Starting phenix.real_space_refine on Fri Dec 27 20:04:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdh_31543/12_2024/7fdh_31543.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 4150 2.51 5 N 1069 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6488 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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 Time building chain proxies: 6.67, per 1000 atoms: 1.03 Number of scatterers: 6488 At special positions: 0 Unit cell: (122.72, 78, 76.96, 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 1232 8.00 N 1069 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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 NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 704 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 1.3 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 57.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.872A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.565A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.609A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.560A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.779A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.812A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.756A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.588A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.974A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.846A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.962A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.211A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.963A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.970A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.808A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.955A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.531A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 Processing helix chain 'E' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.960A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.692A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 320 hydrogen bonds defined for protein. 893 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: 1.81 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2079 1.35 - 1.47: 1767 1.47 - 1.59: 2768 1.59 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6672 Sorted by residual: bond pdb=" C1 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" C5 NAG E 601 " pdb=" O5 NAG E 601 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 6667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8902 2.20 - 4.39: 150 4.39 - 6.59: 15 6.59 - 8.79: 3 8.79 - 10.98: 1 Bond angle restraints: 9071 Sorted by residual: angle pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " ideal model delta sigma weight residual 114.40 125.38 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" N CYS A 141 " pdb=" CA CYS A 141 " pdb=" C CYS A 141 " ideal model delta sigma weight residual 108.96 115.21 -6.25 1.49e+00 4.50e-01 1.76e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 108.60 114.00 -5.40 1.46e+00 4.69e-01 1.37e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 121.73 -7.33 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA CYS A 133 " pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " ideal model delta sigma weight residual 114.40 121.68 -7.28 2.30e+00 1.89e-01 1.00e+01 ... (remaining 9066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3552 17.59 - 35.19: 350 35.19 - 52.78: 73 52.78 - 70.37: 12 70.37 - 87.96: 10 Dihedral angle restraints: 3997 sinusoidal: 1672 harmonic: 2325 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 11.10 81.90 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 51.66 41.34 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 862 0.078 - 0.156: 97 0.156 - 0.234: 1 0.234 - 0.312: 1 0.312 - 0.390: 1 Chirality restraints: 962 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA CYS A 141 " pdb=" N CYS A 141 " pdb=" C CYS A 141 " pdb=" CB CYS A 141 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASN E 343 " pdb=" N ASN E 343 " pdb=" C ASN E 343 " pdb=" CB ASN E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 959 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO A 146 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 33 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.07e+00 pdb=" C ASN A 33 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN A 33 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS A 34 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO A 