Starting phenix.real_space_refine on Wed Jan 17 15:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c02_16353/01_2024/8c02_16353.pdb" } resolution = 4.09 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2767 2.51 5 N 695 2.21 5 O 749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 4242 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 2.71, per 1000 atoms: 0.64 Number of scatterers: 4242 At special positions: 0 Unit cell: (76.818, 100.254, 72.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 749 8.00 N 695 7.00 C 2767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " 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: 1.79 Conformation dependent library (CDL) restraints added in 810.5 milliseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 72.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.897A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 127 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.077A pdb=" N VAL A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'A' and resid 288 through 305 removed outlier: 3.856A pdb=" N PHE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.695A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 393 Processing helix chain 'A' and resid 451 through 483 removed outlier: 3.642A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 546 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 37 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET B 36 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.523A pdb=" N VAL B 14 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS B 101 " --> pdb=" O TYR B 112 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR B 112 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 103 " --> pdb=" O TYR B 110 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1014 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: 1.57 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1312 1.34 - 1.46: 1032 1.46 - 1.58: 1939 1.58 - 1.70: 0 1.70 - 1.81: 52 Bond restraints: 4335 Sorted by residual: bond pdb=" N MET A 288 " pdb=" CA MET A 288 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.25e-02 6.40e+03 8.87e+00 bond pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.32e-02 5.74e+03 5.40e+00 bond pdb=" CG GLN A 93 " pdb=" CD GLN A 93 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.31e+00 bond pdb=" CG1 ILE A 136 " pdb=" CD1 ILE A 136 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.14e+00 bond pdb=" CG LEU A 222 " pdb=" CD1 LEU A 222 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 ... (remaining 4330 not shown) Histogram of bond angle deviations from ideal: 96.25 - 103.84: 45 103.84 - 111.43: 1933 111.43 - 119.02: 1569 119.02 - 126.61: 2280 126.61 - 134.19: 71 Bond angle restraints: 5898 Sorted by residual: angle pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 114.10 121.78 -7.68 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CA GLU A 486 " pdb=" CB GLU A 486 " pdb=" CG GLU A 486 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" N GLN A 93 " pdb=" CA GLN A 93 " pdb=" CB GLN A 93 " ideal model delta sigma weight residual 110.28 115.21 -4.93 1.55e+00 4.16e-01 1.01e+01 angle pdb=" CB LYS A 549 " pdb=" CG LYS A 549 " pdb=" CD LYS A 549 " ideal model delta sigma weight residual 111.30 118.34 -7.04 2.30e+00 1.89e-01 9.36e+00 angle pdb=" CA GLU A 290 " pdb=" CB GLU A 290 " pdb=" CG GLU A 290 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.81e+00 ... (remaining 5893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 2262 16.19 - 32.38: 187 32.38 - 48.57: 43 48.57 - 64.76: 7 64.76 - 80.95: 5 Dihedral angle restraints: 2504 sinusoidal: 930 harmonic: 1574 Sorted by