Starting phenix.real_space_refine on Tue May 13 06:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792.map" model { file = "/net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzb_38792/05_2025/8xzb_38792_neut.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4271 atoms to isotropic. 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 Zn 1 6.06 5 S 38 5.16 5 C 4110 2.51 5 N 1058 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4885 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 29, 'TRANS': 566} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.72 Number of scatterers: 6412 At special positions: 0 Unit cell: (75.21, 83.49, 120.75, 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) Zn 1 29.99 S 38 16.00 O 1205 8.00 N 1058 7.00 C 4110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.65 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: 1.43 Conformation dependent library (CDL) restraints added in 884.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 56.8% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.746A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.742A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.817A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.521A pdb=" N ASP A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 removed outlier: 3.935A pdb=" N GLY A 268 " --> pdb=" O HIS A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.695A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 397 through 414 removed outlier: 4.119A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 466 removed outlier: 3.512A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.623A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 503' Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.062A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.581A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.552A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 602 removed outlier: 4.636A pdb=" N ASN A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.642A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 395 removed outlier: 3.765A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 392 through 395' Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.310A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.445A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.690A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 386 " --> pdb=" O GLU C 341 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 439 through 441 311 hydrogen bonds defined for protein. 924 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: 1.63 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1962 1.33 - 1.45: 1141 1.45 - 1.57: 3437 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 6601 Sorted by residual: bond pdb=" C LYS A 564 " pdb=" N PRO A 565 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.25e-02 6.40e+03 2.26e+01 bond pdb=" CA ILE A 233 " pdb=" C ILE A 233 " ideal model delta sigma weight residual 1.518 1.568 -0.049 1.13e-02 7.83e+03 1.91e+01 bond pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.73e+01 bond pdb=" C PRO C 469 " pdb=" N PRO C 470 " ideal model delta sigma weight residual 1.333 1.362 -0.029 7.80e-03 1.64e+04 1.37e+01 bond pdb=" CA GLN A 325 " pdb=" C GLN A 325 " ideal model delta sigma weight residual 1.524 1.571 -0.047 1.28e-02 6.10e+03 1.34e+01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 8279 2.75 - 5.49: 522 5.49 - 8.24: 122 8.24 - 10.98: 44 10.98 - 13.73: 12 Bond angle restraints: 8979 Sorted by residual: angle pdb=" N TYR A 202 " pdb=" CA TYR A 202 " pdb=" C TYR A 202 " ideal model delta sigma weight residual 111.07 97.66 13.41 1.07e+00 8.73e-01 1.57e+02 angle pdb=" N LYS A 112 " pdb=" CA LYS A 112 " pdb=" C LYS A 112 " ideal model delta sigma weight residual 111.36 98.79 12.57 1.09e+00 8.42e-01 1.33e+02 angle pdb=" N GLU C 327 " pdb=" CA GLU C 327 " pdb=" C GLU C 327 " ideal model delta sigma weight residual 111.28 123.82 -12.54 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N PRO C 469 " pdb=" CA PRO C 469 " pdb=" C PRO C 469 " ideal model delta sigma weight residual 110.70 124.43 -13.73 1.22e+00 6.72e-01 1.27e+02 angle pdb=" N GLU A 212 " pdb=" CA GLU A 212 " pdb=" C GLU A 212 " ideal model delta sigma weight residual 111.07 122.83 -11.76 1.07e+00 8.73e-01 1.21e+02 ... (remaining 8974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3375 17.64 - 35.27: 334 35.27 - 52.90: 121 52.90 - 70.54: 41 70.54 - 88.17: 12 Dihedral angle restraints: 3883 sinusoidal: 1561 harmonic: 2322 Sorted by residual: dihedral pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CA PRO C 469 " pdb=" CB PRO C 469 " ideal model delta harmonic sigma weight residual 115.10 127.99 -12.89 0 2.50e+00 1.60e-01 2.66e+01 dihedral pdb=" N PHE A 512 " pdb=" C PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual 122.80 110.27 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C PHE A 512 " pdb=" N PHE A 512 " pdb=" CA PHE