Starting phenix.real_space_refine on Fri Dec 27 11:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqs_25392/12_2024/7sqs_25392.cif" } resolution = 3.1 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= 0.010 sd= 0.044 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 14 5.16 5 C 2730 2.51 5 N 789 2.21 5 O 843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4376 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3970 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 23, 'TRANS': 484} Chain breaks: 1 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 83 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 163 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Time building chain proxies: 3.49, per 1000 atoms: 0.80 Number of scatterers: 4376 At special positions: 0 Unit cell: (78.4536, 68.9851, 86.5695, 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 14 16.00 O 843 8.00 N 789 7.00 C 2730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 597.2 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1032 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 5 sheets defined 40.4% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.770A pdb=" N VAL A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 202 through 226 Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.021A pdb=" N LYS A 236 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.660A pdb=" N TYR A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 360 through 367 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 378 through 386 removed outlier: 3.971A pdb=" N ALA A 381 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.699A pdb=" N GLY A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.704A pdb=" N LEU A 434 " --> pdb=" O GLN A 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.620A pdb=" N ARG A 465 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 removed outlier: 3.855A pdb=" N GLN A 472 " --> pdb=" O HIS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.720A pdb=" N GLN A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 560 through 574 removed outlier: 3.568A pdb=" N ILE A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 565 " --> pdb=" O ALA A 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.676A pdb=" N ASN B 601 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AA4, first strand: chain 'A' and resid 493 through 495 removed outlier: 5.949A pdb=" N GLU A 476 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR A 559 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 478 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N CYS A 557 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLN A 480 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU A 555 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 482 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS A 553 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 484 " --> pdb=" O THR A 551 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE A 418 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 331 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA A 294 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 332 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN A 292 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 291 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 270 " --> pdb=" O ASN A 291 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 243 " --> pdb=" O THR A 579 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 255 195 hydrogen bonds defined for protein. 501 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: 1.14 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1527 1.34 - 1.46: 761 1.46 - 1.57: 2141 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4455 Sorted by residual: bond pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 9.81e-01 bond pdb=" N GLN A 238 " pdb=" CA GLN A 238 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.47e-01 bond pdb=" CB GLN A 278 " pdb=" CG GLN A 278 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.27e-01 bond pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.10e-02 2.27e+03 8.14e-01 bond pdb=" N TYR A 543 " pdb=" CA TYR A 543 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.22e-02 6.72e+03 6.59e-01 ... (remaining 4450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 5902 1.25 - 2.50: 93 2.50 - 3.75: 33 3.75 - 5.01: 6 5.01 - 6.26: 2 Bond angle restraints: 6036 Sorted by residual: angle pdb=" N ASP A 375 " pdb=" CA ASP A 375 " pdb=" C ASP A 375 " ideal model delta sigma weight residual 113.56 109.64 3.92 1.39e+00 5.18e-01 7.94e+00 angle pdb=" CA GLN A 278 " pdb=" CB GLN A 278 " pdb=" CG GLN A 278 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.41e+00 angle pdb=" C THR A 286 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " ideal model delta sigma weight residual 122.46 125.41 -2.95 1.41e+00 5.03e-01 4.38e+00 angle pdb=" C GLN A 278 " pdb=" CA GLN A 278 " pdb=" CB GLN A 278 " ideal model delta sigma weight residual 111.91 114.82 -2.91 1.52e+00 4.33e-01 3.67e+00 angle pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " pdb=" CG ASP