Starting phenix.real_space_refine on Thu Nov 14 01:40:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9je0_61403/11_2024/9je0_61403_neut.cif" } resolution = 3.23 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 2 7.06 5 S 28 5.16 5 C 2176 2.51 5 N 554 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 26, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'R75': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.95, per 1000 atoms: 0.89 Number of scatterers: 3321 At special positions: 0 Unit cell: (94.9, 52.56, 66.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 2 34.99 S 28 16.00 O 561 8.00 N 554 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.96 Conformation dependent library (CDL) restraints added in 536.5 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 83.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 4.208A pdb=" N GLU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.765A pdb=" N ASN A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.571A pdb=" N LEU A 98 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.548A pdb=" N HIS A 142 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.261A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.530A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 4.311A pdb=" N GLU A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 255 Processing helix chain 'A' and resid 257 through 273 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 339 through 343 removed outlier: 4.040A pdb=" N ARG A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 343 " --> pdb=" O LEU A 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 339 through 343' Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.600A pdb=" N LEU A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix removed outlier: 4.161A pdb=" N LEU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 426 Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.005A pdb=" N SER A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 465 No H-bonds generated for 'chain 'A' and resid 464 through 465' Processing helix chain 'A' and resid 467 through 467 No H-bonds generated for 'chain 'A' and resid 467 through 467' Processing helix chain 'A' and resid 468 through 487 Proline residue: A 484 - end of helix removed outlier: 3.732A pdb=" N ARG A 487 " --> pdb=" O GLY A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.682A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 513 Proline residue: A 505 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.645A pdb=" N ARG A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) 237 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: 0.93 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 934 1.34 - 1.49: 1009 1.49 - 1.64: 1419 1.64 - 1.79: 0 1.79 - 1.94: 46 Bond restraints: 3408 Sorted by residual: bond pdb=" CAC R75 A 601 " pdb=" OAG R75 A 601 " ideal model delta sigma weight residual 1.326 1.399 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CAJ R75 A 601 " pdb=" CAL R75 A 601 " ideal model delta sigma weight residual 1.465 1.528 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" CAB R75 A 601 " pdb="BR2 R75 A 601 " ideal model delta sigma weight residual 1.880 1.940 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" CAD R75 A 601 " pdb="BR1 R75 A 601 " ideal model delta sigma weight residual 1.884 1.940 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " ideal model delta sigma weight residual 1.483 1.528 -0.045 2.00e-02 2.50e+03 4.96e+00 ... (remaining 3403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 4591 1.96 - 3.93: 47 3.93 - 5.89: 13 5.89 - 7.85: 2 7.85 - 9.82: 1 Bond angle restraints: 4654 Sorted by residual: angle pdb=" CAQ R75 A 601 " pdb=" CAM R75 A 601 " pdb=" OAN R75 A 601 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " ideal model delta sigma weight residual 132.81 126.27 6.54 3.00e+00 1.11e-01 4.75e+00 angle pdb=" C HIS A 245 " pdb=" N GLY A 246 " pdb=" CA GLY A 246 " ideal model delta sigma weight residual 119.94 122.23 -2.29 1.11e+00 8.12e-01 4.26e+00 angle pdb=" CA LEU A 37 " pdb=" CB LEU A 37 " pdb=" CG LEU A 37 " ideal model delta sigma weight residual 116.30 122.73 -6.43 3.50e+00 8.16e-02 3.37e+00 angle pdb=" CAD R75 A 601 " pdb=" CAC R75 A 601 " pdb=" OAG R75 A 601 " ideal model delta sigma weight residual 125.05 119.82 5.23 3.00e+00 1.11e-01 3.03e+00 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.98: 1828 20.98 - 41.95: 123 41.95 - 62.93: 17 62.93 - 83.90: 4 83.90 - 104.88: 2 Dihedral angle restraints: 1974 sinusoidal: 738 harmonic: 1236 Sorted by residual: dihedral pdb=" CAL R75 A 601 " pdb=" CAM R75 A 601 " pdb=" CAQ R75 A 601 " pdb=" CAR R75 A 601 " ideal model delta sinusoidal sigma weight residual 263.96 159.08 104.88 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -114.54 28.54 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 118 " pdb=" CB ASP A 118 " pdb=" CG ASP A 118 " pdb=" OD1 ASP