A 512 " pdb=" CB PHE A 512 " ideal model delta harmonic sigma weight residual -122.60 -110.20 -12.40 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 3880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 700 0.126 - 0.252: 180 0.252 - 0.378: 40 0.378 - 0.504: 11 0.504 - 0.630: 2 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA PRO C 469 " pdb=" N PRO C 469 " pdb=" C PRO C 469 " pdb=" CB PRO C 469 " both_signs ideal model delta sigma weight residual False 2.72 2.09 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA PHE C 460 " pdb=" N PHE C 460 " pdb=" C PHE C 460 " pdb=" CB PHE C 460 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CA ASN C 473 " pdb=" N ASN C 473 " pdb=" C ASN C 473 " pdb=" CB ASN C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 ... (remaining 930 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 468 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 469 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO C 469 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 469 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 332 " -0.019 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" C THR C 332 " 0.066 2.00e-02 2.50e+03 pdb=" O THR C 332 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS C 333 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.063 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO A 146 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.055 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 35 2.53 - 3.12: 5026 3.12 - 3.72: 10271 3.72 - 4.31: 14654 4.31 - 4.90: 23115 Nonbonded interactions: 53101 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.941 2.230 nonbonded pdb=" O ASN C 330 " pdb=" OD1 ASN C 330 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN C 427 " pdb=" N ILE C 428 " model vdw 2.106 3.120 nonbonded pdb=" OD1 ASP C 351 " pdb=" N TYR C 352 " model vdw 2.188 3.120 nonbonded pdb=" CB TYR C 440 " pdb=" OH TYR C 481 " model vdw 2.198 3.440 ... (remaining 53096 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: 0.00 ========== 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.011 0.616 6604 Z= 0.645 Angle : 1.655 18.865 8981 Z= 1.187 Chirality : 0.126 0.630 933 Planarity : 0.009 0.114 1160 Dihedral : 17.473 88.173 2390 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.51 % Allowed : 1.66 % Favored : 97.83 % Rotamer: Outliers : 4.45 % Allowed : 14.49 % Favored : 81.06 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.29), residues: 783 helix: 3.39 (0.25), residues: 379 sheet: 2.08 (0.69), residues: 49 loop : 0.02 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.018 0.002 PHE A 512 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.24909 ( 311) hydrogen bonds : angle 6.38830 ( 924) metal coordination : bond 0.23436 ( 2) SS BOND : bond 0.61589 ( 1) SS BOND : angle 14.79944 ( 2) covalent geometry : bond 0.00669 ( 6601) covalent geometry : angle 1.64010 ( 8979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 329 PHE cc_start: 0.6610 (t80) cc_final: 0.6032 (t80) REVERT: C 419 CYS cc_start: 0.6266 (m) cc_final: 0.5481 (m) outliers start: 31 outliers final: 2 residues processed: 144 average time/residue: 0.2355 time to fit residues: 42.5125 Evaluate side-chains 62 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain C residue 465 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 96 GLN A 194 ASN A 373 HIS A 401 HIS A 546 ASN A 598 GLN C 330 ASN C 381 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.054737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.039356 restraints weight = 27723.674| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 5.32 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6604 Z= 0.227 Angle : 0.728 10.032 8981 Z= 0.398 Chirality : 0.046 0.218 933 Planarity : 0.006 0.044 1160 Dihedral : 5.901 57.014 869 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.53 % Favored : 98.21 % Rotamer: Outliers : 3.01 % Allowed : 16.50 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.29), residues: 783 helix: 2.61 (0.26), residues: 383 sheet: 0.83 (0.68), residues: 51 loop : 0.01 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 271 HIS 0.005 0.001 HIS A 265 PHE 0.028 0.002 PHE C 483 TYR 0.024 0.002 TYR A 613 ARG 0.004 0.001 ARG C 395 Details of bonding type rmsd hydrogen bonds : bond 0.07992 ( 311) hydrogen bonds : angle 5.47077 ( 924) metal coordination : bond 0.01386 ( 2) SS BOND : bond 0.00190 ( 1) SS BOND : angle 1.15485 ( 2) covalent geometry : bond 0.00493 ( 6601) covalent geometry : angle 0.72739 ( 8979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 CYS cc_start: 0.9367 (p) cc_final: 0.9158 (p) REVERT: A 194 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8236 (m110) REVERT: A 249 MET cc_start: 0.8876 (tpp) cc_final: 0.8617 (mmt) REVERT: A 481 LYS cc_start: 0.9522 (OUTLIER) cc_final: 0.9268 (ttmt) REVERT: C 334 PHE cc_start: 0.8527 (m-80) cc_final: 0.8286 (m-80) REVERT: C 357 ASN cc_start: 0.9043 (m-40) cc_final: 