residual: dihedral pdb=" CA THR A 122 " pdb=" C THR A 122 " pdb=" N MET A 123 " pdb=" CA MET A 123 " ideal model delta harmonic sigma weight residual 180.00 -162.55 -17.45 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA GLU B 46 " pdb=" C GLU B 46 " pdb=" N ARG B 47 " pdb=" CA ARG B 47 " ideal model delta harmonic sigma weight residual 180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA MET B 105 " pdb=" C MET B 105 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " ideal model delta harmonic sigma weight residual 180.00 162.97 17.03 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 2501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 473 0.039 - 0.077: 164 0.077 - 0.116: 48 0.116 - 0.155: 7 0.155 - 0.193: 4 Chirality restraints: 696 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA GLN A 93 " pdb=" N GLN A 93 " pdb=" C GLN A 93 " pdb=" CB GLN A 93 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.84e-01 chirality pdb=" CB ILE B 56 " pdb=" CA ILE B 56 " pdb=" CG1 ILE B 56 " pdb=" CG2 ILE B 56 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 693 not shown) Planarity restraints: 719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 514 " -0.054 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO A 515 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 29 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO B 30 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 317 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C LEU A 317 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU A 317 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 318 " -0.015 2.00e-02 2.50e+03 ... (remaining 716 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 718 2.76 - 3.29: 4563 3.29 - 3.83: 7381 3.83 - 4.36: 7786 4.36 - 4.90: 13676 Nonbonded interactions: 34124 Sorted by model distance: nonbonded pdb=" O CYS B 24 " pdb=" OG1 THR B 80 " model vdw 2.225 2.440 nonbonded pdb=" O VAL A 358 " pdb=" OG1 THR A 361 " model vdw 2.279 2.440 nonbonded pdb=" O ALA B 54 " pdb=" NH2 ARG B 74 " model vdw 2.298 2.520 nonbonded pdb=" N MET B 105 " pdb=" O TRP B 108 " model vdw 2.323 2.520 nonbonded pdb=" O THR A 230 " pdb=" OG1 THR A 230 " model vdw 2.339 2.440 ... (remaining 34119 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: 0.240 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: 1.430 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.290 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.004 0.057 4335 Z= 0.259 Angle : 0.832 9.920 5898 Z= 0.419 Chirality : 0.045 0.193 696 Planarity : 0.007 0.083 719 Dihedral : 13.159 80.949 1497 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.44 % Allowed : 0.00 % Favored : 99.56 % 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: 1.51 (0.35), residues: 541 helix: 2.10 (0.26), residues: 367 sheet: -1.31 (0.64), residues: 39 loop : -1.40 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 38 HIS 0.002 0.001 HIS A 32 PHE 0.016 0.002 PHE A 530 TYR 0.030 0.002 TYR A 29 ARG 0.007 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80) REVERT: A 36 THR cc_start: 0.9349 (m) cc_final: 0.9145 (t) REVERT: A 111 MET cc_start: 0.8545 (tpt) cc_final: 0.8277 (mmm) REVERT: A 184 THR cc_start: 0.9334 (m) cc_final: 0.8956 (t) REVERT: A 290 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20) REVERT: A 312 MET cc_start: 0.8837 (tpt) cc_final: 0.8058 (tpp) REVERT: A 473 ASP cc_start: 0.9390 (t70) cc_final: 0.9177 (t0) REVERT: A 536 ILE cc_start: 0.8342 (mm) cc_final: 0.8104 (mm) REVERT: B 20 LEU cc_start: 0.8822 (tt) cc_final: 0.8434 (mt) REVERT: B 70 PHE cc_start: 0.7802 (m-10) cc_final: 0.7413 (m-80) REVERT: B 92 ASP cc_start: 0.7493 (m-30) cc_final: 