Starting phenix.real_space_refine on Wed Mar 12 05:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.map" model { file = "/net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zya_60560/03_2025/8zya_60560.cif" } resolution = 2.5 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= 0.002 sd= 0.126 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 40 5.16 5 C 4663 2.51 5 N 1211 2.21 5 O 1392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 7306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 5730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5730 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 34, 'TRANS': 663} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.73, per 1000 atoms: 0.65 Number of scatterers: 7306 At special positions: 0 Unit cell: (77.745, 102.93, 133.59, 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 40 16.00 O 1392 8.00 N 1211 7.00 C 4663 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 1 " - " ASN D 53 " " NAG C 1 " - " ASN D 689 " " NAG D 901 " - " ASN D 322 " " NAG D 902 " - " ASN D 432 " " NAG E 1 " - " ASN D 546 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 923.3 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 49.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.736A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'D' and resid 24 through 53 removed outlier: 3.514A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU D 35 " --> pdb=" O ASN D 31 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.724A pdb=" N GLN D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 81 removed outlier: 4.544A pdb=" N ALA D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 100 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 172 through 193 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.709A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D 224 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.569A 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 removed outlier: 3.669A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.545A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.574A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.012A 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 399 through 409 removed outlier: 3.772A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.799A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 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 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.391A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.987A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.032A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.635A pdb=" N GLU D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 657 removed outlier: 3.842A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR D 641 " --> pdb=" O ASP D 637 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 642 " --> pdb=" O ASN D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 371 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA3, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.928A 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: 6.218A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 618 through 621 302 hydrogen bonds defined for protein. 858 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: 2.00 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1246 1.32 - 1.45: 2165 1.45 - 1.57: 4032 1.57 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 7508 Sorted by residual: bond pdb=" N VAL D 560 " pdb=" CA VAL D 560 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.77e+00 bond pdb=" C GLN D 556 " pdb=" O GLN D 556 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.35e-02 5.49e+03 8.35e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" N LYS D 562 " pdb=" CA LYS D 562 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.33e-02 5.65e+03 5.65e+00 bond pdb=" N SER D 559 " pdb=" CA SER D 559 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.28e-02 6.10e+03 5.37e+00 ... (remaining 7503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 9925 2.04 - 4.09: 219 4.09 - 6.13: 33 6.13 - 8.17: 11 8.17 - 10.22: 3 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N VAL A 331 " pdb=" CA VAL A 331 " pdb=" C VAL A 331 " ideal model delta sigma weight residual 113.71 106.57 7.14 9.50e-01 1.11e+00 5.65e+01 angle pdb=" C THR D 90 " pdb=" N VAL D 91 " pdb=" CA VAL D 91 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 115.61 108.51 7.10 1.74e+00 3.30e-01 1.66e+01 angle pdb=" N MET D 557 " pdb=" CA MET D 557 " pdb=" C MET D 557 " ideal model delta sigma weight residual 113.55 108.67 4.88 1.26e+00 6.30e-01 1.50e+01 angle pdb=" N GLN D 556 " pdb=" CA GLN D 556 " pdb=" C