Starting phenix.real_space_refine on Sun Mar 10 23:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vyh_21460/03_2024/6vyh_21460.pdb" } resolution = 3.0 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= 0.006 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: 5 Type Number sf(0) Gaussians Co 2 6.85 5 S 33 5.16 5 C 3898 2.51 5 N 1030 2.21 5 O 1130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6093 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3305 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 8, 'TRANS': 419} Chain breaks: 2 Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1348 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 177 Chain: "D" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1437 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2017 SG CYS A 326 43.574 81.441 42.997 1.00 77.54 S Time building chain proxies: 3.87, per 1000 atoms: 0.64 Number of scatterers: 6093 At special positions: 0 Unit cell: (132.566, 112.514, 83.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Co 2 26.99 S 33 16.00 O 1130 8.00 N 1030 7.00 C 3898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 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: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 25 through 50 removed outlier: 3.710A pdb=" N TYR A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 85 removed outlier: 5.624A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.543A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 163 removed outlier: 3.995A pdb=" N TYR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 199 removed outlier: 3.614A pdb=" N ASN A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix removed outlier: 3.579A pdb=" N GLY A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 230 removed outlier: 3.772A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.686A pdb=" N ARG A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.505A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.642A pdb=" N THR A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.786A pdb=" N SER A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.533A pdb=" N PHE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 379 removed outlier: 3.636A pdb=" N TRP A 378 " --> pdb=" O LEU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 393 removed outlier: 4.057A pdb=" N VAL A 391 " --> pdb=" O CYS A 387 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.601A pdb=" N PHE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 484 removed outlier: 3.854A pdb=" N LEU A 475 " --> pdb=" O TRP A 471 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 513 removed outlier: 3.593A pdb=" N ASN A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 504 " --> pdb=" O MET A 500 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 4.421A pdb=" N PHE A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.552A pdb=" N PHE A 540 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.524A pdb=" N ARG C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 204 through 209' Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.799A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.154A pdb=" N THR C 117 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.809A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER C 87 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138 removed outlier: 3.581A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 211 through 216 removed outlier: 3.685A pdb=" N TYR C 212 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA8, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.491A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.773A pdb=" N VAL D 167 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 179 321 hydrogen bonds defined for protein. 