0.6904 (m-30) REVERT: B 119 VAL cc_start: 0.9269 (t) cc_final: 0.9062 (t) outliers start: 2 outliers final: 1 residues processed: 192 average time/residue: 0.1340 time to fit residues: 32.8698 Evaluate side-chains 159 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 335 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4335 Z= 0.200 Angle : 0.643 7.862 5898 Z= 0.327 Chirality : 0.040 0.174 696 Planarity : 0.004 0.040 719 Dihedral : 4.042 15.816 590 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % 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: 2.05 (0.36), residues: 541 helix: 2.43 (0.26), residues: 370 sheet: -0.08 (0.76), residues: 43 loop : -1.46 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 38 HIS 0.003 0.001 HIS A 32 PHE 0.011 0.001 PHE A 530 TYR 0.025 0.002 TYR A 29 ARG 0.005 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.7978 (p0) cc_final: 0.7703 (p0) REVERT: A 26 PHE cc_start: 0.8726 (t80) cc_final: 0.8518 (t80) REVERT: A 111 MET cc_start: 0.8478 (tpt) cc_final: 0.8178 (mmm) REVERT: A 488 GLU cc_start: 0.7330 (tp30) cc_final: 0.7064 (tp30) REVERT: A 536 ILE cc_start: 0.8246 (mm) cc_final: 0.8034 (mm) REVERT: B 6 LEU cc_start: 0.8568 (pp) cc_final: 0.8196 (pp) REVERT: B 8 GLU cc_start: 0.6905 (mp0) cc_final: 0.4964 (mp0) REVERT: B 34 ASN cc_start: 0.8121 (m-40) cc_final: 0.7558 (m110) REVERT: B 38 TRP cc_start: 0.8330 (m100) cc_final: 0.7981 (m100) REVERT: B 92 ASP cc_start: 0.7473 (m-30) cc_final: 0.7092 (m-30) REVERT: B 108 TRP cc_start: 0.8067 (t-100) cc_final: 0.7324 (t-100) REVERT: B 115 GLN cc_start: 0.8320 (pm20) cc_final: 0.8055 (pm20) REVERT: B 117 THR cc_start: 0.8799 (p) cc_final: 0.8466 (t) REVERT: B 119 VAL cc_start: 0.9319 (t) cc_final: 0.9089 (t) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1438 time to fit residues: 35.7778 Evaluate side-chains 158 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4335 Z= 0.245 Angle : 0.650 8.827 5898 Z= 0.336 Chirality : 0.040 0.161 696 Planarity : 0.004 0.030 719 Dihedral : 3.938 17.377 590 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.22 % Allowed : 3.30 % Favored : 96.48 % 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: 2.01 (0.37), residues: 541 helix: 2.33 (0.26), residues: 373 sheet: 0.18 (0.89), residues: 38 loop : -1.38 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 42 HIS 0.004 0.001 HIS A 32 PHE 0.008 0.001 PHE A 292 TYR 0.019 0.002 TYR A 302 ARG 0.005 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8744 (t80) cc_final: 0.8417 (t80) REVERT: A 79 ILE cc_start: 0.9015 (mm) cc_final: 0.8806 (tp) REVERT: A 309 LEU cc_start: 0.8815 (mt) cc_final: 0.8377 (mt) REVERT: A 473 ASP cc_start: 0.9464 (t70) cc_final: 0.9174 (t0) REVERT: A 495 VAL cc_start: 0.9541 (m) cc_final: 0.9334 (m) REVERT: A 536 ILE cc_start: 0.8292 (mm) cc_final: 0.8086 (mm) REVERT: B 21 ARG cc_start: 0.8729 (tpt-90) cc_final: 0.8157 (tpt-90) REVERT: B 34 ASN cc_start: 0.8334 (m-40) cc_final: 0.7749 (m110) REVERT: B 36 MET cc_start: 0.9014 (mmm) cc_final: 0.8748 (mmm) REVERT: B 38 TRP cc_start: 0.8283 (m100) cc_final: 0.7913 (m100) REVERT: B 70 PHE cc_start: 0.7645 (m-10) cc_final: 0.7407 (m-80) REVERT: B 92 ASP cc_start: 0.7567 (m-30) cc_final: 0.7054 (m-30) REVERT: B 97 TYR cc_start: 0.7993 (m-80) cc_final: 0.7442 (m-10) REVERT: B 115 GLN cc_start: 0.8248 (pm20) cc_final: 0.7819 (pm20) REVERT: B 119 VAL cc_start: 0.9178 (t) cc_final: 0.8970 (t) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1470 time to fit residues: 35.3061 Evaluate side-chains 152 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4335 Z= 0.253 Angle : 0.665 8.869 5898 Z= 0.338 Chirality : 0.040 0.148 696 Planarity : 0.004 0.049 719 Dihedral : 3.869 16.101 590 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.22 % Allowed : 4.19 % Favored : 95.59 % 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: 2.14 (0.36), residues: 541 helix: 2.40 (0.26), residues: 371 sheet: 0.26 (0.88), residues: 38 loop : -1.19 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE A 530 TYR 0.023 0.002 TYR A 29 ARG 0.006 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8791 (t80) cc_final: 0.8379 (t80) REVERT: A 111 MET cc_start: 0.8170 (mmm) cc_final: 0.7952 (mmm) REVERT: A 119 GLU cc_start: 0.8140 (pm20) cc_final: 0.7889 (pm20) REVERT: A 335 GLN cc_start: 0.7558 (tp40) cc_final: 0.6505 (tt0) REVERT: A 473 ASP cc_start: 0.9439 (t70) cc_final: 0.9230 (t0) REVERT: B 34 ASN cc_start: 0.8659 (m-40) cc_final: 0.8191 (m110) REVERT: B 36 MET cc_start: 0.8980 (mmm) cc_final: 0.8711 (mmm) REVERT: B 38 TRP cc_start: 0.8365 (m100) cc_final: 0.8029 (m100) REVERT: B 70 PHE cc_start: 0.7688 (m-10) cc_final: 0.7449 (m-80) REVERT: B 92 ASP cc_start: 0.7795 (m-30) cc_final: 0.7103 (m-30) REVERT: B 97 TYR cc_start: 0.7985 (m-80) cc_final: 0.7761 (m-10) REVERT: B 119 VAL cc_start: 0.9226 (t) cc_final: 0.8988 (t) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1336 time to fit residues: 31.8627 Evaluate side-chains 152 residues out of total 454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 65.9423 > 50: distance: 16 - 115: 31.410 distance: 29 - 95: 25.118 distance: 32 - 92: 28.473 distance: 49 - 52: 17.851 distance: 52 - 53: 36.394 distance: 52 - 58: 17.071 distance: 53 - 54: 31.297 distance: 53 - 56: 28.605 distance: 54 - 55: 28.737 distance: 54 - 59: 18.867 distance: 56 - 57: 26.374 distance: 57 - 58: 45.799 distance: 59 - 60: 40.697 distance: 60 - 61: 44.875 distance: 61 - 62: 45.385 distance: 61 - 63: 30.666 distance: 63 - 64: 39.697 distance: 64 - 65: 29.840 distance: 64 - 67: 23.885 distance: 65 - 66: 51.869 distance: 65 - 72: 23.708 distance: 67 - 68: 25.538 distance: 68 - 69: 11.323 distance: 69 - 70: 22.952 distance: 70 - 71: 47.462 distance: 72 - 73: 15.656 distance: 73 - 74: 42.638 distance: 73 - 76: 38.179 distance: 74 - 75: 41.914 distance: 74 - 81: 11.607 distance: 76 - 77: 13.797 distance: 77 - 78: 30.616 distance: 78 - 79: 43.338 distance: 78 - 80: 25.709 distance: 81 - 82: 9.193 distance: 82 - 83: 42.496 distance: 82 - 85: 27.372 distance: 83 - 84: 7.309 distance: 83 - 92: 6.617 distance: 85 - 86: 37.409 distance: 86 - 87: 31.185 distance: 87 - 88: 40.368 distance: 88 - 89: 18.464 distance: 89 - 90: 6.716 distance: 89 - 91: 51.374 distance: 92 - 93: 20.825 distance: 93 - 94: 14.315 distance: 93 - 96: 32.880 distance: 94 - 95: 30.227 distance: 94 - 101: 41.572 distance: 96 - 97: 32.380 distance: 97 - 98: 27.845 distance: 98 - 99: 24.632 distance: 98 - 100: 21.898 distance: 101 - 102: 19.038 distance: 102 - 103: 25.142 distance: 102 - 105: 34.422 distance: 103 - 104: 12.655 distance: 103 - 115: 25.399 distance: 105 - 106: 21.860 distance: 106 - 107: 23.072 distance: 106 - 108: 14.554 distance: 107 - 109: 20.268 distance: 108 - 110: 4.649 distance: 108 - 111: 16.207 distance: 109 - 110: 13.672 distance: 110 - 112: 27.199 distance: 111 - 113: 20.537 distance: 112 - 114: 21.197 distance: 113 - 114: 23.269 distance: 115 - 116: 4.665 distance: 116 - 117: 14.511 distance: 116 - 119: 41.153 distance: 117 - 118: 9.695 distance: 117 - 122: 18.081 distance: 119 - 120: 13.009 distance: 119 - 121: 8.460 distance: 122 - 123: 15.234 distance: 123 - 124: 18.269 distance: 123 - 126: 58.952 distance: 124 - 125: 24.224 distance: 124 - 127: 39.346 distance: 127 - 128: 53.199 distance: 128 - 129: 33.137 distance: 128 - 131: 14.062 distance: 129 - 130: 16.458 distance: 129 - 132: 28.877