A 118 " ideal model delta sinusoidal sigma weight residual -30.00 -84.71 54.71 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 314 0.023 - 0.046: 133 0.046 - 0.070: 62 0.070 - 0.093: 25 0.093 - 0.116: 10 Chirality restraints: 544 Sorted by residual: chirality pdb=" CA VAL A 426 " pdb=" N VAL A 426 " pdb=" C VAL A 426 " pdb=" CB VAL A 426 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.59e-01 chirality pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" C PRO A 115 " pdb=" CB PRO A 115 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.49e-01 ... (remaining 541 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 268 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 44 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 45 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 483 " -0.015 5.00e-02 4.00e+02 2.33e-02 8.72e-01 pdb=" N PRO A 484 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 484 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 484 " -0.013 5.00e-02 4.00e+02 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 916 2.80 - 3.33: 3286 3.33 - 3.85: 5702 3.85 - 4.38: 6346 4.38 - 4.90: 10742 Nonbonded interactions: 26992 Sorted by model distance: nonbonded pdb=" OG SER A 27 " pdb=" OH TYR A 180 " model vdw 2.281 3.040 nonbonded pdb=" O VAL A 504 " pdb=" OG SER A 508 " model vdw 2.332 3.040 nonbonded pdb=" O TRP A 50 " pdb=" NH1 ARG A 90 " model vdw 2.371 3.120 nonbonded pdb=" OG1 THR A 339 " pdb=" OG1 THR A 467 " model vdw 2.375 3.040 nonbonded pdb=" N GLY A 80 " pdb=" O ARG A 84 " model vdw 2.387 3.120 ... (remaining 26987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.180 Find NCS groups from input model: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 : 0.003 0.073 3408 Z= 0.219 Angle : 0.579 9.815 4654 Z= 0.294 Chirality : 0.035 0.116 544 Planarity : 0.004 0.030 574 Dihedral : 14.224 104.881 1170 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.61 % Allowed : 8.70 % Favored : 88.70 % 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: -0.32 (0.40), residues: 425 helix: 0.19 (0.29), residues: 290 sheet: None (None), residues: 0 loop : -0.85 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 224 HIS 0.004 0.001 HIS A 245 PHE 0.009 0.001 PHE A 358 TYR 0.004 0.001 TYR A 455 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7798 (ttp) cc_final: 0.7577 (ttm) REVERT: A 169 ARG cc_start: 0.6394 (mmm-85) cc_final: 0.6139 (mtt90) REVERT: A 222 MET cc_start: 0.5510 (ppp) cc_final: 0.4780 (mtm) REVERT: A 270 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.4744 (m-80) REVERT: A 474 MET cc_start: 0.5866 (tpp) cc_final: 0.5478 (mmt) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.1511 time to fit residues: 19.0079 Evaluate side-chains 82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 270 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3408 Z= 0.202 Angle : 0.601 5.936 4654 Z= 0.285 Chirality : 0.039 0.110 544 Planarity : 0.004 0.030 574 Dihedral : 6.771 84.539 468 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.19 % Allowed : 18.55 % Favored : 78.26 % 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: 1.07 (0.42), residues: 425 helix: 1.09 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.02 (0.62), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 47 PHE 0.024 0.002 PHE A 362 TYR 0.014 0.001 TYR A 122 ARG 0.003 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.7912 (ttp) cc_final: 0.7665 (ttm) REVERT: A 118 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6863 (t0) REVERT: A 149 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7059 (mt0) REVERT: A 169 ARG cc_start: 0.6565 (mmm-85) cc_final: 0.6297 (mtt90) REVERT: A 222 MET cc_start: 0.5589 (ppp) cc_final: 0.4800 (mtm) REVERT: A 270 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.5110 (m-10) REVERT: A 342 ARG cc_start: 0.6620 (ptt90) cc_final: 0.4427 (ptt90) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 0.1193 time to fit residues: 12.5079 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3408 Z= 0.212 Angle : 0.582 6.002 4654 Z= 0.284 Chirality : 0.040 0.169 544 Planarity : 0.004 0.030 574 Dihedral : 5.803 68.056 467 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 4.06 % Allowed : 18.84 % Favored : 77.10 % 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: 1.52 (0.43), residues: 425 helix: 1.38 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.29 (0.64), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 50 HIS 0.003 0.001 HIS A 47 PHE 0.013 0.001 PHE A 362 TYR 0.013 0.002 TYR A 122 ARG 0.003 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 29 MET cc_start: 0.8024 (ttp) cc_final: 0.7767 (ttm) REVERT: A 149 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.6980 (mp10) REVERT: A 169 ARG cc_start: 0.6604 (mmm-85) cc_final: 0.6280 (mtt180) REVERT: A 186 MET cc_start: 0.7948 (mmm) cc_final: 0.7622 (mmp) REVERT: A 222 MET cc_start: 0.5558 (ppp) cc_final: 