Starting phenix.real_space_refine on Thu Dec 7 19:07:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuz_26807/12_2023/7uuz_26807_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.095 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: 7 Type Number sf(0) Gaussians Re 1 12.26 5 P 1 5.49 5 S 26 5.16 5 Na 1 4.78 5 C 2500 2.51 5 N 591 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3786 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3786 Unusual residues: {' NA': 1, '3PH': 1, 'REO': 1} Classifications: {'peptide': 501, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 476, None: 3} Not linked: pdbres="TRP A 560 " pdbres=" NA A 701 " Not linked: pdbres=" NA A 701 " pdbres="REO A 702 " Not linked: pdbres="REO A 702 " pdbres="3PH A 703 " Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.71, per 1000 atoms: 0.72 Number of scatterers: 3786 At special positions: 0 Unit cell: (69.42, 77.964, 83.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Re 1 74.95 S 26 16.00 P 1 15.00 Na 1 11.00 O 666 8.00 N 591 7.00 C 2500 6.00 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: 1.79 Conformation dependent library (CDL) restraints added in 735.5 milliseconds 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 0 sheets defined 76.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 Processing helix chain 'A' and resid 56 through 67 removed outlier: 4.477A pdb=" N PHE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 87 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 127 through 159 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 164 through 180 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.546A pdb=" N VAL A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.685A pdb=" N VAL A 249 " --> pdb=" O TRP A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.682A pdb=" N CYS A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 307 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.138A pdb=" N MET A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.640A pdb=" N VAL A 329 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.702A pdb=" N TYR A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 374 No H-bonds generated for 'chain 'A' and resid 371 through 374' Processing helix chain 'A' and resid 380 through 407 Processing helix chain 'A' and resid 412 through 436 removed outlier: 3.635A pdb=" N SER A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 442 through 465 Processing helix chain 'A' and resid 470 through 473 No H-bonds generated for 'chain 'A' and resid 470 through 473' Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 523 through 545 removed outlier: 4.298A pdb=" N GLY A 527 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 531 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 532 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 537 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY A 538 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 541 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR A 545 " --> pdb=" O SER A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' 260 hydrogen bonds defined for protein. 690 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: 1.06 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 585 1.32 - 1.45: 1036 1.45 - 1.57: 2204 1.57 - 1.69: 2 1.69 - 1.81: 45 Bond restraints: 3872 Sorted by residual: bond pdb=" O12 REO A 702 " pdb="RE REO A 702 " ideal model delta sigma weight residual 2.000 1.735 0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" O14 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.527 1.654 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" O11 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.703 1.643 0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.526 1.491 0.035 2.00e-02 2.50e+03 3.08e+00 bond pdb=" O13 3PH A 703 " pdb=" P 3PH A 703 " ideal model delta sigma weight residual 1.522 1.491 0.031 2.00e-02 2.50e+03 2.35e+00 ... (remaining 3867 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.58: 127 106.58 - 113.45: 2168 113.45 - 120.33: 1469 120.33 - 127.20: 1469 127.20 - 134.07: 49 Bond angle restraints: 5282 Sorted by residual: angle pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O14 3PH A 703 " ideal model delta sigma weight residual 113.84 104.72 9.12 3.00e+00 1.11e-01 9.23e+00 angle pdb=" O12 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O13 3PH A 703 " ideal model delta sigma weight residual 115.12 123.73 -8.61 3.00e+00 1.11e-01 8.23e+00 angle pdb=" O13 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O14 3PH A 703 " ideal model delta sigma weight residual 115.01 109.59 5.42 3.00e+00 1.11e-01 3.27e+00 angle pdb=" CA TYR A 269 " pdb=" CB TYR A 269 " pdb=" CG TYR A 269 " ideal model delta sigma weight residual 113.90 117.11 -3.21 1.80e+00 3.09e-01 3.18e+00 angle pdb=" O11 3PH A 703 " pdb=" P 3PH A 703 " pdb=" O12 3PH A 703 " ideal model delta sigma weight residual 105.09 110.06 -4.97 3.00e+00 1.11e-01 2.75e+00 ... (remaining 