897 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: 1.76 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1303 1.33 - 1.45: 1455 1.45 - 1.57: 3390 1.57 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6202 Sorted by residual: bond pdb=" N ILE C 126 " pdb=" CA ILE C 126 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.97e+00 bond pdb=" N GLU C 128 " pdb=" CA GLU C 128 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 9.16e+00 bond pdb=" CA VAL D 208 " pdb=" CB VAL D 208 " ideal model delta sigma weight residual 1.553 1.531 0.022 7.40e-03 1.83e+04 9.05e+00 bond pdb=" N VAL A 341 " pdb=" CA VAL A 341 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.00e+00 bond pdb=" N TYR D 128 " pdb=" CA TYR D 128 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.95e+00 ... (remaining 6197 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.76: 88 105.76 - 112.90: 3400 112.90 - 120.03: 2189 120.03 - 127.17: 2718 127.17 - 134.30: 64 Bond angle restraints: 8459 Sorted by residual: angle pdb=" N PRO D 151 " pdb=" CA PRO D 151 " pdb=" CB PRO D 151 " ideal model delta sigma weight residual 103.25 111.38 -8.13 1.05e+00 9.07e-01 5.99e+01 angle pdb=" N PRO D 192 " pdb=" CA PRO D 192 " pdb=" CB PRO D 192 " ideal model delta sigma weight residual 103.31 109.48 -6.17 8.90e-01 1.26e+00 4.80e+01 angle pdb=" N PRO D 174 " pdb=" CA PRO D 174 " pdb=" CB PRO D 174 " ideal model delta sigma weight residual 103.25 110.32 -7.07 1.05e+00 9.07e-01 4.54e+01 angle pdb=" N PRO D 237 " pdb=" CA PRO D 237 " pdb=" CB PRO D 237 " ideal model delta sigma weight residual 103.25 110.21 -6.96 1.05e+00 9.07e-01 4.39e+01 angle pdb=" N PRO D 144 " pdb=" CA PRO D 144 " pdb=" CB PRO D 144 " ideal model delta sigma weight residual 102.85 110.34 -7.49 1.13e+00 7.83e-01 4.39e+01 ... (remaining 8454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3225 17.08 - 34.16: 299 34.16 - 51.24: 64 51.24 - 68.32: 3 68.32 - 85.41: 9 Dihedral angle restraints: 3600 sinusoidal: 1139 harmonic: 2461 Sorted by residual: dihedral pdb=" CA GLY D 27 " pdb=" C GLY D 27 " pdb=" N ALA D 28 " pdb=" CA ALA D 28 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" C THR A 334 " pdb=" N THR A 334 " pdb=" CA THR A 334 " pdb=" CB THR A 334 " ideal model delta harmonic sigma weight residual -122.00 -133.98 11.98 0 2.50e+00 1.60e-01 2.30e+01 dihedral pdb=" CA TRP A 127 " pdb=" C TRP A 127 " pdb=" N VAL A 128 " pdb=" CA VAL A 128 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 796 0.072 - 0.144: 181 0.144 - 0.216: 23 0.216 - 0.287: 7 0.287 - 0.359: 2 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA THR A 334 " pdb=" N THR A 334 " pdb=" C THR A 334 " pdb=" CB THR A 334 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA TYR D 121 " pdb=" N TYR D 121 " pdb=" C TYR D 121 " pdb=" CB TYR D 121 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE A 513 " pdb=" N ILE A 513 " pdb=" C ILE A 513 " pdb=" CB ILE A 513 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1006 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 512 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C VAL A 512 " -0.061 2.00e-02 2.50e+03 pdb=" O VAL A 512 " 0.023 2.00e-02 2.50e+03 pdb=" N ILE A 513 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C GLN A 155 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 63 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO C 64 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.031 5.00e-02 4.00e+02 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 29 2.52 - 3.11: 4569 3.11 - 3.71: 8663 3.71 - 4.30: 12478 4.30 - 4.90: 21677 Nonbonded interactions: 47416 Sorted by model distance: nonbonded pdb=" OD2 ASP A 39 " pdb="CO CO A 601 " model vdw 1.922 2.220 nonbonded pdb=" SG CYS A 326 " pdb="CO CO A 602 " model vdw 2.112 2.580 nonbonded pdb=" OD1 ASP A 39 " pdb="CO CO A 601 " model vdw 2.141 2.220 nonbonded pdb=" O GLY A 368 " pdb=" OG1 THR A 372 " model vdw 2.215 2.440 nonbonded pdb=" OG SER A 376 " pdb=" OG SER A 472 " model vdw 2.236 2.440 ... (remaining 47411 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.170 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.180 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.013 0.086 6202 Z= 0.829 Angle : 1.112 10.479 8459 Z= 0.707 Chirality : 0.064 0.359 1009 Planarity : 0.005 0.056 1072 Dihedral : 14.405 85.406 2020 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 1.18 % Allowed : 8.82 % Favored : 90.00 % Rotamer: Outliers : 2.00 % Allowed : 10.71 % Favored : 87.30 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.24), residues: 850 helix: -3.32 (0.20), residues: 354 sheet: -1.58 (0.36), residues: 188 loop : -3.29 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 69 HIS 0.007 0.002 HIS A 508 PHE 0.021 0.003 PHE D 126 TYR 0.021 