GLN D 556 " ideal model delta sigma weight residual 113.20 108.93 4.27 1.21e+00 6.83e-01 1.24e+01 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 4072 17.67 - 35.33: 397 35.33 - 53.00: 62 53.00 - 70.67: 11 70.67 - 88.33: 7 Dihedral angle restraints: 4549 sinusoidal: 1954 harmonic: 2595 Sorted by residual: dihedral pdb=" CA GLN D 102 " pdb=" C GLN D 102 " pdb=" N SER D 103 " pdb=" CA SER D 103 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN D 101 " pdb=" C GLN D 101 " pdb=" N GLN D 102 " pdb=" CA GLN D 102 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ASP D 250 " pdb=" C ASP D 250 " pdb=" N THR D 251 " pdb=" CA THR D 251 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 911 0.063 - 0.125: 164 0.125 - 0.188: 10 0.188 - 0.251: 1 0.251 - 0.314: 2 Chirality restraints: 1088 Sorted by residual: chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB VAL D 581 " pdb=" CA VAL D 581 " pdb=" CG1 VAL D 581 " pdb=" CG2 VAL D 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB ILE D 678 " pdb=" CA ILE D 678 " pdb=" CG1 ILE D 678 " pdb=" CG2 ILE D 678 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1085 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO D 346 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO D 146 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 555 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C HIS D 555 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS D 555 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN D 556 " 0.015 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2026 2.81 - 3.33: 6520 3.33 - 3.86: 12403 3.86 - 4.38: 14715 4.38 - 4.90: 25038 Nonbonded interactions: 60702 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.290 3.040 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.290 3.040 nonbonded pdb=" OD1 ASP D 382 " pdb=" OH TYR D 385 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR A 442 " pdb=" ND1 HIS D 34 " model vdw 2.323 3.120 ... (remaining 60697 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } 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=0.00 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: 18.920 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.004 0.063 7508 Z= 0.266 Angle : 0.731 10.217 10191 Z= 0.405 Chirality : 0.049 0.314 1088 Planarity : 0.007 0.115 1304 Dihedral : 14.034 88.333 2865 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 0.13 % Allowed : 0.51 % Favored : 99.37 % 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: -1.47 (0.27), residues: 876 helix: -0.80 (0.24), residues: 409 sheet: 1.58 (0.70), residues: 42 loop : -1.37 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 566 HIS 0.007 0.001 HIS D 378 PHE 0.022 0.002 PHE A 337 TYR 0.017 0.001 TYR D 385 ARG 0.004 0.000 ARG D 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.872 Fit side-chains REVERT: D 49 GLU cc_start: 0.7506 (tp30) cc_final: 0.7255 (tp30) REVERT: D 60 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 82 ASN cc_start: 0.7880 (m110) cc_final: 0.7605 (m-40) REVERT: D 472 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7536 (mt-10) outliers start: 1 outliers final: 2 residues processed: 108 average time/residue: 1.8087 time to fit residues: 206.0869 Evaluate side-chains 84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 457 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN D 42 GLN D 58 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.150904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115783 restraints weight = 8355.439| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.50 r_work: 0.3432 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7508 Z= 0.167 Angle : 0.549 9.703 10191 Z= 0.280 Chirality : 0.041 0.256 1088 Planarity : 0.005 0.067 1304 Dihedral : 6.968 56.942 1143 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.90 % Allowed : 6.59 % Favored : 91.51 % 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: -0.77 (0.28), residues: 876 helix: -0.00 (0.26), residues: 420 sheet: 1.72 (0.72), residues: 42 loop : -1.26 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.006 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.013 0.001 TYR D 385 ARG 0.004 0.000 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: D 64 GLU cc_start: 0.6877 (mm-30) cc_final: 0.5996 (tm-30) REVERT: D 74 GLU cc_start: 0.6747 (pp20) cc_final: 0.6436 (pt0) REVERT: D 140 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6677 (pm20) REVERT: D 208 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: D 401 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: D 465 ARG cc_start: 0.8140 (ttp80) cc_final: 0.7710 (ttp80) REVERT: D 467 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8557 (mt-10) REVERT: D 472 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7635 (mt-10) REVERT: D 564 GLN cc_start: 0.7913 (tt0) cc_final: 0.7709 (tt0) outliers start: 15 outliers final: 5 residues processed: 94 average time/residue: 1.4173 time to fit residues: 140.2250 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.145579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109875 restraints weight = 8394.516| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.51 r_work: 0.3355 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7508 Z= 0.263 Angle : 0.578 9.512 10191 Z= 0.294 Chirality : 0.043 0.256 1088 Planarity : 0.005 0.054 1304 Dihedral : 6.483 56.401 1140 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.28 % Allowed : 9.51 % Favored : 88.21 % 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: -0.58 (0.29), residues: 876 helix: 0.24 (0.26), residues: 422 sheet: 1.55 (0.74), residues: 42 loop : -1.22 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 349 HIS 0.006 0.001 HIS D 241 PHE 0.023 0.002 PHE D 400 TYR 0.014 0.001 TYR D 385 ARG 0.005 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: D 49 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6050 (tm-30) REVERT: D 62 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.5886 (mtp) REVERT: D 64 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6186 (mp0) REVERT: D 74 GLU cc_start: 0.6660 (pp20) cc_final: 0.6332 (pt0) REVERT: D 140 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: D 208 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: D 367 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6363 (pp20) REVERT: D 401 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7664 (t-90) REVERT: D 465 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7952 (ttp80) REVERT: D 472 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7662 (mt-10) REVERT: D 640 MET cc_start: 0.7687 (tpt) cc_final: 0.7345 (mmm) outliers start: 18 outliers final: 7 residues processed: 96 average time/residue: 1.9418 time to fit residues: 196.7925 Evaluate side-chains 95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.0070 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112077 restraints weight = 8400.770| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.51 r_work: 0.3391 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7508 Z= 0.165 Angle : 0.527 9.504 10191 Z= 0.267 Chirality : 0.041 0.252 1088 Planarity : 0.004 0.050 1304 Dihedral : 6.146 56.121 1140 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.53 % Allowed : 11.03 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.29), residues: 876 helix: 0.51 (0.27), residues: 413 sheet: 0.96 (0.67), residues: 52 loop : -1.10 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.014 0.001 PHE D 369 TYR 0.013 0.001 TYR D 516 ARG 0.004 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: D 49 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6014 (tm-30) REVERT: D 62 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6240 (mpp) REVERT: D 64 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6027 (mp0) REVERT: D 74 GLU cc_start: 0.6675 (pp20) cc_final: 0.6349 (pt0) REVERT: D 140 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: D 208 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: D 227 ASP cc_start: 0.7104 (p0) cc_final: 0.6902 (p0) REVERT: D 465 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7921 (ttp80) REVERT: D 472 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 640 MET cc_start: 0.7691 (tpt) cc_final: 0.7406 (mmm) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 1.5793 time to fit residues: 165.8294 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 10 optimal weight: 0.0000 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.145848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110325 restraints weight = 8370.190| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.50 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7508 Z= 0.216 Angle : 0.539 9.505 10191 Z= 0.272 Chirality : 0.042 0.254 1088 Planarity : 0.004 0.046 1304 Dihedral : 6.077 56.190 1140 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.79 % Allowed : 11.66 % Favored : 85.55 % 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: -0.28 (0.29), residues: 876 helix: 0.59 (0.27), residues: 413 sheet: 0.90 (0.67), residues: 52 loop : -1.11 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 163 HIS 0.005 0.001 HIS D 241 PHE 0.016 0.001 PHE D 523 TYR 0.012 0.001 TYR D 516 ARG 0.004 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 49 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: D 62 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.6240 (mpp) REVERT: D 64 