0.4870 (mtp) REVERT: A 243 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7135 (m-10) REVERT: A 270 PHE cc_start: 0.5533 (OUTLIER) cc_final: 0.5118 (m-80) outliers start: 14 outliers final: 5 residues processed: 83 average time/residue: 0.1169 time to fit residues: 12.7363 Evaluate side-chains 77 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3408 Z= 0.186 Angle : 0.575 6.472 4654 Z= 0.275 Chirality : 0.040 0.143 544 Planarity : 0.004 0.030 574 Dihedral : 5.065 43.510 466 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.32 % Allowed : 22.03 % Favored : 75.65 % 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: 1.79 (0.43), residues: 425 helix: 1.55 (0.30), residues: 299 sheet: None (None), residues: 0 loop : 0.49 (0.65), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 50 HIS 0.001 0.000 HIS A 245 PHE 0.012 0.001 PHE A 362 TYR 0.009 0.001 TYR A 122 ARG 0.001 0.000 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.345 Fit side-chains REVERT: A 29 MET cc_start: 0.8039 (ttp) cc_final: 0.7792 (ttm) REVERT: A 38 GLU cc_start: 0.7685 (tp30) cc_final: 0.7420 (tp30) REVERT: A 149 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7139 (mt0) REVERT: A 169 ARG cc_start: 0.6687 (mmm-85) cc_final: 0.6361 (mtt90) REVERT: A 222 MET cc_start: 0.5590 (ppp) cc_final: 0.4879 (mtm) REVERT: A 270 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: A 394 MET cc_start: 0.6598 (tmm) cc_final: 0.5756 (tmm) outliers start: 8 outliers final: 4 residues processed: 77 average time/residue: 0.1233 time to fit residues: 12.2058 Evaluate side-chains 75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 455 TYR Chi-restraints excluded: chain A residue 486 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/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-5513/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-5513/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-5513/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-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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-5513/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-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.1373 > 50: distance: 75 - 78: 25.729 distance: 78 - 79: 32.675 distance: 78 - 84: 31.077 distance: 79 - 80: 7.767 distance: 79 - 82: 19.818 distance: 80 - 81: 5.941 distance: 80 - 85: 13.288 distance: 82 - 83: 14.932 distance: 83 - 84: 9.107 distance: 85 - 86: 17.348 distance: 86 - 87: 27.315 distance: 86 - 89: 51.590 distance: 87 - 88: 37.305 distance: 87 - 90: 18.029 distance: 88 - 115: 32.489 distance: 90 - 91: 3.651 distance: 91 - 92: 21.896 distance: 91 - 94: 36.154 distance: 92 - 93: 41.512 distance: 92 - 101: 16.445 distance: 93 - 127: 23.156 distance: 94 - 95: 36.693 distance: 95 - 96: 45.860 distance: 95 - 97: 19.172 distance: 96 - 98: 9.855 distance: 97 - 99: 14.876 distance: 98 - 100: 22.780 distance: 99 - 100: 24.234 distance: 101 - 102: 21.965 distance: 101 - 107: 26.885 distance: 102 - 103: 22.139 distance: 102 - 105: 14.970 distance: 103 - 104: 10.638 distance: 103 - 108: 23.627 distance: 104 - 133: 25.391 distance: 105 - 106: 32.277 distance: 106 - 107: 18.345 distance: 108 - 109: 31.047 distance: 109 - 110: 30.632 distance: 109 - 112: 30.928 distance: 110 - 111: 27.143 distance: 110 - 115: 35.653 distance: 111 - 141: 30.702 distance: 112 - 113: 29.571 distance: 112 - 114: 24.148 distance: 115 - 116: 31.052 distance: 116 - 117: 23.629 distance: 116 - 119: 26.367 distance: 117 - 118: 23.885 distance: 117 - 127: 13.020 distance: 118 - 152: 24.233 distance: 119 - 120: 9.994 distance: 120 - 121: 19.717 distance: 120 - 122: 32.717 distance: 121 - 123: 16.146 distance: 122 - 124: 19.236 distance: 123 - 125: 5.612 distance: 124 - 125: 18.483 distance: 125 - 126: 11.400 distance: 127 - 128: 12.419 distance: 128 - 129: 41.919 distance: 128 - 131: 28.184 distance: 129 - 130: 29.281 distance: 129 - 133: 38.029 distance: 130 - 163: 26.026 distance: 131 - 132: 27.129 distance: 133 - 134: 11.863 distance: 134 - 135: 18.290 distance: 134 - 137: 27.854 distance: 135 - 136: 25.608 distance: 135 - 141: 21.896 distance: 136 - 170: 24.996 distance: 137 - 138: 15.846 distance: 138 - 139: 32.708 distance: 138 - 140: 13.596 distance: 141 - 142: 22.673 distance: 142 - 143: 41.332 distance: 142 - 145: 29.814 distance: 143 - 144: 27.968 distance: 143 - 152: 31.981 distance: 144 - 178: 9.696 distance: 145 - 146: 11.113 distance: 146 - 147: 28.961 distance: 146 - 148: 32.465 distance: 147 - 149: 45.478 distance: 148 - 150: 41.889 distance: 149 - 151: 48.833 distance: 150 - 151: 16.335 distance: 152 - 153: 20.541 distance: 153 - 154: 15.351 distance: 153 - 156: 26.150 distance: 154 - 155: 25.900 distance: 154 - 163: 16.106 distance: 155 - 185: 19.722 distance: 156 - 157: 17.041 distance: 157 - 158: 10.885 distance: 158 - 159: 11.707 distance: 159 - 160: 6.838 distance: 160 - 161: 17.283 distance: 160 - 162: 16.294