Starting phenix.real_space_refine on Tue Feb 11 20:52:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.map" model { file = "/net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j53_61141/02_2025/9j53_61141.cif" } resolution = 3.3 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= 0.061 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 P 6 5.49 5 S 30 5.16 5 C 4462 2.51 5 N 1024 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6598 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'PC1': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'PC1': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.60, per 1000 atoms: 0.70 Number of scatterers: 6598 At special positions: 0 Unit cell: (125.19, 69.55, 78.11, 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) S 30 16.00 P 6 15.00 O 1076 8.00 N 1024 7.00 C 4462 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 - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 902.1 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 265 through 295 removed outlier: 4.645A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.690A pdb=" N PHE B 303 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.537A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.636A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 419 removed outlier: 3.606A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 Proline residue: B 455 - end of helix removed outlier: 3.740A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 500 removed outlier: 3.668A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.627A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 removed outlier: 3.675A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 562 " --> pdb=" O TYR B 558 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 578 " --> pdb=" O THR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 615 Proline residue: B 598 - end of helix removed outlier: 3.656A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 256 removed outlier: 3.832A pdb=" N VAL A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 5.166A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 removed outlier: 4.135A pdb=" N GLU A 304 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.264A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.786A pdb=" N PHE A 379 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.814A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.540A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.698A pdb=" N CYS A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.685A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 503 removed outlier: 4.146A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.945A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 513 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.394A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 Proline residue: A 598 - end of helix removed outlier: 3.664A pdb=" N LEU A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1233 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: 1.65 Time building geometry restraints manager: 2.18 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: 986 1.32 - 1.44: 2069 1.44 - 1.57: 3695 1.57 - 1.69: 12 1.69 - 1.81: 42 Bond restraints: 6804 Sorted by residual: bond pdb=" C ALA B 337 " pdb=" N PRO B 338 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.47e-01 bond pdb=" CB GLN B 399 " pdb=" CG GLN B 399 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.45e-01 bond pdb=" C TYR B 347 " pdb=" N PRO B 348 " ideal model delta sigma weight residual 1.335 1.347 -0.011 1.36e-02 5.41e+03 6.86e-01 bond pdb=" CA ILE B 279 " pdb=" C ILE B 279 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.22e-02 6.72e+03 6.66e-01 bond pdb=" CB PRO A 385 " pdb=" CG PRO A 385 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.10e-01 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 8965 1.52 - 3.04: 209 3.04 - 4.56: 27 4.56 - 6.08: 10 6.08 - 7.60: 3 Bond angle restraints: 9214 Sorted by residual: angle pdb=" N ILE B 577 " pdb=" CA ILE B 577 " pdb=" C ILE B 577 " ideal model delta sigma weight residual 113.00 109.53 3.47 1.30e+00 5.92e-01 7.10e+00 angle pdb=" C SER B 402 " pdb=" N LEU B 403 " pdb=" CA LEU B 403 " ideal model delta sigma weight residual 122.73 118.80 3.93 1.61e+00 3.86e-01 5.96e+00 angle pdb=" C GLY B 621 " pdb=" N GLU B 622 " pdb=" CA GLU B 622 " ideal model delta sigma weight residual 122.40 125.93 -3.53 1.45e+00 4.76e-01 5.91e+00 angle pdb=" N