5277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 2046 17.48 - 34.96: 137 34.96 - 52.44: 43 52.44 - 69.92: 5 69.92 - 87.40: 2 Dihedral angle restraints: 2233 sinusoidal: 819 harmonic: 1414 Sorted by residual: dihedral pdb=" CA PRO A 555 " pdb=" C PRO A 555 " pdb=" N GLY A 556 " pdb=" CA GLY A 556 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA TYR A 83 " pdb=" C TYR A 83 " pdb=" N GLY A 84 " pdb=" CA GLY A 84 " ideal model delta harmonic sigma weight residual 180.00 164.28 15.72 0 5.00e+00 4.00e-02 9.88e+00 dihedral pdb=" CB MET A 258 " pdb=" CG MET A 258 " pdb=" SD MET A 258 " pdb=" CE MET A 258 " ideal model delta sinusoidal sigma weight residual 60.00 2.21 57.79 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 500 0.041 - 0.082: 112 0.082 - 0.123: 23 0.123 - 0.165: 0 0.165 - 0.206: 1 Chirality restraints: 636 Sorted by residual: chirality pdb=" C2 3PH A 703 " pdb=" C1 3PH A 703 " pdb=" C3 3PH A 703 " pdb=" O21 3PH A 703 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CB THR A 357 " pdb=" CA THR A 357 " pdb=" OG1 THR A 357 " pdb=" CG2 THR A 357 " both_signs ideal model delta sigma weight residual False 2.55 2.45 0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 633 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 101 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR A 101 " -0.030 2.00e-02 2.50e+03 pdb=" O THR A 101 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 102 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 99 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C LEU A 99 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 99 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 100 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 98 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C SER A 98 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 98 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 262 2.73 - 3.27: 4252 3.27 - 3.81: 6798 3.81 - 4.36: 7975 4.36 - 4.90: 13833 Nonbonded interactions: 33120 Sorted by model distance: nonbonded pdb=" OE1 GLU A 122 " pdb=" NH1 ARG A 130 " model vdw 2.186 2.520 nonbonded pdb=" O LYS A 549 " pdb=" OG SER A 552 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR A 110 " pdb=" N THR A 274 " model vdw 2.240 2.520 nonbonded pdb=" OH TYR A 307 " pdb=" OD2 ASP A 331 " model vdw 2.325 2.440 nonbonded pdb=" NH2 ARG A 241 " pdb=" OE1 GLN A 414 " model vdw 2.349 2.520 ... (remaining 33115 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: 1.260 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: 0.010 Extract box with map and model: 5.080 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.360 Find NCS groups from input model: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.006 0.265 3872 Z= 0.388 Angle : 0.570 9.115 5282 Z= 0.282 Chirality : 0.035 0.206 636 Planarity : 0.004 0.038 636 Dihedral : 13.544 87.401 1339 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.51 % Allowed : 9.16 % Favored : 90.33 % 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: 1.14 (0.40), residues: 493 helix: 1.42 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -1.71 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 165 HIS 0.001 0.000 HIS A 226 PHE 0.010 0.001 PHE A 304 TYR 0.009 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.489 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.1558 time to fit residues: 12.2550 Evaluate side-chains 60 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.404 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0404 time to fit residues: 0.6746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3872 Z= 0.171 Angle : 0.558 6.794 5282 Z= 0.274 Chirality : 0.037 0.148 636 Planarity : 0.004 0.042 636 Dihedral : 7.358 58.023 573 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.27 % Allowed : 11.70 % Favored : 87.02 % 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: 1.20 (0.40), residues: 493 helix: 1.44 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.52 (0.66), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.000 0.000 HIS A 226 PHE 0.012 0.001 PHE A 304 TYR 0.013 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.407 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 74 average time/residue: 0.1359 time to fit residues: 13.1274 Evaluate side-chains 63 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.413 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0396 time to fit residues: 0.6754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 30 optimal weight: 0.2980 chunk 12 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.0370 overall best weight: 0.1012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3872 Z= 0.140 Angle : 0.544 6.664 5282 Z= 0.261 Chirality : 0.036 0.142 636 Planarity : 0.004 0.043 636 Dihedral : 7.278 51.137 573 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.53 % Allowed : 16.03 % Favored : 82.44 % 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: 1.43 (0.40), residues: 493 helix: 1.61 