583 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.024 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 196 2.70 - 3.25: 6959 3.25 - 3.80: 10455 3.80 - 4.35: 13483 4.35 - 4.90: 22150 Nonbonded interactions: 53243 Sorted by model distance: nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.145 3.040 nonbonded pdb=" O VAL E 367 " pdb=" OG SER E 371 " model vdw 2.147 3.040 nonbonded pdb=" NE2 GLN A 221 " pdb=" OD1 ASP A 225 " model vdw 2.213 3.120 nonbonded pdb=" OG SER A 511 " pdb=" NH2 ARG A 514 " model vdw 2.224 3.120 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.236 3.040 ... (remaining 53238 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.032 6672 Z= 0.273 Angle : 0.735 10.983 9071 Z= 0.425 Chirality : 0.048 0.390 962 Planarity : 0.005 0.051 1170 Dihedral : 14.493 87.964 2486 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.29 % Allowed : 2.88 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.25), residues: 788 helix: -1.53 (0.22), residues: 377 sheet: -0.84 (0.69), residues: 50 loop : -2.49 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 473 HIS 0.004 0.001 HIS A 540 PHE 0.015 0.002 PHE A 314 TYR 0.021 0.002 TYR E 453 ARG 0.003 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (t0) REVERT: A 98 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7859 (tp-100) REVERT: A 123 MET cc_start: 0.7787 (mtm) cc_final: 0.7464 (mtt) REVERT: A 165 TRP cc_start: 0.7254 (t60) cc_final: 0.5965 (t60) REVERT: A 455 MET cc_start: 0.8600 (tmm) cc_final: 0.8285 (tmm) REVERT: A 478 TRP cc_start: 0.7962 (m100) cc_final: 0.7587 (m100) REVERT: A 497 TYR cc_start: 0.7564 (m-80) cc_final: 0.6574 (m-80) REVERT: A 505 HIS cc_start: 0.7573 (m90) cc_final: 0.7157 (m-70) REVERT: E 366 SER cc_start: 0.8329 (m) cc_final: 0.8047 (p) REVERT: E 396 TYR cc_start: 0.7613 (m-80) cc_final: 0.6939 (m-10) outliers start: 1 outliers final: 1 residues processed: 125 average time/residue: 0.2154 time to fit residues: 34.7064 Evaluate side-chains 84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 221 GLN A 239 HIS A 290 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN E 334 ASN E 388 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6672 Z= 0.215 Angle : 0.650 9.405 9071 Z= 0.331 Chirality : 0.046 0.312 962 Planarity : 0.005 0.063 1170 Dihedral : 5.393 33.884 968 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.29 % Allowed : 11.22 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.82 (0.28), residues: 788 helix: 0.16 (0.25), residues: 386 sheet: -0.27 (0.72), residues: 51 loop : -1.34 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 473 HIS 0.003 0.001 HIS A 401 PHE 0.013 0.001 PHE E 392 TYR 0.020 0.002 TYR A 183 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.7870 (mtm) cc_final: 0.7502 (mtt) REVERT: A 165 TRP cc_start: 0.7166 (t60) cc_final: 0.6396 (t60) REVERT: A 222 LEU cc_start: 0.8610 (tp) cc_final: 0.8379 (tp) REVERT: A 455 MET cc_start: 0.8490 (tmm) cc_final: 0.8192 (tmm) REVERT: A 497 TYR cc_start: 0.7802 (m-80) cc_final: 0.6673 (m-80) REVERT: A 505 HIS cc_start: 0.7343 (m90) cc_final: 0.6992 (m-70) REVERT: A 557 MET cc_start: 0.9172 (tmm) cc_final: 0.8768 (tmm) REVERT: E 340 GLU cc_start: 0.7582 (pt0) cc_final: 0.7284 (mm-30) REVERT: E 392 PHE cc_start: 0.8489 (m-80) cc_final: 0.8223 (m-10) REVERT: E 507 PRO cc_start: 0.9343 (Cg_exo) cc_final: 0.9135 (Cg_endo) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.2432 time to fit residues: 36.6682 Evaluate side-chains 89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN A 599 ASN E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6672 Z= 0.198 Angle : 0.622 8.948 9071 Z= 0.317 Chirality : 0.044 0.247 962 Planarity : 0.005 0.042 1170 Dihedral : 4.943 30.244 967 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.29 % Allowed : 12.95 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.09 (0.29), residues: 788 helix: 0.72 (0.26), residues: 390 sheet: 0.08 (0.72), residues: 51 loop : -0.93 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 168 HIS 0.003 0.001 HIS A 505 PHE 0.010 0.001 PHE A 230 TYR 0.019 0.002 TYR A 183 ARG 0.004 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TRP cc_start: 0.7165 (t60) cc_final: 0.6601 (t60) REVERT: A 222 LEU cc_start: 0.8647 (tp) cc_final: 0.8436 (tp) REVERT: A 455 MET cc_start: 0.8456 (tmm) cc_final: 0.8153 (tmm) REVERT: A 481 LYS cc_start: 0.7666 (mttt) cc_final: 0.7344 (mttt) REVERT: A 497 TYR cc_start: 0.7781 (m-80) cc_final: 0.6642 (m-80) REVERT: A 505 HIS cc_start: 0.7355 (m90) cc_final: 0.6987 (m-70) REVERT: A 557 MET cc_start: 0.9158 (tmm) cc_final: 0.8750 (tmm) REVERT: E 340 GLU cc_start: 0.7561 (pt0) cc_final: 0.7311 (mm-30) REVERT: E 392 PHE cc_start: 0.8496 (m-80) cc_final: 0.8212 (m-10) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.2128 time to fit residues: 28.4883 Evaluate side-chains 91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6672 Z= 0.195 Angle : 0.628 11.066 9071 Z= 0.310 Chirality : 0.044 0.233 962 Planarity : 0.004 0.037 1170 Dihedral : 4.758 27.146 967 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 13.67 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.30 (0.30), residues: 788 helix: 1.04 (0.26), residues: 387 sheet: 0.21 (0.71), residues: 51 loop : -0.70 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 478 HIS 0.002 0.001 HIS A 505 PHE 0.016 0.001 PHE A 603 TYR 0.019 0.002 TYR A 183 ARG 0.004 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TRP cc_start: 0.7075 (t60) cc_final: 0.5996 (t60) REVERT: A 222 LEU cc_start: 0.8588 (tp) cc_final: 0.8385 (tp) REVERT: A 455 MET cc_start: 0.8400 (tmm) cc_final: 0.8143 (tmm) REVERT: A 481 LYS cc_start: 0.7496 (mttt) cc_final: 0.7236 (mttt) REVERT: A 505 HIS cc_start: 0.7289 (m90) cc_final: 0.6886 (m-70) REVERT: A 557 MET cc_start: 0.9147 (tmm) cc_final: 0.8702 (tmm) REVERT: E 340 GLU cc_start: 0.7563 (pt0) cc_final: 0.7260 (mm-30) outliers start: 11 outliers final: 11 residues processed: 99 average time/residue: 0.2100 time to fit residues: 27.9307 Evaluate side-chains 93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 64 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 8.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6672 Z= 0.155 Angle : 0.605 10.083 9071 Z= 0.300 Chirality : 0.042 0.223 962 Planarity : 0.004 0.037 1170 Dihedral : 4.369 22.660 967 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.73 % Allowed : 15.40 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.66 (0.30), residues: 788 helix: 1.30 (0.27), residues: 380 sheet: 0.46 (0.72), residues: 50 loop : -0.47 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 478 HIS 0.002 0.001 HIS A 505 PHE 0.012 0.001 PHE A 603 TYR 0.019 0.001 TYR A 183 ARG 0.006 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 TRP cc_start: 0.7064 (t60) cc_final: 0.6090 (t60) REVERT: A 249 MET cc_start: 0.7827 (mmm) cc_final: 0.7612 (mmm) REVERT: A 350 ASP cc_start: 0.7433 (t0) cc_final: 0.7169 (t0) REVERT: A 455 MET cc_start: 0.8256 (tmm) cc_final: 0.7957 (tmm) REVERT: A 481 LYS cc_start: 0.7130 (mttt) cc_final: 0.6917 (mttt) REVERT: A 505 HIS cc_start: 0.7335 (m90) cc_final: 0.6960 (m-70) REVERT: E 340 GLU cc_start: 0.7424 (pt0) cc_final: 0.7121 (mm-30) REVERT: E 392 PHE cc_start: 0.8215 (m-10) cc_final: 0.7981 (m-10) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.2058 time to fit residues: 29.6090 Evaluate side-chains 98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6672 Z= 0.194 Angle : 0.614 9.417 9071 Z= 0.305 Chirality : 0.043 0.227 962 Planarity : 0.004 0.038 1170 Dihedral : 4.367 23.405 967 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.30 % Allowed : 15.83 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.72 (0.30), residues: 788 helix: 1.25 (0.26), residues: 385 sheet: 0.65 (0.72), residues: 50 loop : -0.34 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.001 PHE A 504 TYR 0.018 0.001 TYR A 183 ARG 0.006 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8280 (tmm) cc_final: 0.7972 (tmm) REVERT: A 481 LYS cc_start: 0.7179 (mttt) cc_final: 0.6950 (mttt) REVERT: A 505 HIS cc_start: 0.7363 (m90) cc_final: 0.7003 (m-70) REVERT: A 557 MET cc_start: 0.9069 (tmm) cc_final: 0.8645 (tmm) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.1971 time to fit residues: 28.3142 Evaluate side-chains 102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6672 Z= 0.199 Angle : 0.635 9.566 9071 Z= 0.315 Chirality : 0.043 0.226 962 Planarity : 0.005 0.069 1170 Dihedral : 4.379 21.706 967 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 17.55 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.76 (0.30), residues: 788 helix: 1.13 (0.26), residues: 386 sheet: 0.69 (0.72), residues: 50 loop : -0.14 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 PHE 0.019 0.001 PHE A 603 TYR 0.018 0.001 TYR A 183 ARG 0.012 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8244 (tmm) cc_final: 0.7833 (tmm) REVERT: A 481 LYS cc_start: 0.7254 (mttt) cc_final: 0.6994 (mttt) REVERT: A 505 HIS cc_start: 0.7337 (m90) cc_final: 0.6982 (m-70) outliers start: 15 outliers final: 14 residues processed: 105 average time/residue: 0.1988 time to fit