GLY A 296 " pdb=" CA GLY A 296 " pdb=" C GLY A 296 " ideal model delta sigma weight residual 113.18 118.53 -5.35 2.37e+00 1.78e-01 5.09e+00 angle pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " pdb=" CG LEU B 259 " ideal model delta sigma weight residual 116.30 123.90 -7.60 3.50e+00 8.16e-02 4.72e+00 ... (remaining 9209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3529 18.00 - 35.99: 278 35.99 - 53.99: 90 53.99 - 71.98: 15 71.98 - 89.98: 6 Dihedral angle restraints: 3918 sinusoidal: 1668 harmonic: 2250 Sorted by residual: dihedral pdb=" CA ASN B 298 " pdb=" C ASN B 298 " pdb=" N HIS B 299 " pdb=" CA HIS B 299 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ILE A 302 " pdb=" C ILE A 302 " pdb=" N PHE A 303 " pdb=" CA PHE A 303 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PHE A 303 " pdb=" C PHE A 303 " pdb=" N GLU A 304 " pdb=" CA GLU A 304 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 579 0.029 - 0.057: 267 0.057 - 0.086: 102 0.086 - 0.114: 35 0.114 - 0.143: 3 Chirality restraints: 986 Sorted by residual: chirality pdb=" CA TRP A 266 " pdb=" N TRP A 266 " pdb=" C TRP A 266 " pdb=" CB TRP A 266 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA TRP B 266 " pdb=" N TRP B 266 " pdb=" C TRP B 266 " pdb=" CB TRP B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 337 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B 338 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 561 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C CYS A 561 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS A 561 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 562 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 563 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C ILE A 563 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 563 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE A 564 " 0.010 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 119 2.67 - 3.23: 6919 3.23 - 3.79: 10613 3.79 - 4.34: 14363 4.34 - 4.90: 23141 Nonbonded interactions: 55155 Sorted by model distance: nonbonded pdb=" O LYS A 482 " pdb=" OG1 THR A 485 " model vdw 2.117 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.123 3.040 nonbonded pdb=" O ILE A 551 " pdb=" OH TYR A 559 " model vdw 2.131 3.040 nonbonded pdb=" O ARG B 466 " pdb=" OG1 THR B 470 " model vdw 2.163 3.040 nonbonded pdb=" O TRP A 395 " pdb=" NE2 GLN A 399 " model vdw 2.174 3.120 ... (remaining 55150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.060 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.630 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.039 6804 Z= 0.210 Angle : 0.575 7.601 9214 Z= 0.321 Chirality : 0.038 0.143 986 Planarity : 0.004 0.049 1098 Dihedral : 14.752 89.975 2466 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.13 % Allowed : 9.00 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.49 (0.31), residues: 756 helix: 0.71 (0.22), residues: 526 sheet: None (None), residues: 0 loop : -2.81 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 266 HIS 0.004 0.001 HIS A 313 PHE 0.014 0.001 PHE A 605 TYR 0.010 0.001 TYR B 518 ARG 0.003 0.000 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 1.290 Fit side-chains REVERT: B 283 PHE cc_start: 0.7347 (t80) cc_final: 0.6946 (t80) REVERT: B 345 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: B 408 MET cc_start: 0.8108 (mmm) cc_final: 0.7793 (mmm) REVERT: B 415 CYS cc_start: 0.8719 (t) cc_final: 0.8372 (p) REVERT: B 452 GLN cc_start: 0.9122 (tp40) cc_final: 0.8225 (tp40) REVERT: B 462 GLN cc_start: 0.8359 (mt0) cc_final: 0.8042 (mt0) REVERT: B 599 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (mm) REVERT: A 290 TYR cc_start: 0.8364 (t80) cc_final: 0.8114 (t80) REVERT: A 308 ARG cc_start: 0.7489 (ptt180) cc_final: 0.7238 (ptt-90) REVERT: A 379 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6315 (t80) REVERT: A 408 MET cc_start: 0.7630 (mmt) cc_final: 0.7381 (mmt) REVERT: A 409 ASP cc_start: 0.6501 (OUTLIER) cc_final: 0.5568 (t70) REVERT: A 410 LEU cc_start: 0.7347 (tt) cc_final: 0.7090 (tt) REVERT: A 461 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8465 (tp) REVERT: A 495 LEU cc_start: 0.9322 (mm) cc_final: 0.8887 (mm) REVERT: A 548 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7470 (ptt90) REVERT: A 565 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 605 PHE cc_start: 0.7836 (t80) cc_final: 0.7439 (t80) outliers start: 28 outliers final: 10 residues processed: 224 average time/residue: 0.1895 time