.862A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.633A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 318 through 320 removed outlier: 3.555A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.627A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET E 34 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.740A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'E' and resid 214 through 219 removed outlier: 3.647A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1011 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: 2.29 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1289 1.26 - 1.41: 2048 1.41 - 1.55: 4643 1.55 - 1.70: 1 1.70 - 1.84: 61 Bond restraints: 8042 Sorted by residual: bond pdb=" C05 U0G A 501 " pdb=" C06 U0G A 501 " ideal model delta sigma weight residual 1.422 1.536 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C22 U0G A 501 " pdb=" O23 U0G A 501 " ideal model delta sigma weight residual 1.354 1.464 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL E 135 " pdb=" CA VAL E 135 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.68e+01 bond pdb=" N VAL D 54 " pdb=" CA VAL D 54 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.46e+01 ... (remaining 8037 not shown) Histogram of bond angle deviations from ideal: 98.52 - 114.81: 4909 114.81 - 131.09: 6010 131.09 - 147.37: 33 147.37 - 163.65: 0 163.65 - 179.94: 1 Bond angle restraints: 10953 Sorted by residual: angle pdb=" CA GLY E 10 " pdb=" C GLY E 10 " pdb=" O GLY E 10 " ideal model delta sigma weight residual 122.37 117.88 4.49 7.30e-01 1.88e+00 3.78e+01 angle pdb=" N PRO A 209 " pdb=" CA PRO A 209 " pdb=" C PRO A 209 " ideal model delta sigma weight residual 113.53 120.38 -6.85 1.39e+00 5.18e-01 2.43e+01 angle pdb=" CA GLY E 230 " pdb=" C GLY E 230 " pdb=" O GLY E 230 " ideal model delta sigma weight residual 121.88 118.38 3.50 7.80e-01 1.64e+00 2.02e+01 angle pdb=" N CYS A 337 " pdb=" CA CYS A 337 " pdb=" C CYS A 337 " ideal model delta sigma weight residual 109.81 119.50 -9.69 2.21e+00 2.05e-01 1.92e+01 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" O VAL B 86 " ideal model delta sigma weight residual 121.68 118.42 3.26 7.90e-01 1.60e+00 1.70e+01 ... (remaining 10948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 4381 21.04 - 42.09: 272 42.09 - 63.13: 38 63.13 - 84.18: 5 84.18 - 105.22: 3 Dihedral angle restraints: 4699 sinusoidal: 1595 harmonic: 3104 Sorted by residual: dihedral pdb=" C THR E 198 " pdb=" N THR E 198 " pdb=" CA THR E 198 " pdb=" CB THR E 198 " ideal model delta harmonic sigma weight residual -122.00 -132.23 10.23 0 2.50e+00 1.60e-01 1.67e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR E 102 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" CB TYR E 102 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 748 0.063 - 0.126: 357 0.126 - 0.189: 144 0.189 - 0.251: 32 0.251 - 0.314: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CA THR E 198 " pdb=" N THR E 198 " pdb=" C THR E 198 " pdb=" CB THR E 198 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ARG E 179 " pdb=" N ARG E 179 " pdb=" C ARG E 179 " pdb=" CB ARG E 179 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1282 not shown) Planarity restraints: 1392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 240 " -0.017 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PHE A 240 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE A 240 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 163 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ILE A 163 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE A 163 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 164 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 179 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG E 179 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG E 179 " -0.015 2.00e-02 2.50e+03 pdb=" N MET E 180 " -0.013 2.00e-02 2.50e+03 ... (remaining 1389 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1875 2.81 - 3.33: 6958 3.33 - 3.85: 11351 3.85 - 4.38: 13094 4.38 - 4.90: 23538 Nonbonded interactions: 56816 Sorted by model distance: nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 204 " pdb=" OG SER B 204 " model vdw 2.291 2.440 nonbonded pdb=" O ASP C 195 " pdb=" OG1 THR C 196 " model vdw 2.381 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.384 2.440 nonbonded pdb=" OG SER C 161 " pdb=" N GLY C 162 " model vdw 2.391 2.520 ... (remaining 56811 