residues: 27.8166 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN E 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6672 Z= 0.406 Angle : 0.783 13.284 9071 Z= 0.395 Chirality : 0.051 0.346 962 Planarity : 0.005 0.077 1170 Dihedral : 5.315 26.827 967 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.02 % Allowed : 17.70 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.24 (0.30), residues: 788 helix: 0.70 (0.26), residues: 390 sheet: 0.10 (0.72), residues: 50 loop : -0.34 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 477 HIS 0.003 0.001 HIS A 34 PHE 0.017 0.002 PHE E 392 TYR 0.029 0.002 TYR E 453 ARG 0.007 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8313 (tmm) cc_final: 0.8020 (tmm) REVERT: A 497 TYR cc_start: 0.7971 (m-80) cc_final: 0.6691 (m-80) REVERT: A 503 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 505 HIS cc_start: 0.7408 (m90) cc_final: 0.7056 (m-70) REVERT: A 557 MET cc_start: 0.9123 (tmm) cc_final: 0.8708 (tmm) outliers start: 20 outliers final: 14 residues processed: 103 average time/residue: 0.1965 time to fit residues: 26.6717 Evaluate side-chains 100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6672 Z= 0.193 Angle : 0.690 12.638 9071 Z= 0.341 Chirality : 0.044 0.231 962 Planarity : 0.004 0.046 1170 Dihedral : 4.696 24.484 967 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.01 % Allowed : 18.85 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.63 (0.30), residues: 788 helix: 1.01 (0.26), residues: 388 sheet: 0.34 (0.70), residues: 49 loop : -0.13 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.026 0.002 PHE A 603 TYR 0.018 0.001 TYR A 183 ARG 0.006 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7950 (tpp) cc_final: 0.7516 (tpt) REVERT: A 161 ARG cc_start: 0.6983 (mtp85) cc_final: 0.6670 (mtp85) REVERT: A 503 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7740 (mm) REVERT: A 505 HIS cc_start: 0.7368 (m90) cc_final: 0.6999 (m-70) REVERT: A 557 MET cc_start: 0.8974 (tmm) cc_final: 0.8587 (tmm) REVERT: E 469 SER cc_start: 0.8903 (t) cc_final: 0.8636 (p) outliers start: 13 outliers final: 10 residues processed: 102 average time/residue: 0.2185 time to fit residues: 29.0432 Evaluate side-chains 99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 0.0670 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6672 Z= 0.197 Angle : 0.693 12.196 9071 Z= 0.343 Chirality : 0.044 0.211 962 Planarity : 0.004 0.048 1170 Dihedral : 4.616 24.322 967 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.01 % Allowed : 18.99 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.71 (0.31), residues: 788 helix: 1.07 (0.27), residues: 388 sheet: 0.36 (0.70), residues: 49 loop : -0.07 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 477 HIS 0.003 0.001 HIS A 374 PHE 0.026 0.001 PHE A 603 TYR 0.018 0.001 TYR A 183 ARG 0.008 0.001 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7942 (tpp) cc_final: 0.7330 (tpt) REVERT: A 497 TYR cc_start: 0.7579 (m-80) cc_final: 0.6267 (m-80) REVERT: A 498 CYS cc_start: 0.7094 (p) cc_final: 0.6791 (t) REVERT: A 503 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7681 (mm) REVERT: A 505 HIS cc_start: 0.7403 (m90) cc_final: 0.7067 (m-70) REVERT: A 572 ASN cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (m-40) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.2040 time to fit residues: 27.6899 Evaluate side-chains 101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 440 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 GLN ** 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 = 0.3742 r_free = 0.3742 target = 0.110354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.085056 restraints weight = 19691.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088066 restraints weight = 9606.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089754 restraints weight = 5453.610| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6672 Z= 0.225 Angle : 0.694 11.969 9071 Z= 0.344 Chirality : 0.044 0.207 962 Planarity : 0.005 0.054 1170 Dihedral : 4.595 24.824 967 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 19.71 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.72 (0.31), residues: 788 helix: 1.08 (0.27), residues: 387 sheet: 0.18 (0.69), residues: 49 loop : -0.03 (0.36), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 478 HIS 0.003 0.001 HIS A 505 PHE 0.024 0.002 PHE A 603 TYR 0.017 0.001 TYR A 183 ARG 0.008 0.001 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.59 seconds wall clock time: 31 minutes 32.77 seconds (1892.77 seconds total)