Starting phenix.real_space_refine on Mon Mar 18 19:05:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lc6_23269/03_2024/7lc6_23269_trim_updated.pdb" } resolution = 3.7 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= 0.012 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 P 1 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 6954 2.51 5 N 1814 2.21 5 O 1954 1.98 5 H 11106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "B GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21891 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8445 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 10166 Classifications: {'peptide': 672} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 646} Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2815 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 13, 'TRANS': 171} Chain: "D" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 402 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' K': 1, '9Y0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 9.57, per 1000 atoms: 0.44 Number of scatterers: 21891 At special positions: 0 Unit cell: (82.004, 105.742, 169.403, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) K 1 19.00 S 60 16.00 P 1 15.00 Mg 1 11.99 O 1954 8.00 N 1814 7.00 C 6954 6.00 H 11106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2620 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 6 sheets defined 57.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 2 through 32 removed outlier: 3.534A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 128 through 156 removed outlier: 3.699A pdb=" N THR A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 179 through 192 Processing helix chain 'A' and resid 220 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.938A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.753A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.585A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 509 Proline residue: A 499 - end of helix removed outlier: 3.801A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.532A pdb=" N TRP B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 98 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 216 through 246 removed outlier: 3.570A pdb=" N LEU B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.578A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 266 through 285 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 496 through 509 removed outlier: 4.047A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 543 No H-bonds generated for 'chain 'B' and resid 540 through 543' Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.912A pdb=" N SER B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 613 through 637 Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 187 Processing helix chain 'D' and resid 3 through 24 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 106 through 108 Processing sheet with id= C, first strand: chain 'B' and resid 131 through 134 removed outlier: 4.142A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 466 through 470 Processing sheet with id= F, first strand: chain 'B' and resid 321 through 324 removed outlier: 3.595A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA B 444 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 429 " --> pdb=" O ALA B 444 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1671 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: 7.91 Time building geometry restraints manager: 20.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11094 1.02 - 1.22: 17 1.22 - 1.42: 4344 1.42 - 1.62: 6518 1.62 - 1.82: 110 Bond restraints: 22083 Sorted by residual: bond pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" ND2 ASN B 624 " pdb="HD22 ASN B 624 " ideal model delta sigma weight residual 0.860 0.977 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" ND2 ASN B 624 " pdb="HD21 ASN B 624 " ideal model delta sigma weight residual 0.860 0.976 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C5 9Y0 A 602 " pdb=" O5 9Y0 A 602 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C21 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 2.00e+01 ... (remaining 22078 not shown) Histogram of bond angle deviations from ideal: 85.41 - 95.16: 2 95.16 - 104.91: 288 104.91 - 114.67: 27880 114.67 - 124.42: 10575 124.42 - 134.17: 1322 Bond angle restraints: 40067 Sorted by residual: angle pdb=" C11 9Y0 A 602 " pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " ideal model delta sigma weight residual 111.77 85.41 26.36 3.00e+00 1.11e-01 7.72e+01 angle pdb=" C12 9Y0 A 602 " pdb=" C13 9Y0 A 602 " pdb=" C14 9Y0 A 602 " ideal model delta sigma weight residual 127.16 112.84 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CD1 ILE C 141 " pdb=" CG1 ILE C 141 " pdb="HG13 ILE C 141 " ideal model delta sigma weight residual 108.00 94.49 13.51 3.00e+00 1.11e-01 2.03e+01 angle pdb=" CB ILE C 141 " pdb=" CG1 ILE C 141 " pdb=" CD1 ILE C 141 " ideal model delta sigma weight residual 113.80 122.90 -9.10 2.10e+00 2.27e-01 1.88e+01 angle pdb=" N ASN A 32 " pdb=" CA ASN A 32 " pdb=" C ASN A 32 " ideal model delta sigma weight residual 112.59 107.49 5.10 1.22e+00 6.72e-01 1.75e+01 ... (remaining 40062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 9918 28.91 - 57.83: 379 57.83 - 86.74: 39 86.74 - 115.65: 4 115.65 - 144.57: 5 Dihedral angle restraints: 10345 sinusoidal: 5701 harmonic: 4644 Sorted by residual: dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O7 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 181.02 36.45 144.57 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C23 9Y0 A 602 " pdb=" C21 9Y0 A 602 " pdb=" C22 9Y0 A 602 " pdb=" O6 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 0.61 -143.51 144.12 1 3.00e+01 1.11e-03 1.93e+01 dihedral pdb=" C3 9Y0 A 602 " pdb=" O1 9Y0 A 602 " pdb=" P 9Y0 A 602 " pdb=" O3 9Y0 A 602 " ideal model delta sinusoidal sigma weight residual 291.93 150.21 141.72 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 10342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1323 0.060 - 0.120: 395 0.120 - 0.180: 65 0.180 - 0.240: 11 0.240 - 0.300: 4 Chirality restraints: 1798 Sorted by residual: chirality pdb=" CG LEU B 225 " pdb=" CB LEU B 225 " pdb=" CD1 LEU B 225 " pdb=" CD2 LEU B 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE A 148 " pdb=" CA ILE A 148 " pdb=" CG1 ILE A 148 " pdb=" CG2 ILE A 148 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1795 not shown) Planarity restraints: 3264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.313 2.00e-02 2.50e+03 3.84e-01 2.21e+03 pdb=" CG ASN B 624 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.303 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.595 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 A 602 " 0.039 2.00e-02 2.50e+03 3.09e-01 9.57e+02 pdb=" C13 9Y0 A 602 " 0.203 2.00e-02 2.50e+03 pdb=" C14 9Y0 A 602 " -0.515 2.00e-02 2.50e+03 pdb=" C15 9Y0 A 602 " 0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 86 " 0.048 2.00e-02 2.50e+03 8.93e-02 1.20e+02 pdb=" CG ASN C 86 " -0.096 2.00e-02 2.50e+03 pdb=" OD1 ASN C 86 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 86 " 0.152 2.00e-02 2.50e+03 pdb="HD21 ASN C 86 " 0.022 2.00e-02 2.50e+03 pdb="HD22 ASN C 86 " -0.112 2.00e-02 2.50e+03 ... (remaining 3261 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.33: 6143 2.33 - 3.03: 62554 3.03 - 3.73: 79513 3.73 - 4.44: 122834 4.44 - 5.14: 191225 Nonbonded interactions: 462269 Sorted by model distance: nonbonded pdb=" O ASP B 329 " pdb=" H THR B 332 " model vdw 1.626 1.850 nonbonded pdb=" HZ1 LYS B 499 " pdb=" OD2 ASP B 522 " model vdw 1.644 1.850 nonbonded pdb=" O THR B 645 " pdb=" H MET B 649 " model vdw 1.645 1.850 nonbonded pdb=" H ASP B 154 " pdb=" O ARG B 181 " model vdw 1.648 1.850 nonbonded pdb=" OE1 GLN B 601 " pdb=" H GLN B 601 " model vdw 1.651 1.850 ... (remaining 462264 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.410 Extract box with map and model: 8.160 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 75.330 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.010 0.212 10977 Z= 0.637 Angle : 1.124 26.360 14930 Z= 0.623 Chirality : 0.058 0.300 1798 Planarity : 0.011 0.309 1891 Dihedral : 12.510 144.567 3923 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.51 % Allowed : 5.15 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.96 (0.18), residues: 1432 helix: -1.05 (0.15), residues: 857 sheet: -3.62 (0.38), residues: 97 loop : -3.13 (0.22), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 176 HIS 0.009 0.002 HIS C 66 PHE 0.036 0.005 PHE A 392 TYR 0.035 0.004 TYR C 22 ARG 0.008 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLU cc_start: 0.7800 (tp30) cc_final: 0.7298 (tm-30) REVERT: A 350 MET cc_start: 0.7926 (mmt) cc_final: 0.7702 (mmt) REVERT: B 190 GLU cc_start: 0.7016 (tt0) cc_final: 0.6369 (tp30) REVERT: B 192 SER cc_start: 0.7970 (t) cc_final: 0.7449 (m) REVERT: B 350 ARG cc_start: 0.8420 (mtm-85) cc_final: 0.7634 (mmm160) REVERT: C 48 THR cc_start: 0.6938 (p) cc_final: 0.6507 (p) REVERT: C 111 ASP cc_start: 0.7698 (m-30) cc_final: 0.7314 (t0) outliers start: 17 outliers final: 5 residues processed: 190 