Starting phenix.real_space_refine on Tue Mar 11 21:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.map" model { file = "/net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dm6_27528/03_2025/8dm6_27528.cif" } resolution = 2.77 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4200 2.51 5 N 1082 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1604 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.20, per 1000 atoms: 0.79 Number of scatterers: 6559 At special positions: 0 Unit cell: (79, 86, 122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1240 8.00 N 1082 7.00 C 4200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 865.0 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1500 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 57.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.866A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.572A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.284A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 20 through 53 Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.166A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.609A pdb=" N SER D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix removed outlier: 3.807A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 removed outlier: 4.500A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.824A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.744A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.340A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.531A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.335A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.747A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.372A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.992A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 6.539A pdb=" N ALA A 435 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.976A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.246A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 984 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: 1.87 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2084 1.35 - 1.48: 1851 1.48 - 1.61: 2752 1.61 - 1.73: 0 1.73 - 1.86: 58 Bond restraints: 6745 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C1 NAG D 706 " pdb=" O5 NAG D 706 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" CG PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 1.503 1.575 -0.072 3.40e-02 8.65e+02 4.47e+00 bond pdb=" C1 NAG D 704 " pdb=" O5 NAG D 704 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG D 702 " pdb=" O5 NAG D 702 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.52e+00 ... (remaining 6740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 8890 2.44 - 4.87: 244 4.87 - 7.31: 21 7.31 - 9.74: 7 9.74 - 12.18: 4 Bond angle restraints: 9166 Sorted by residual: angle pdb=" N ALA A 372 " pdb=" CA ALA A 372 " pdb=" C ALA A 372 " ideal model delta sigma weight residual 109.81 120.82 -11.01 2.21e+00 2.05e-01 2.48e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 125.13 -10.73 2.30e+00 1.89e-01 2.18e+01 angle pdb=" CB MET D 152 " pdb=" CG MET D 152 " pdb=" SD MET D 152 " ideal model delta sigma weight residual 112.70 124.88 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB LYS D 534 " pdb=" CG LYS D 534 " pdb=" CD LYS D 534 " ideal model delta sigma weight residual 111.30 120.35 -9.05 2.30e+00 1.89e-01 1.55e+01 angle pdb=" CA PRO A 330 " pdb=" N PRO A 330 " pdb=" CD PRO A 330 " ideal model delta sigma weight residual 112.00 106.58 5.42 1.40e+00 5.10e-01 1.50e+01 ... (remaining 9161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 3648 17.48 - 34.97: 340 34.97 - 52.45: 60 52.45 - 69.94: 14 69.94 - 87.42: 8 Dihedral angle restraints: 4070 sinusoidal: 1733 harmonic: 2337 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.29 54.71 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 55.17 37.83 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 588 0.046 - 0.093: 273 0.093 - 0.139: 86 0.139 - 0.185: 24 0.185 - 0.231: 5 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA ASN A 360 " pdb=" N ASN A 360 " pdb=" C ASN A 360 " pdb=" CB ASN A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU D 267 " pdb=" CB LEU D 267 " pdb=" CD1 LEU D 267 " pdb=" CD2 LEU D 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB THR A 333 " pdb=" CA THR A 333 " pdb=" OG1 THR A 333 " pdb=" CG2 THR A 333 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 973 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS D 241 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.90e+00 pdb=" C HIS D 241 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA D 242 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 244 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C VAL D 244 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 244 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG D 245 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 226 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C VAL D 226 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL D 226 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU D 227 " -0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1832 2.81 - 3.33: 5953 3.33 - 3.85: 11478 3.85 - 4.38: 13089 4.38 - 4.90: 22516 Nonbonded interactions: 54868 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.282 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.342 3.040 nonbonded pdb=" OE2 GLU D 435 " pdb=" NZ LYS D 541 " model vdw 2.343 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.350 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.360 3.040 ... (remaining 54863 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: 2.570 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: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6745 Z= 0.392 Angle : 0.937 12.179 9166 Z= 0.510 Chirality : 0.059 0.231 976 Planarity : 0.007 0.063 1179 Dihedral : 14.081 87.420 2552 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.57 % Allowed : 4.29 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.27), residues: 792 helix: 0.27 (0.23), residues: 389 sheet: 2.01 (0.81), residues: 34 loop : -0.50 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 594 HIS 0.007 0.002 HIS A 505 PHE 0.024 0.003 PHE A 377 TYR 0.031 0.002 TYR D 385 ARG 0.012 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7820 (ttt90) REVERT: A 465 GLU cc_start: 0.8263 (tt0) cc_final: 0.8028 (tt0) REVERT: D 55 THR cc_start: 0.8054 (m) cc_final: 0.7796 (p) REVERT: D 270 MET cc_start: 0.8145 (tpt) cc_final: 0.7927 (tpp) REVERT: D 366 MET cc_start: 0.8582 (ttp) cc_final: 0.8362 (ttp) REVERT: D 483 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 534 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8302 (mmtm) REVERT: D 582 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7744 (mmm160) REVERT: D 603 PHE cc_start: 0.8656 (t80) cc_final: 0.8027 (t80) REVERT: D 604 VAL cc_start: 0.9243 (p) cc_final: 0.8911 (t) outliers start: 4 outliers final: 1 residues processed: 192 average time/residue: 1.3055 time to fit residues: 262.2694 Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 609 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.0470 chunk 33 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 76 GLN ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.080202 restraints weight = 12126.955| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.79 r_work: 0.2986 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6745 Z= 0.226 Angle : 0.604 8.060 9166 Z= 0.311 Chirality : 0.044 0.274 976 Planarity : 0.005 0.036 1179 Dihedral : 5.662 53.377 1014 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.43 % Allowed : 13.88 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.29), residues: 792 helix: 1.04 (0.25), residues: 402 sheet: 1.21 (0.75), residues: 43 loop : -0.07 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 165 HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.016 0.001 TYR D 41 ARG 0.004 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8089 (p0) cc_final: 0.7760 (p0) REVERT: A 340 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8688 (mp0) REVERT: A 357 ARG cc_start: 0.8777 (ptm160) cc_final: 0.8275 (ttt90) REVERT: A 465 GLU cc_start: 0.8595 (tt0) cc_final: 0.8211 (tt0) REVERT: D 26 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8334 (mtmm) REVERT: D 55 THR cc_start: 0.8071 (m) cc_final: 0.7691 (p) REVERT: D 182 GLU cc_start: 0.8556 (tt0) cc_final: 0.8160 (tt0) REVERT: D 228 HIS cc_start: 0.8435 (t70) cc_final: 0.7962 (m90) REVERT: D 270 MET cc_start: 0.8222 (tpt) cc_final: 0.7930 (tpp) REVERT: D 287 GLN cc_start: 0.8692 (mp10) cc_final: 0.8264 (pm20) REVERT: D 408 MET cc_start: 0.9222 (mmt) cc_final: 0.8949 (mmt) REVERT: D 429 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8155 (mm-40) REVERT: D 467 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7701 (mp0) REVERT: D 470 LYS cc_start: 0.8779 (tppp) cc_final: 0.8573 (tppp) REVERT: D 472 GLN cc_start: 0.8277 (mm-40) cc_final: 0.8060 (mm-40) REVERT: D 483 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8284 (tm-30) REVERT: D 497 TYR cc_start: 0.8809 (m-80) cc_final: 0.8521 (m-80) REVERT: D 582 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8184 (mmm160) REVERT: D 603 PHE cc_start: 0.8740 (t80) cc_final: 0.8321 (t80) outliers start: 17 outliers final: 4 residues processed: 125 average time/residue: 1.5114 time to fit residues: 197.9736 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 549 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.100762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078012 restraints weight = 12285.316| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.85 r_work: 0.2923 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6745 Z= 0.237 Angle : 0.567 6.240 9166 Z= 0.289 Chirality : 0.043 0.244 976 Planarity : 0.004 0.034 1179 Dihedral : 4.997 44.938 1012 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.15 % Allowed : 15.31 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 792 helix: 1.24 (0.25), residues: 408 sheet: 2.09 (0.87), residues: 33 loop : 0.07 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 165 HIS 0.002 0.001 HIS D 535 PHE 0.014 0.001 PHE D 369 TYR 0.016 0.001 TYR D 50 ARG 0.004 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.8362 (p0) cc_final: 0.7814 (p0) REVERT: A 340 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8653 (mp0) REVERT: A 357 ARG cc_start: 0.8759 (ptm160) cc_final: 0.8234 (ttt90) REVERT: A 465 GLU cc_start: 0.8648 (tt0) cc_final: 0.8348 (tt0) REVERT: D 26 LYS cc_start: 0.8671 (mtpt) cc_final: 0.8324 (mttm) REVERT: D 55 THR cc_start: 0.8045 (m) cc_final: 0.7661 (p) REVERT: D 115 ARG cc_start: 0.8547 (tpm-80) cc_final: 0.8023 (tpm170) REVERT: D 182 GLU cc_start: 0.8621 (tt0) cc_final: 0.8273 (tt0) REVERT: D 243 TYR cc_start: 0.8895 (t80) cc_final: 0.8678 (t80) REVERT: D 270 MET cc_start: 0.8232 (tpt) cc_final: 0.7927 (tpp) REVERT: D 287 GLN cc_start: 0.8675 (mp10) cc_final: 0.8172 (pm20) REVERT: D 305 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: D 408 MET cc_start: 0.9222 (mmt) cc_final: 0.9008 (mmt) REVERT: D 470 LYS cc_start: 0.8706 (tppp) cc_final: 0.8450 (tppp) REVERT: D 483 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8291 (tm-30) REVERT: D 582 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8214 (mmm160) REVERT: D 603 PHE cc_start: 0.8784 (t80) cc_final: 0.8327 (t80) outliers start: 22 outliers final: 8 residues processed: 126 average time/residue: 1.3265 time to fit residues: 175.2391 Evaluate side-chains 114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 49 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN D 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078430 restraints weight = 12400.907| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.88 r_work: 0.2942 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6745 Z= 0.206 Angle : 0.551 6.522 9166 Z= 0.280 Chirality : 0.042 0.192 976 Planarity : 0.004 0.030 1179 Dihedral : 4.389 27.983 1012 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.00 % Allowed : 16.88 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 792 helix: 1.41 (0.26), residues: 408 sheet: 2.12 (0.89), residues: 33 loop : 0.22 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 168 HIS 0.003 0.001 HIS D 239 PHE 0.014 0.001 PHE D 369 TYR 0.013 0.001 TYR D 50 ARG 0.003 0.000 ARG D 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.8763 (ptm160) cc_final: 0.8166 (ttt90) REVERT: A 465 GLU cc_start: 0.8663 (tt0) cc_final: 0.8318 (tt0) REVERT: A 500 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9013 (p) REVERT: D 26 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8305 (mttp) REVERT: D 115 ARG cc_start: 0.8597 (tpm-80) cc_final: 0.8136 (tpm170) REVERT: D 182 GLU cc_start: 0.8676 (tt0) cc_final: 0.8331 (tt0) REVERT: D 243 TYR cc_start: 0.8926 (t80) cc_final: 0.8721 (t80) REVERT: D 270 MET cc_start: 0.8173 (tpt) cc_final: 0.7888 (tpp) REVERT: D 287 GLN cc_start: 0.8669 (mp10) cc_final: 0.8178 (pm20) REVERT: D 467 GLU cc_start: 0.8290 (mp0) cc_final: 0.7452 (mp0) REVERT: D 470 LYS cc_start: 0.8754 (tppp) cc_final: 0.8529 (tppp) REVERT: D 479 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8330 (mt-10) REVERT: D 483 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8271 (tm-30) REVERT: D 531 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: D 582 ARG cc_start: 0.8437 (mmm160) cc_final: 0.8206 (mmm160) REVERT: D 603 PHE cc_start: 0.8798 (t80) cc_final: 0.8353 (t80) outliers start: 21 outliers final: 11 residues processed: 118 average time/residue: 1.3099 time to fit residues: 162.0861 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 549 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 477 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.077306 restraints weight = 12161.430| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.86 r_work: 0.2910 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6745 Z= 0.238 Angle : 0.560 6.872 9166 Z= 0.282 Chirality : 0.042 0.165 976 Planarity : 0.004 0.030 1179 Dihedral : 4.296 26.256 1012 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.43 % Allowed : 18.17 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.30), residues: 792 helix: 1.49 (0.26), residues: 409 sheet: 1.99 (0.89), residues: 33 loop : 0.26 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 165 HIS 0.003 0.001 HIS D 239 PHE 0.015 0.001 PHE D 369 TYR 0.014 0.001 TYR D 50 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8334 (t0) REVERT: A 465 GLU cc_start: 0.8649 (tt0) cc_final: 0.8314 (tt0) REVERT: D 26 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8347 (mttm) REVERT: D 115 ARG cc_start: 0.8684 (tpm-80) cc_final: 0.7970 (tpm170) REVERT: D 182 GLU cc_start: 0.8728 (tt0) cc_final: 0.8382 (tt0) REVERT: D 243 TYR cc_start: 0.9000 (t80) cc_final: 0.8773 (t80) REVERT: D 270 MET cc_start: 0.8244 (tpt) cc_final: 0.7959 (tpp) REVERT: D 287 GLN cc_start: 0.8689 (mp10) cc_final: 0.8205 (pm20) REVERT: D 467 GLU cc_start: 0.8292 (mp0) cc_final: 0.7233 (mp0) REVERT: D 470 LYS cc_start: 0.8733 (tppp) cc_final: 0.8521 (tppp) REVERT: D 479 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8245 (mt-10) REVERT: D 483 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 497 TYR cc_start: 0.8706 (m-80) cc_final: 0.8202 (m-80) REVERT: D 531 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: D 603 PHE cc_start: 0.8822 (t80) cc_final: 0.8388 (t80) outliers start: 24 outliers final: 13 residues processed: 122 average time/residue: 1.1640 time to fit residues: 149.6107 Evaluate side-chains 114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 429 GLN Chi-restraints excluded: chain D residue 531 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 57.7081 > 50: distance: 24 - 46: 21.138 distance: 29 - 54: 29.905 distance: 37 - 62: 9.904 distance: 40 - 46: 21.684 distance: 41 - 70: 13.361 distance: 46 - 47: 28.292 distance: 47 - 48: 28.458 distance: 47 - 50: 38.469 distance: 48 - 49: 19.993 distance: 48 - 54: 52.316 distance: 49 - 75: 18.710 distance: 50 - 51: 23.386 distance: 51 - 52: 8.897 distance: 51 - 53: 3.875 distance: 54 - 55: 16.814 distance: 55 - 56: 17.530 distance: 55 - 58: 14.030 distance: 56 - 57: 13.428 distance: 56 - 62: 4.907 distance: 58 - 59: 12.517 distance: 59 - 60: 7.700 distance: 60 - 61: 4.954 distance: 62 - 63: 9.302 distance: 63 - 64: 7.496 distance: 63 - 66: 5.012 distance: 64 - 65: 9.209 distance: 64 - 70: 17.369 distance: 66 - 67: 7.575 distance: 67 - 69: 4.436 distance: 70 - 71: 16.190 distance: 71 - 72: 7.305 distance: 71 - 74: 10.321 distance: 72 - 73: 10.990 distance: 75 - 76: 21.484 distance: 76 - 77: 37.013 distance: 76 - 79: 22.313 distance: 77 - 78: 46.681 distance: 77 - 87: 27.414 distance: 79 - 80: 6.420 distance: 80 - 81: 4.072 distance: 80 - 82: 6.600 distance: 82 - 84: 4.677 distance: 87 - 88: 21.086 distance: 87 - 93: 18.737 distance: 88 - 89: 28.505 distance: 88 - 91: 57.708 distance: 89 - 90: 10.359 distance: 89 - 94: 10.494 distance: 91 - 92: 38.222 distance: 92 - 93: 26.392 distance: 94 - 95: 11.762 distance: 95 - 96: 14.553 distance: 95 - 98: 23.352 distance: 96 - 97: 14.273 distance: 96 - 100: 12.901 distance: 98 - 99: 6.972 distance: 100 - 101: 26.196 distance: 101 - 102: 33.663 distance: 101 - 104: 27.497 distance: 102 - 103: 26.251 distance: 102 - 112: 18.243 distance: 104 - 105: 6.620 distance: 105 - 106: 9.808 distance: 105 - 107: 7.099 distance: 106 - 108: 6.245 distance: 107 - 109: 8.319 distance: 108 - 110: 10.997 distance: 109 - 110: 12.398 distance: 110 - 111: 3.583 distance: 112 - 113: 6.686 distance: 113 - 114: 24.341 distance: 113 - 116: 13.518 distance: 114 - 115: 51.257 distance: 114 - 120: 31.671 distance: 116 - 117: 17.099 distance: 116 - 118: 12.309 distance: 117 - 119: 6.268 distance: 120 - 121: 16.729 distance: 121 - 122: 46.542 distance: 121 - 124: 30.048 distance: 122 - 123: 39.055 distance: 122 - 126: 29.284 distance: 124 - 125: 24.990