to fit residues: 56.9649 Evaluate side-chains 183 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN B 504 HIS B 618 ASN A 288 ASN A 310 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.189096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165625 restraints weight = 10550.409| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.65 r_work: 0.3967 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6804 Z= 0.209 Angle : 0.613 8.667 9214 Z= 0.321 Chirality : 0.042 0.197 986 Planarity : 0.005 0.053 1098 Dihedral : 12.886 79.445 1066 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.42 % Allowed : 14.45 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.08 (0.31), residues: 756 helix: 1.05 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.88 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 528 HIS 0.004 0.001 HIS A 313 PHE 0.016 0.001 PHE B 391 TYR 0.011 0.001 TYR A 417 ARG 0.004 0.001 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: B 263 ARG cc_start: 0.7480 (tpp-160) cc_final: 0.6852 (tpp-160) REVERT: B 345 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: B 415 CYS cc_start: 0.8544 (t) cc_final: 0.8265 (p) REVERT: B 462 GLN cc_start: 0.8339 (mt0) cc_final: 0.7994 (mt0) REVERT: B 496 TYR cc_start: 0.8316 (t80) cc_final: 0.8114 (t80) REVERT: B 500 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8428 (tptm) REVERT: B 576 GLN cc_start: 0.7783 (tp40) cc_final: 0.7541 (tp40) REVERT: A 283 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6927 (t80) REVERT: A 288 ASN cc_start: 0.8250 (m110) cc_final: 0.8040 (m110) REVERT: A 290 TYR cc_start: 0.8307 (t80) cc_final: 0.7938 (t80) REVERT: A 308 ARG cc_start: 0.7425 (ptt180) cc_final: 0.7115 (ptt-90) REVERT: A 379 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 409 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.4897 (t70) REVERT: A 477 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 495 LEU cc_start: 0.9235 (mm) cc_final: 0.8836 (mm) REVERT: A 603 ARG cc_start: 0.8057 (tmm-80) cc_final: 0.7720 (tmm-80) outliers start: 30 outliers final: 11 residues processed: 201 average time/residue: 0.1625 time to fit residues: 44.5096 Evaluate side-chains 204 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 345 TYR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 500 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 409 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 609 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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-5592/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-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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-5592/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-5592/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-5592/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-5592/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: 50.9518 > 50: distance: 73 - 89: 5.269 distance: 77 - 98: 15.288 distance: 81 - 106: 24.474 distance: 85 - 89: 3.752 distance: 86 - 111: 9.205 distance: 89 - 90: 3.935 distance: 90 - 91: 7.309 distance: 91 - 98: 4.807 distance: 92 - 115: 13.839 distance: 93 - 94: 3.199 distance: 94 - 95: 7.034 distance: 95 - 97: 4.633 distance: 99 - 100: 8.289 distance: 100 - 101: 8.029 distance: 100 - 106: 18.503 distance: 101 - 126: 9.627 distance: 102 - 104: 5.824 distance: 103 - 105: 6.811 distance: 106 - 107: 37.337 distance: 107 - 108: 7.966 distance: 107 - 110: 30.507 distance: 108 - 109: 7.470 distance: 108 - 111: 8.378 distance: 109 - 134: 9.258 distance: 111 - 112: 5.634 distance: 112 - 113: 4.575 distance: 114 - 138: 3.459 distance: 118 - 146: 7.428 distance: 120 - 121: 4.160 distance: 120 - 122: 4.168 distance: 121 - 123: 3.181 distance: 123 - 125: 4.480 distance: 124 - 125: 5.888 distance: 127 - 128: 3.276 distance: 128 - 134: 3.725 distance: 129 - 154: 6.509 distance: 131 - 132: 3.204 distance: 131 - 133: 4.440 distance: 134 - 135: 5.514 distance: 135 - 136: 4.974 distance: 136 - 137: 7.348 distance: 136 - 138: 4.246 distance: 137 - 168: 13.094 distance: 138 - 139: 3.038 distance: 141 - 174: 3.927 distance: 142 - 143: 3.247 distance: 149 - 182: 4.656 distance: 150 - 151: 4.756 distance: 151 - 152: 4.179 distance: 151 - 153: 13.306 distance: 155 - 158: 3.213 distance: 158 - 159: 5.338 distance: 159 - 160: 4.503 distance: 159 - 161: 3.974 distance: 161 - 163: 3.216 distance: 161 - 164: 5.902 distance: 162 - 163: 3.952 distance: 165 - 167: 6.308