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6015 (mp0) REVERT: D 74 GLU cc_start: 0.6571 (pp20) cc_final: 0.6249 (pt0) REVERT: D 208 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: D 401 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7734 (t-90) REVERT: D 465 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7912 (ttp80) REVERT: D 472 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7592 (mt-10) outliers start: 22 outliers final: 12 residues processed: 95 average time/residue: 1.2081 time to fit residues: 121.5688 Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111340 restraints weight = 8366.924| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.50 r_work: 0.3384 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7508 Z= 0.175 Angle : 0.522 9.519 10191 Z= 0.263 Chirality : 0.041 0.249 1088 Planarity : 0.004 0.039 1304 Dihedral : 5.964 55.981 1140 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.04 % Allowed : 12.29 % Favored : 84.66 % 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: -0.20 (0.29), residues: 876 helix: 0.67 (0.27), residues: 413 sheet: 0.85 (0.66), residues: 52 loop : -1.09 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 241 PHE 0.014 0.001 PHE D 523 TYR 0.012 0.001 TYR D 516 ARG 0.006 0.000 ARG D 621 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 27 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.6531 (mp) REVERT: D 49 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5874 (tm-30) REVERT: D 62 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6325 (mpp) REVERT: D 64 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5984 (mp0) REVERT: D 74 GLU cc_start: 0.6590 (pp20) cc_final: 0.6254 (pt0) REVERT: D 140 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: D 208 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: D 465 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7875 (ttp80) REVERT: D 472 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7566 (mt-10) outliers start: 24 outliers final: 12 residues processed: 99 average time/residue: 1.1718 time to fit residues: 122.8231 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 208 GLU Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 637 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 69.6118 > 50: distance: 72 - 74: 20.388 distance: 73 - 94: 25.431 distance: 74 - 75: 7.244 distance: 75 - 76: 20.007 distance: 75 - 78: 30.336 distance: 76 - 77: 26.528 distance: 76 - 81: 30.395 distance: 77 - 102: 25.769 distance: 78 - 79: 25.671 distance: 78 - 80: 19.736 distance: 81 - 82: 6.008 distance: 82 - 83: 28.787 distance: 82 - 85: 28.728 distance: 83 - 84: 19.201 distance: 83 - 89: 25.426 distance: 84 - 114: 47.001 distance: 85 - 86: 21.611 distance: 85 - 87: 20.290 distance: 86 - 88: 19.116 distance: 89 - 90: 31.153 distance: 90 - 91: 18.573 distance: 90 - 93: 23.574 distance: 91 - 92: 19.415 distance: 91 - 94: 31.727 distance: 94 - 95: 11.778 distance: 95 - 96: 31.354 distance: 95 - 98: 32.715 distance: 96 - 97: 30.324 distance: 96 - 102: 30.868 distance: 98 - 99: 40.929 distance: 99 - 100: 55.933 distance: 99 - 101: 50.639 distance: 102 - 103: 7.810 distance: 103 - 104: 13.272 distance: 103 - 106: 27.237 distance: 104 - 105: 38.224 distance: 104 - 114: 27.234 distance: 106 - 107: 22.314 distance: 107 - 108: 17.322 distance: 107 - 109: 17.382 distance: 108 - 110: 13.352 distance: 109 - 111: 23.586 distance: 110 - 112: 20.558 distance: 111 - 112: 20.312 distance: 112 - 113: 11.007 distance: 114 - 115: 46.785 distance: 115 - 116: 56.005 distance: 115 - 118: 40.336 distance: 116 - 117: 26.535 distance: 116 - 122: 41.050 distance: 118 - 119: 46.111 distance: 119 - 120: 69.612 distance: 119 - 121: 57.309 distance: 122 - 123: 37.295 distance: 123 - 124: 13.009 distance: 123 - 126: 29.565 distance: 124 - 125: 21.062 distance: 124 - 134: 35.685 distance: 126 - 127: 28.327 distance: 127 - 128: 18.089 distance: 127 - 129: 17.814 distance: 128 - 130: 13.798 distance: 129 - 131: 19.961 distance: 130 - 132: 10.229 distance: 131 - 132: 11.984 distance: 132 - 133: 11.426 distance: 134 - 135: 29.488 distance: 135 - 136: 40.578 distance: 135 - 138: 44.607 distance: 136 - 143: 53.672 distance: 138 - 139: 55.088 distance: 139 - 140: 20.247 distance: 140 - 141: 46.874 distance: 141 - 142: 21.727 distance: 143 - 144: 39.284 distance: 144 - 145: 19.760 distance: 144 - 147: 56.335 distance: 145 - 146: 38.698 distance: 145 - 151: 6.930 distance: 147 - 148: 52.706 distance: 148 - 149: 10.688 distance: 148 - 150: 19.122 distance: 151 - 152: 36.563 distance: 151 - 157: 21.956 distance: 152 - 153: 39.067 distance: 152 - 155: 21.570 distance: 153 - 154: 39.254 distance: 153 - 158: 31.182 distance: 155 - 156: 16.097 distance: 156 - 157: 41.453