0.003 TYR A 220 ARG 0.015 0.002 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.690 Fit side-chains REVERT: A 112 MET cc_start: 0.6879 (mtp) cc_final: 0.6285 (mtt) REVERT: A 195 ILE cc_start: 0.7868 (mm) cc_final: 0.7656 (mm) REVERT: A 538 MET cc_start: 0.8818 (mtp) cc_final: 0.8392 (mtp) REVERT: C 123 LYS cc_start: 0.8010 (tttp) cc_final: 0.7677 (tmtt) REVERT: C 128 GLU cc_start: 0.6730 (tt0) cc_final: 0.5650 (pm20) REVERT: D 106 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (m) outliers start: 11 outliers final: 6 residues processed: 134 average time/residue: 1.0367 time to fit residues: 146.6374 Evaluate side-chains 105 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 86 ASN A 497 GLN C 26 GLN C 73 ASN D 25 GLN D 62 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6202 Z= 0.209 Angle : 0.631 10.519 8459 Z= 0.328 Chirality : 0.042 0.140 1009 Planarity : 0.005 0.066 1072 Dihedral : 5.673 35.787 919 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.18 % Favored : 94.35 % Rotamer: Outliers : 4.17 % Allowed : 21.05 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.04 (0.27), residues: 850 helix: -1.79 (0.25), residues: 366 sheet: -1.10 (0.36), residues: 193 loop : -2.73 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.011 0.001 PHE D 126 TYR 0.013 0.001 TYR A 133 ARG 0.008 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.6643 (mtp) cc_final: 0.6121 (mtt) REVERT: A 195 ILE cc_start: 0.7651 (mm) cc_final: 0.7201 (mt) REVERT: A 393 MET cc_start: 0.0563 (ptt) cc_final: -0.0222 (mmt) REVERT: A 507 LEU cc_start: 0.8266 (tp) cc_final: 0.7846 (mt) REVERT: A 538 MET cc_start: 0.8713 (mtp) cc_final: 0.8423 (mtp) REVERT: C 32 SER cc_start: 0.8311 (t) cc_final: 0.7976 (p) REVERT: C 59 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: C 123 LYS cc_start: 0.7956 (tttp) cc_final: 0.7594 (tmtt) REVERT: C 125 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: C 128 GLU cc_start: 0.6636 (tt0) cc_final: 0.5386 (pm20) outliers start: 23 outliers final: 11 residues processed: 116 average time/residue: 0.9917 time to fit residues: 121.6355 Evaluate side-chains 108 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 82 optimal weight: 0.1980 chunk 68 optimal weight: 0.0370 chunk 75 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 61 optimal weight: 40.0000 overall best weight: 1.0074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6202 Z= 0.211 Angle : 0.573 8.990 8459 Z= 0.295 Chirality : 0.041 0.145 1009 Planarity : 0.004 0.062 1072 Dihedral : 4.793 39.818 911 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.29 % Favored : 94.24 % Rotamer: Outliers : 5.08 % Allowed : 22.14 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.29), residues: 850 helix: -0.74 (0.27), residues: 365 sheet: -0.56 (0.36), residues: 191 loop : -2.31 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.002 0.001 HIS D 54 PHE 0.012 0.001 PHE D 126 TYR 0.014 0.001 TYR A 502 ARG 0.006 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.672 Fit side-chains REVERT: A 112 MET cc_start: 0.6561 (mtp) cc_final: 0.6128 (mtt) REVERT: A 195 ILE cc_start: 0.7665 (mm) cc_final: 0.7202 (mt) REVERT: A 296 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6510 (mmp-170) REVERT: A 393 MET cc_start: 0.0875 (ptt) cc_final: -0.0041 (mmt) REVERT: A 507 LEU cc_start: 0.7869 (tp) cc_final: 0.7620 (mt) REVERT: A 538 MET cc_start: 0.8745 (mtp) cc_final: 0.8320 (mtp) REVERT: C 123 LYS cc_start: 0.7912 (tttp) cc_final: 0.7524 (tmtt) REVERT: C 125 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6760 (pt0) REVERT: C 128 GLU cc_start: 0.6840 (tt0) cc_final: 0.5390 (pm20) outliers start: 28 outliers final: 13 residues processed: 119 average time/residue: 1.0666 time to fit residues: 133.8306 Evaluate side-chains 111 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.0670 chunk 81 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6202 Z= 0.190 Angle : 0.541 8.662 8459 Z= 0.279 Chirality : 0.041 0.145 1009 Planarity : 0.004 0.063 1072 Dihedral : 4.420 27.033 909 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.82 % Favored : 94.71 % Rotamer: Outliers : 5.81 % Allowed : 23.05 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.29), residues: 850 helix: -0.22 (0.28), residues: 364 sheet: -0.21 (0.37), residues: 191 loop : -2.10 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.001 0.000 HIS D 54 PHE 0.011 0.001 PHE C 107 TYR 0.009 0.001 TYR A 220 ARG 0.005 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.595 Fit side-chains REVERT: A 112 MET cc_start: 0.6493 (mtp) cc_final: 0.6072 (mtt) REVERT: A 195 ILE cc_start: 0.7781 (mm) cc_final: 0.7314 (mt) REVERT: A 324 PHE cc_start: 0.8023 (t80) cc_final: 0.7812 (t80) REVERT: A 393 MET cc_start: 0.0631 (ptt) cc_final: -0.0070 (mmt) REVERT: A 538 MET cc_start: 0.8711 (mtp) cc_final: 0.8199 (mtp) REVERT: C 123 LYS cc_start: 0.7917 (tttp) cc_final: 0.7506 (tmtt) REVERT: C 125 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6744 (pt0) REVERT: C 128 GLU cc_start: 0.7106 (tt0) cc_final: 0.5739 (pm20) REVERT: D 42 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7824 (tttp) outliers start: 32 outliers final: 18 residues processed: 114 average time/residue: 0.9474 time to fit residues: 114.5628 Evaluate side-chains 117 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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: 0.7696 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6202 Z= 0.144 Angle : 0.507 8.346 8459 Z= 0.258 Chirality : 0.040 0.143 1009 Planarity : 0.004 0.059 1072 Dihedral : 4.124 23.326 909 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.00 % Favored : 95.53 % Rotamer: Outliers : 5.26 % Allowed : 24.32 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.30), residues: 850 helix: 0.19 (0.29), residues: 367 sheet: 0.10 (0.37), residues: 187 loop : -1.87 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 127 HIS 0.001 0.000 HIS D 54 PHE 0.010 0.001 PHE C 107 TYR 0.011 0.001 TYR A 502 ARG 0.007 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.599 Fit side-chains REVERT: A 112 MET cc_start: 0.6470 (mtp) cc_final: 0.6137 (mtt) REVERT: A 195 ILE cc_start: 0.7792 (mm) cc_final: 0.7424 (mm) REVERT: A 296 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6528 (mmp-170) REVERT: A 324 PHE cc_start: 0.8044 (t80) cc_final: 0.7814 (t80) REVERT: A 383 CYS cc_start: 0.7513 (m) cc_final: 0.7221 (m) REVERT: A 393 MET cc_start: 0.0824 (ptt) cc_final: 0.0294 (mmt) REVERT: A 538 MET cc_start: 0.8665 (mtp) cc_final: 0.8155 (mtp) REVERT: C 59 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7928 (mttt) REVERT: C 123 LYS cc_start: 0.7901 (tttp) cc_final: 0.7497 (tmtt) REVERT: C 125 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: C 128 GLU cc_start: 0.7127 (tt0) cc_final: 0.5796 (pm20) outliers start: 29 outliers final: 13 residues processed: 120 average time/residue: 1.0144 time to fit residues: 128.8354 Evaluate side-chains 115 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6202 Z= 0.297 Angle : 0.584 8.662 8459 Z= 0.300 Chirality : 0.043 0.144 1009 Planarity : 0.004 0.062 1072 Dihedral : 4.403 17.430 908 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.18 % Favored : 94.35 % Rotamer: Outliers : 6.17 % Allowed : 24.50 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.30), residues: 850 helix: 0.00 (0.28), residues: 370 sheet: 0.12 (0.37), residues: 194 loop : -1.99 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 127 HIS 0.003 0.001 HIS D 54 PHE 0.015 0.001 PHE D 126 TYR 0.017 0.002 TYR A 133 ARG 0.006 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 0.724 Fit side-chains REVERT: A 195 ILE cc_start: 0.7791 (mm) cc_final: 0.7507 (mm) REVERT: A 296 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7036 (mmt180) REVERT: A 393 MET cc_start: 0.0640 (ptt) cc_final: -0.0119 (mmt) REVERT: A 530 SER cc_start: 0.8306 (m) cc_final: 0.7960 (m) REVERT: A 538 MET cc_start: 0.8667 (mtp) cc_final: 0.8208 (mtp) REVERT: C 123 LYS cc_start: 0.7947 (tttp) cc_final: 0.7492 (tmtt) REVERT: C 125 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6852 (pt0) REVERT: C 128 GLU cc_start: 0.7222 (tt0) cc_final: 0.5889 (pm20) outliers start: 34 outliers final: 21 residues processed: 120 average time/residue: 0.9600 time to fit residues: 122.1368 Evaluate side-chains 119 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.0040 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6202 Z= 0.162 Angle : 0.528 8.125 8459 Z= 0.269 Chirality : 0.040 0.143 1009 Planarity : 0.004 0.061 1072 Dihedral : 4.113 15.703 908 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.71 % Favored : 94.82 % Rotamer: Outliers : 5.99 % Allowed : 25.41 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.66 (0.30), residues: 850 helix: 0.35 (0.29), residues: 369 sheet: 0.16 (0.38), residues: 194 loop : -1.82 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 69 HIS 0.001 0.000 HIS D 54 PHE 0.010 0.001 PHE C 107 TYR 0.026 0.001 TYR A 133 ARG 0.009 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1700 Ramachandran restraints generated. 