0.8817 (m110) REVERT: C 411 LYS cc_start: 0.8530 (tppt) cc_final: 0.8238 (tppt) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.1865 time to fit residues: 20.7763 Evaluate side-chains 72 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 360 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.055879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.040280 restraints weight = 28111.172| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 5.41 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6604 Z= 0.142 Angle : 0.604 10.636 8981 Z= 0.324 Chirality : 0.042 0.236 933 Planarity : 0.004 0.036 1160 Dihedral : 5.300 53.653 865 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 2.30 % Allowed : 15.64 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.30), residues: 783 helix: 2.64 (0.25), residues: 382 sheet: 0.63 (0.72), residues: 46 loop : 0.14 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.011 0.001 HIS A 401 PHE 0.015 0.001 PHE C 483 TYR 0.028 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 Details of bonding type rmsd hydrogen bonds : bond 0.06720 ( 311) hydrogen bonds : angle 5.01900 ( 924) metal coordination : bond 0.00143 ( 2) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.64808 ( 2) covalent geometry : bond 0.00286 ( 6601) covalent geometry : angle 0.60374 ( 8979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8567 (t0) REVERT: A 270 MET cc_start: 0.9181 (tpt) cc_final: 0.8956 (tpt) REVERT: A 481 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9310 (ttmt) REVERT: A 512 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.9005 (m-80) REVERT: C 411 LYS cc_start: 0.8537 (tppt) cc_final: 0.8258 (tppt) outliers start: 16 outliers final: 6 residues processed: 78 average time/residue: 0.2051 time to fit residues: 21.1579 Evaluate side-chains 67 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 0.0060 chunk 24 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 69 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN C 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.054430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.038978 restraints weight = 28662.275| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 5.31 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6604 Z= 0.154 Angle : 0.585 11.882 8981 Z= 0.309 Chirality : 0.041 0.190 933 Planarity : 0.004 0.039 1160 Dihedral : 4.887 25.860 861 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.30 % Favored : 97.57 % Rotamer: Outliers : 2.15 % Allowed : 15.78 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.30), residues: 783 helix: 2.59 (0.25), residues: 384 sheet: 0.68 (0.78), residues: 40 loop : 0.16 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.003 0.001 HIS A 401 PHE 0.012 0.001 PHE A 523 TYR 0.026 0.001 TYR A 613 ARG 0.003 0.000 ARG C 395 Details of bonding type rmsd hydrogen bonds : bond 0.06314 ( 311) hydrogen bonds : angle 4.91259 ( 924) metal coordination : bond 0.00079 ( 2) SS BOND : bond 0.00200 ( 1) SS BOND : angle 0.45827 ( 2) covalent geometry : bond 0.00338 ( 6601) covalent geometry : angle 0.58544 ( 8979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 481 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9305 (ttmt) REVERT: C 501 PHE cc_start: 0.7068 (p90) cc_final: 0.6322 (t80) REVERT: C 502 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8435 (pp20) outliers start: 15 outliers final: 10 residues processed: 68 average time/residue: 0.2009 time to fit residues: 18.2619 Evaluate side-chains 69 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN C 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.055319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.039908 restraints weight = 28215.043| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 5.29 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6604 Z= 0.124 Angle : 0.547 10.193 8981 Z= 0.288 Chirality : 0.040 0.183 933 Planarity : 0.004 0.042 1160 Dihedral : 4.635 23.800 861 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.81 % Favored : 97.06 % Rotamer: Outliers : 2.15 % Allowed : 16.50 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.30), residues: 783 helix: 2.52 (0.25), residues: 390 sheet: 0.43 (0.80), residues: 40 loop : 0.14 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.002 0.001 HIS A 265 PHE 0.010 0.001 PHE C 387 TYR 0.023 0.001 TYR A 613 ARG 0.002 0.000 ARG C 395 Details of bonding type rmsd hydrogen bonds : bond 0.05301 ( 311) hydrogen bonds : angle 4.67825 ( 924) metal coordination : bond 0.00102 ( 2) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.35277 ( 2) covalent geometry : bond 0.00263 ( 6601) covalent geometry : angle 0.54667 ( 8979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9109 (mmm) cc_final: 0.8897 (tpp) REVERT: A 512 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: C 414 ASP cc_start: 0.8713 (p0) cc_final: 0.8278 (p0) REVERT: C 417 MET cc_start: 0.6604 (mpp) cc_final: 0.5824 (mpp) REVERT: C 501 PHE