average time/residue: 0.6282 time to fit residues: 159.9049 Evaluate side-chains 104 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 453 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 465 ASN B 316 ASN B 390 ASN B 582 ASN C 58 ASN C 86 ASN C 135 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10977 Z= 0.207 Angle : 0.608 5.885 14930 Z= 0.322 Chirality : 0.039 0.148 1798 Planarity : 0.005 0.071 1891 Dihedral : 11.549 174.593 1569 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.80 % Allowed : 9.05 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.20), residues: 1432 helix: -0.13 (0.16), residues: 858 sheet: -3.33 (0.45), residues: 81 loop : -2.70 (0.23), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 176 HIS 0.003 0.001 HIS C 66 PHE 0.013 0.002 PHE A 109 TYR 0.024 0.001 TYR A 381 ARG 0.006 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 279 MET cc_start: 0.5789 (mmp) cc_final: 0.5486 (mmp) REVERT: B 350 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.7664 (mmm160) REVERT: B 383 MET cc_start: 0.2928 (ptp) cc_final: 0.2709 (ptp) REVERT: C 75 MET cc_start: 0.6753 (ptm) cc_final: 0.6270 (ptm) outliers start: 9 outliers final: 9 residues processed: 119 average time/residue: 0.5814 time to fit residues: 98.0122 Evaluate side-chains 104 residues out of total 1127 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 245 TRP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 516 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 56.8421 > 50: distance: 91 - 100: 5.003 distance: 100 - 101: 7.638 distance: 100 - 104: 6.327 distance: 101 - 102: 8.849 distance: 101 - 105: 7.645 distance: 101 - 106: 26.504 distance: 102 - 103: 10.560 distance: 102 - 107: 12.376 distance: 107 - 108: 8.896 distance: 107 - 119: 20.879 distance: 108 - 109: 15.644 distance: 108 - 111: 14.349 distance: 108 - 120: 12.557 distance: 109 - 110: 7.366 distance: 109 - 128: 28.457 distance: 111 - 112: 4.759 distance: 111 - 122: 4.234 distance: 112 - 114: 3.025 distance: 128 - 129: 9.213 distance: 128 - 139: 15.810 distance: 129 - 130: 6.870 distance: 129 - 132: 11.922 distance: 129 - 140: 6.233 distance: 130 - 131: 13.963 distance: 130 - 148: 26.984 distance: 132 - 133: 5.417 distance: 132 - 141: 7.524 distance: 132 - 142: 16.343 distance: 133 - 134: 3.545 distance: 134 - 136: 3.844 distance: 134 - 143: 4.071 distance: 135 - 144: 3.289 distance: 136 - 138: 3.481 distance: 148 - 149: 20.356 distance: 148 - 158: 13.345 distance: 149 - 150: 15.821 distance: 149 - 152: 17.092 distance: 149 - 159: 13.901 distance: 150 - 151: 12.583 distance: 150 - 165: 25.771 distance: 152 - 153: 7.449 distance: 152 - 160: 6.580 distance: 152 - 161: 12.186 distance: 153 - 154: 6.740 distance: 153 - 155: 9.451 distance: 154 - 156: 10.030 distance: 155 - 157: 9.937 distance: 155 - 162: 5.289 distance: 156 - 163: 8.836 distance: 157 - 164: 6.130 distance: 165 - 166: 18.035 distance: 165 - 169: 15.897 distance: 166 - 167: 22.259 distance: 166 - 170: 27.091 distance: 166 - 171: 13.751 distance: 167 - 168: 24.577 distance: 167 - 172: 20.004 distance: 172 - 173: 10.279 distance: 172 - 183: 10.242 distance: 173 - 174: 9.516 distance: 173 - 176: 14.829 distance: 173 - 184: 12.044 distance: 174 - 175: 15.575 distance: 174 - 196: 4.073 distance: 176 - 177: 9.877 distance: 176 - 185: 8.279 distance: 176 - 186: 8.439 distance: 177 - 178: 7.177 distance: 177 - 187: 3.172 distance: 177 - 188: 7.625 distance: 178 - 179: 3.117 distance: 178 - 189: 3.630 distance: 196 - 197: 10.396 distance: 196 - 202: 8.140 distance: 197 - 198: 12.602 distance: 197 - 200: 9.832 distance: 197 - 203: 13.455 distance: 198 - 199: 14.216 distance: 198 - 210: 35.268 distance: 200 - 201: 4.128 distance: 200 - 204: 10.251 distance: 200 - 205: 10.820 distance: 201 - 202: 8.928 distance: 201 - 206: 5.154 distance: 201 - 207: 8.437 distance: 202 - 208: 4.011 distance: 202 - 209: 14.735 distance: 210 - 211: 10.475 distance: 210 - 216: 13.743 distance: 211 - 212: 4.326 distance: 211 - 214: 6.429 distance: 211 - 217: 7.019 distance: 212 - 213: 11.029 distance: 212 - 221: 4.244 distance: 214 - 215: 13.908 distance: 214 - 218: 6.083 distance: 214 - 219: 5.651 distance: 215 - 220: 11.765 distance: 221 - 222: 6.599 distance: 221 - 226: 6.217 distance: 222 - 227: 7.720 distance: 223 - 224: 6.367 distance: 223 - 231: 9.341 distance: 225 - 229: 3.163 distance: 225 - 230: 5.071 distance: 231 - 232: 6.055 distance: 231 - 238: 4.004 distance: 232 - 233: 17.479 distance: 232 - 235: 4.079 distance: 232 - 239: 15.400 distance: 233 - 234: 17.150 distance: 233 - 245: 19.126 distance: 575 - 600: 3.248