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.45 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.000 0.000 HIS A 226 PHE 0.015 0.002 PHE A 304 TYR 0.012 0.001 TYR A 118 ARG 0.001 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.374 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 73 average time/residue: 0.1431 time to fit residues: 13.4610 Evaluate side-chains 62 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0426 time to fit residues: 0.6121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3872 Z= 0.198 Angle : 0.567 8.594 5282 Z= 0.272 Chirality : 0.037 0.148 636 Planarity : 0.004 0.046 636 Dihedral : 7.210 52.629 573 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.29 % Allowed : 15.78 % Favored : 81.93 % 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: 1.29 (0.39), residues: 493 helix: 1.50 (0.27), residues: 384 sheet: None (None), residues: 0 loop : -1.43 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.000 0.000 HIS A 226 PHE 0.019 0.002 PHE A 333 TYR 0.011 0.001 TYR A 118 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.360 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.1393 time to fit residues: 13.0340 Evaluate side-chains 69 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0520 time to fit residues: 0.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.0570 chunk 12 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3872 Z= 0.177 Angle : 0.560 8.904 5282 Z= 0.268 Chirality : 0.037 0.162 636 Planarity : 0.004 0.047 636 Dihedral : 7.167 52.286 573 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.78 % Allowed : 16.79 % Favored : 81.42 % 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: 1.27 (0.39), residues: 493 helix: 1.48 (0.27), residues: 385 sheet: None (None), residues: 0 loop : -1.45 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 89 HIS 0.000 0.000 HIS A 273 PHE 0.023 0.002 PHE A 193 TYR 0.010 0.001 TYR A 118 ARG 0.001 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 986 Ramachandran restraints generated. 493 Oldfield, 0 Emsley, 493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.437 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 77 average time/residue: 0.1315 time to fit residues: 13.3311 Evaluate side-chains 67 residues out of total 394 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0394 time to fit residues: 0.5845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.7252 > 50: distance: 2 - 10: 3.144 distance: 74 - 89: 11.191 distance: 78 - 93: 24.605 distance: 82 - 101: 7.800 distance: 85 - 89: 10.424 distance: 86 - 108: 23.500 distance: 89 - 90: 28.897 distance: 90 - 91: 21.638 distance: 91 - 92: 33.353 distance: 91 - 93: 25.296 distance: 92 - 116: 52.725 distance: 93 - 94: 11.202 distance: 94 - 95: 13.672 distance: 94 - 97: 8.789 distance: 95 - 96: 20.652 distance: 95 - 101: 22.614 distance: 96 - 127: 25.323 distance: 97 - 98: 13.191 distance: 97 - 99: 23.504 distance: 98 - 100: 23.178 distance: 101 - 102: 27.056 distance: 102 - 103: 32.061 distance: 102 - 105: 24.817 distance: 103 - 104: 29.867 distance: 103 - 108: 43.561 distance: 104 - 134: 33.152 distance: 105 - 106: 10.291 distance: 105 - 107: 5.862 distance: 108 - 109: 26.968 distance: 109 - 110: 36.000 distance: 109 - 112: 16.123 distance: 110 - 111: 39.178 distance: 110 - 116: 39.492 distance: 111 - 146: 29.331 distance: 112 - 113: 15.595 distance: 113 - 114: 13.054 distance: 114 - 115: 6.768 distance: 116 - 117: 25.840 distance: 117 - 118: 15.472 distance: 117 - 120: 13.897 distance: 118 - 119: 21.417 distance: 118 - 127: 21.101 distance: 120 - 121: 13.267 distance: 121 - 122: 4.462 distance: 121 - 123: 20.919 distance: 122 - 124: 4.271 distance: 123 - 125: 9.111 distance: 124 - 126: 19.103 distance: 125 - 126: 9.280 distance: 127 - 128: 11.158 distance: 128 - 129: 7.001 distance: 128 - 131: 6.420 distance: 129 - 130: 18.516 distance: 129 - 134: 20.603 distance: 131 - 132: 19.313 distance: 131 - 133: 9.891 distance: 134 - 135: 5.203 distance: 135 - 136: 7.831 distance: 135 - 138: 5.283 distance: 136 - 137: 9.906 distance: 136 - 146: 9.257 distance: 139 - 141: 5.771 distance: 140 - 142: 4.833 distance: 141 - 143: 5.517 distance: 143 - 144: 4.698 distance: 144 - 145: 5.340 distance: 146 - 147: 9.712 distance: 147 - 148: 16.361 distance: 147 - 150: 8.334 distance: 148 - 149: 13.312 distance: 148 - 158: 37.649 distance: 150 - 151: 10.227 distance: 151 - 152: 9.046 distance: 151 - 153: 8.709 distance: 152 - 154: 9.619 distance: 153 - 155: 4.509 distance: 154 - 156: 4.843 distance: 156 - 157: 4.598 distance: 158 - 159: 30.679 distance: 159 - 160: 8.924 distance: 159 - 162: 25.971 distance: 160 - 161: 9.394 distance: 160 - 167: 20.401 distance: 162 - 163: 20.167 distance: 163 - 164: 6.559 distance: 164 - 165: 21.391 distance: 165 - 166: 16.894 distance: 167 - 168: 41.040 distance: 168 - 169: 16.551 distance: 168 - 171: 16.819 distance: 169 - 170: 14.459 distance: 169 - 175: 25.477 distance: 171 - 172: 12.620 distance: 172 - 173: 42.935 distance: 172 - 174: 8.700