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.000 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.012 0.114 8042 Z= 0.795 Angle : 1.196 9.929 10953 Z= 0.828 Chirality : 0.084 0.314 1285 Planarity : 0.005 0.049 1392 Dihedral : 13.683 105.222 2683 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.99 % Allowed : 15.99 % Favored : 81.01 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.33 % 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: -0.19 (0.26), residues: 1042 helix: 1.17 (0.28), residues: 352 sheet: 0.33 (0.35), residues: 263 loop : -1.54 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 169 HIS 0.009 0.002 HIS C 54 PHE 0.031 0.002 PHE B 197 TYR 0.023 0.002 TYR C 289 ARG 0.007 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.884 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 146 average time/residue: 0.2172 time to fit residues: 41.9327 Evaluate side-chains 108 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0752 time to fit residues: 3.1216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8042 Z= 0.205 Angle : 0.570 8.108 10953 Z= 0.305 Chirality : 0.044 0.143 1285 Planarity : 0.004 0.041 1392 Dihedral : 5.737 105.362 1146 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.60 % Allowed : 17.43 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.26), residues: 1042 helix: 2.15 (0.27), residues: 353 sheet: 0.28 (0.33), residues: 271 loop : -1.39 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 339 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.002 PHE C 199 TYR 0.011 0.001 TYR A 174 ARG 0.005 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.006 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.1811 time to fit residues: 32.1762 Evaluate side-chains 112 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0699 time to fit residues: 3.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8042 Z= 0.225 Angle : 0.563 9.008 10953 Z= 0.299 Chirality : 0.044 0.139 1285 Planarity : 0.004 0.038 1392 Dihedral : 5.750 105.556 1146 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.08 % Allowed : 19.90 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.71 (0.26), residues: 1042 helix: 2.45 (0.27), residues: 357 sheet: 0.47 (0.33), residues: 265 loop : -1.34 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS C 54 PHE 0.018 0.002 PHE E 80 TYR 0.012 0.001 TYR E 178 ARG 0.006 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.895 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 115 average time/residue: 0.1595 time to fit residues: 26.7833 Evaluate side-chains 106 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0680 time to fit residues: 2.5149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4879 > 50: distance: 38 - 42: 21.066 distance: 42 - 43: 16.722 distance: 43 - 44: 27.740 distance: 43 - 46: 58.633 distance: 44 - 45: 43.820 distance: 44 - 50: 38.980 distance: 46 - 47: 47.595 distance: 47 - 48: 29.578 distance: 47 - 49: 9.636 distance: 50 - 51: 57.298 distance: 51 - 52: 41.177 distance: 51 - 54: 39.633 distance: 52 - 53: 33.948 distance: 52 - 55: 31.632 distance: 55 - 56: 10.159 distance: 55 - 61: 18.964 distance: 56 - 57: 45.934 distance: 56 - 59: 11.656 distance: 57 - 58: 26.211 distance: 57 - 62: 26.175 distance: 59 - 60: 10.952 distance: 60 - 61: 12.682 distance: 62 - 63: 25.809 distance: 63 - 64: 6.011 distance: 63 - 66: 42.338 distance: 64 - 65: 21.481 distance: 64 - 70: 11.497 distance: 66 - 67: 39.828 distance: 70 - 71: 49.237 distance: 71 - 74: 57.514 distance: 72 - 77: 41.080 distance: 77 - 78: 56.156 distance: 78 - 79: 55.464 distance: 78 - 81: 39.926 distance: 79 - 80: 3.457 distance: 79 - 82: 55.019 distance: 82 - 83: 40.062 distance: 83 - 84: 41.299 distance: 83 - 86: 15.439 distance: 84 - 85: 19.972 distance: 86 - 87: 15.557 distance: 87 - 88: 57.586 distance: 87 - 89: 56.321 distance: 90 - 91: 38.041 distance: 90 - 141: 34.425 distance: 91 - 92: 40.622 distance: 91 - 94: 39.609 distance: 92 - 101: 44.304 distance: 93 - 138: 35.126 distance: 94 - 95: 40.932 distance: 96 - 98: 35.594 distance: 97 - 99: 39.526 distance: 98 - 100: 3.755 distance: 101 - 102: 50.104 distance: 102 - 103: 21.706 distance: 102 - 105: 40.475 distance: 105 - 106: 26.398 distance: 105 - 107: 14.358 distance: 108 - 109: 27.850 distance: 108 - 129: 32.524 distance: 109 - 110: 48.609 distance: 109 - 112: 12.531 distance: 110 - 114: 33.006 distance: 111 - 126: 34.620 distance: 112 - 113: 37.031