850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.704 Fit side-chains REVERT: A 195 ILE cc_start: 0.7789 (mm) cc_final: 0.7443 (mm) REVERT: A 296 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.6594 (mmp-170) REVERT: A 383 CYS cc_start: 0.7559 (m) cc_final: 0.7276 (m) REVERT: A 393 MET cc_start: 0.0646 (ptt) cc_final: 0.0049 (mmt) REVERT: A 530 SER cc_start: 0.8273 (m) cc_final: 0.7923 (m) REVERT: A 538 MET cc_start: 0.8649 (mtp) cc_final: 0.8138 (mtp) REVERT: C 38 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.7795 (ttp80) REVERT: C 59 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7960 (mttt) REVERT: C 123 LYS cc_start: 0.7907 (tttp) cc_final: 0.7460 (tmtt) REVERT: C 125 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: C 128 GLU cc_start: 0.7209 (tt0) cc_final: 0.5797 (pm20) REVERT: D 131 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7207 (pm20) outliers start: 33 outliers final: 16 residues processed: 118 average time/residue: 0.9464 time to fit residues: 118.4844 Evaluate side-chains 120 residues out of total 733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 296 ARG Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 517 ASN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 131 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-dev-5265/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-dev-5265/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: 50.6337 > 50: distance: 76 - 83: 21.767 distance: 83 - 84: 19.378 distance: 83 - 144: 26.953 distance: 84 - 85: 24.035 distance: 84 - 87: 34.247 distance: 85 - 86: 18.722 distance: 85 - 92: 11.996 distance: 87 - 88: 29.744 distance: 88 - 89: 11.531 distance: 89 - 90: 21.455 distance: 89 - 91: 19.408 distance: 92 - 93: 10.269 distance: 93 - 94: 11.520 distance: 93 - 96: 6.884 distance: 94 - 95: 20.502 distance: 94 - 104: 17.483 distance: 96 - 97: 21.206 distance: 97 - 98: 19.917 distance: 97 - 99: 27.296 distance: 98 - 100: 26.550 distance: 99 - 101: 11.823 distance: 100 - 102: 20.330 distance: 101 - 102: 8.230 distance: 102 - 103: 11.421 distance: 104 - 105: 29.748 distance: 105 - 106: 17.960 distance: 106 - 107: 19.114 distance: 106 - 108: 3.222 distance: 108 - 109: 15.119 distance: 109 - 110: 22.511 distance: 109 - 112: 28.056 distance: 110 - 111: 32.419 distance: 110 - 114: 7.818 distance: 112 - 113: 45.999 distance: 114 - 115: 8.427 distance: 115 - 116: 21.017 distance: 115 - 118: 28.217 distance: 116 - 117: 14.754 distance: 116 - 126: 18.294 distance: 118 - 119: 16.530 distance: 119 - 120: 11.931 distance: 119 - 121: 14.812 distance: 120 - 122: 13.237 distance: 121 - 123: 14.555 distance: 122 - 124: 5.188 distance: 124 - 125: 11.011 distance: 126 - 127: 17.650 distance: 126 - 132: 14.598 distance: 127 - 128: 12.869 distance: 127 - 130: 32.124 distance: 128 - 129: 31.014 distance: 128 - 133: 29.853 distance: 130 - 131: 24.361 distance: 131 - 132: 30.568 distance: 133 - 134: 14.055 distance: 134 - 135: 11.748 distance: 134 - 137: 3.220 distance: 135 - 136: 13.413 distance: 135 - 141: 8.305 distance: 137 - 138: 23.334 distance: 138 - 139: 22.454 distance: 138 - 140: 25.327 distance: 141 - 142: 9.309 distance: 142 - 143: 7.907 distance: 142 - 145: 12.281 distance: 143 - 144: 13.455 distance: 143 - 148: 10.986 distance: 145 - 146: 15.104 distance: 145 - 147: 12.887 distance: 148 - 149: 5.612 distance: 149 - 150: 3.398 distance: 149 - 152: 14.056 distance: 150 - 151: 4.283 distance: 150 - 159: 8.212 distance: 152 - 153: 12.197 distance: 153 - 154: 10.541 distance: 153 - 155: 8.248 distance: 154 - 156: 16.808 distance: 155 - 157: 6.547 distance: 156 - 158: 14.920 distance: 157 - 158: 20.223 distance: 159 - 160: 3.103 distance: 160 - 161: 4.709 distance: 161 - 162: 3.199 distance: 161 - 163: 5.263