cc_start: 0.7219 (p90) cc_final: 0.6435 (t80) REVERT: C 502 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8424 (tm-30) outliers start: 15 outliers final: 7 residues processed: 75 average time/residue: 0.1948 time to fit residues: 19.5896 Evaluate side-chains 65 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.054016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.038547 restraints weight = 28157.761| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 5.21 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6604 Z= 0.142 Angle : 0.561 13.073 8981 Z= 0.291 Chirality : 0.039 0.159 933 Planarity : 0.004 0.043 1160 Dihedral : 4.575 21.479 861 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 1.87 % Allowed : 16.93 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.30), residues: 783 helix: 2.61 (0.26), residues: 388 sheet: 0.35 (0.80), residues: 40 loop : 0.07 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.002 0.001 HIS A 374 PHE 0.012 0.001 PHE C 325 TYR 0.023 0.001 TYR A 613 ARG 0.003 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.05578 ( 311) hydrogen bonds : angle 4.61640 ( 924) metal coordination : bond 0.00143 ( 2) SS BOND : bond 0.00335 ( 1) SS BOND : angle 0.57565 ( 2) covalent geometry : bond 0.00313 ( 6601) covalent geometry : angle 0.56120 ( 8979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 67 average time/residue: 0.2007 time to fit residues: 17.9597 Evaluate side-chains 63 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 467 CYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.039623 restraints weight = 28445.057| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 5.34 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6604 Z= 0.116 Angle : 0.542 12.458 8981 Z= 0.282 Chirality : 0.039 0.199 933 Planarity : 0.004 0.044 1160 Dihedral : 4.472 21.289 861 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.55 % Favored : 97.32 % Rotamer: Outliers : 1.58 % Allowed : 17.36 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.30), residues: 783 helix: 2.63 (0.26), residues: 388 sheet: 0.29 (0.82), residues: 38 loop : -0.01 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 HIS 0.002 0.000 HIS A 265 PHE 0.017 0.001 PHE C 361 TYR 0.023 0.001 TYR A 613 ARG 0.005 0.000 ARG C 449 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 311) hydrogen bonds : angle 4.47466 ( 924) metal coordination : bond 0.00055 ( 2) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.45122 ( 2) covalent geometry : bond 0.00239 ( 6601) covalent geometry : angle 0.54227 ( 8979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9035 (tpp) cc_final: 0.8688 (tpp) REVERT: C 415 ASP cc_start: 0.8726 (p0) cc_final: 0.8481 (p0) REVERT: C 417 MET cc_start: 0.6393 (mpp) cc_final: 0.5646 (mpp) REVERT: C 501 PHE cc_start: 0.7353 (p90) cc_final: 0.6255 (t80) outliers start: 11 outliers final: 8 residues processed: 66 average time/residue: 0.2020 time to fit residues: 17.8524 Evaluate side-chains 64 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 65.8827 > 50: distance: 35 - 60: 17.847 distance: 39 - 68: 29.851 distance: 45 - 77: 27.776 distance: 52 - 60: 20.549 distance: 53 - 85: 29.533 distance: 60 - 61: 3.704 distance: 61 - 62: 16.796 distance: 61 - 64: 44.651 distance: 62 - 63: 23.062 distance: 62 - 68: 34.160 distance: 63 - 93: 21.799 distance: 64 - 65: 31.549 distance: 65 - 66: 52.002 distance: 65 - 67: 20.157 distance: 68 - 69: 4.027 distance: 69 - 72: 7.599 distance: 70 - 71: 10.456 distance: 70 - 77: 7.321 distance: 72 - 73: 42.283 distance: 73 - 74: 26.959 distance: 74 - 75: 58.831 distance: 75 - 76: 4.775 distance: 78 - 79: 11.298 distance: 78 - 81: 6.670 distance: 79 - 80: 10.560 distance: 79 - 85: 5.709 distance: 81 - 82: 45.147 distance: 82 - 83: 24.087 distance: 82 - 84: 56.427 distance: 85 - 86: 8.442 distance: 86 - 87: 6.099 distance: 86 - 89: 11.515 distance: 87 - 88: 42.908 distance: 87 - 93: 38.085 distance: 89 - 90: 13.867 distance: 89 - 91: 28.431 distance: 90 - 92: 47.496 distance: 93 - 94: 28.988 distance: 94 - 95: 26.833 distance: 95 - 96: 40.796 distance: 95 - 97: 28.847 distance: 97 - 98: 34.542 distance: 98 - 99: 18.809 distance: 98 - 101: 30.314 distance: 99 - 100: 20.074 distance: 99 - 105: 39.676 distance: 101 - 102: 12.993 distance: 102 - 103: 6.113 distance: 102 - 104: 27.177 distance: 106 - 107: 20.765 distance: 106 - 109: 32.252 distance: 107 - 108: 8.151 distance: 107 - 113: 24.962 distance: 109 - 110: 38.738 distance: 110 - 111: 22.671 distance: 110 - 112: 45.384 distance: 113 - 114: 25.304 distance: 113 - 119: 37.885 distance: 114 - 115: 7.155 distance: 114 - 117: 7.419 distance: 115 - 116: 4.163 distance: 115 - 120: 39.726 distance: 117 - 118: 49.149 distance: 118 - 119: 15.344 distance: 120 - 121: 23.379 distance: 120 - 126: 15.916 distance: 121 - 122: 28.121 distance: 121 - 124: 28.914 distance: 122 - 123: 8.551 distance: 125 - 126: 10.947 distance: 128 - 131: 11.251 distance: 129 - 133: 35.446 distance: 131 - 132: 24.362