A 287 " ideal model delta sigma weight residual 112.60 114.50 -1.90 1.00e+00 1.00e+00 3.62e+00 ... (remaining 6031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 2405 17.07 - 34.14: 223 34.14 - 51.20: 34 51.20 - 68.27: 6 68.27 - 85.34: 6 Dihedral angle restraints: 2674 sinusoidal: 1075 harmonic: 1599 Sorted by residual: dihedral pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " ideal model delta sinusoidal sigma weight residual -60.00 -111.92 51.92 3 1.50e+01 4.44e-03 9.06e+00 dihedral pdb=" CA MET A 385 " pdb=" CB MET A 385 " pdb=" CG MET A 385 " pdb=" SD MET A 385 " ideal model delta sinusoidal sigma weight residual 180.00 135.38 44.62 3 1.50e+01 4.44e-03 8.03e+00 dihedral pdb=" CB ARG A 497 " pdb=" CG ARG A 497 " pdb=" CD ARG A 497 " pdb=" NE ARG A 497 " ideal model delta sinusoidal sigma weight residual -60.00 -101.07 41.07 3 1.50e+01 4.44e-03 7.34e+00 ... (remaining 2671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 415 0.028 - 0.055: 154 0.055 - 0.083: 41 0.083 - 0.111: 40 0.111 - 0.138: 12 Chirality restraints: 662 Sorted by residual: chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 193 " pdb=" N ILE A 193 " pdb=" C ILE A 193 " pdb=" CB ILE A 193 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 659 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 320 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 528 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.67e-01 pdb=" N PRO A 529 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 529 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 529 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 287 " 0.005 2.00e-02 2.50e+03 9.39e-03 8.82e-01 pdb=" C ASP A 287 " -0.016 2.00e-02 2.50e+03 pdb=" O ASP A 287 " 0.006 2.00e-02 2.50e+03 pdb=" N VAL A 288 " 0.005 2.00e-02 2.50e+03 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1388 2.83 - 3.35: 3878 3.35 - 3.87: 6531 3.87 - 4.38: 7051 4.38 - 4.90: 13013 Nonbonded interactions: 31861 Sorted by model distance: nonbonded pdb=" O TRP A 384 " pdb=" NH2 ARG A 389 " model vdw 2.317 3.120 nonbonded pdb=" O ASN A 524 " pdb=" NH1 ARG A 532 " model vdw 2.324 3.120 nonbonded pdb=" OE2 GLU A 514 " pdb=" OH TYR A 543 " model vdw 2.335 3.040 nonbonded pdb=" NE2 GLN A 175 " pdb=" O ALA A 183 " model vdw 2.353 3.120 nonbonded pdb=" OD1 ASP A 219 " pdb=" NE ARG E 56 " model vdw 2.375 3.120 ... (remaining 31856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.002 0.029 4455 Z= 0.128 Angle : 0.469 6.258 6036 Z= 0.259 Chirality : 0.040 0.138 662 Planarity : 0.003 0.050 813 Dihedral : 13.610 85.335 1642 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.22 % Allowed : 0.22 % Favored : 99.57 % 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: 1.01 (0.38), residues: 548 helix: 2.17 (0.40), residues: 185 sheet: 0.50 (0.47), residues: 130 loop : -0.42 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 105 HIS 0.001 0.000 HIS A 101 PHE 0.004 0.001 PHE A 399 TYR 0.004 0.001 TYR A 166 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.541 Fit side-chains REVERT: A 388 LEU cc_start: 0.8923 (pt) cc_final: 0.8640 (mm) REVERT: A 491 ASP cc_start: 0.8299 (t0) cc_final: 0.8056 (t0) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1678 time to fit residues: 11.7673 Evaluate side-chains 43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4455 Z= 0.255 Angle : 0.519 8.086 6036 Z= 0.278 Chirality : 0.043 0.154 662 Planarity : 0.004 0.046 813 Dihedral : 3.615 14.019 602 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.86 % Allowed : 4.31 % Favored : 94.83 % 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: 0.86 (0.37), residues: 548 helix: 2.11 (0.39), residues: 190 sheet: 0.21 (0.46), residues: 129 loop : -0.48 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 323 HIS 0.002 0.001 HIS A 224 PHE 0.023 0.002 PHE A 283 TYR 0.010 0.001 TYR A 570 ARG 0.002 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.496 Fit side-chains REVERT: A 248 ASP cc_start: 0.8477 (t0) cc_final: 0.8175 (t0) REVERT: A 491 ASP cc_start: 0.8366 (t0) cc_final: 0.8159 (t0) outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.1389 time to fit residues: 9.6698 Evaluate side-chains 46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4455 Z= 0.170 Angle : 0.481 7.438 6036 Z= 0.252 Chirality : 0.042 0.150 662 Planarity : 0.003 0.043 813 Dihedral : 3.457 12.818 602 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.08 % Allowed : 6.68 % Favored : 92.24 % 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: 0.90 (0.38), residues: 548 helix: 2.20 (0.40), residues: 191 sheet: 0.13 (0.46), residues: 129 loop : -0.47 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.011 0.001 PHE A 296 TYR 0.006 0.001 TYR A 570 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.473 Fit side-chains REVERT: A 248 ASP cc_start: 0.8484 (t0) cc_final: 0.8168 (t0) outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1300 time to fit residues: 8.1408 Evaluate side-chains 43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4455 Z= 0.203 Angle : 0.483 6.096 6036 Z= 0.254 Chirality : 0.042 0.152 662 Planarity : 0.003 0.040 813 Dihedral : 3.527 13.223 602 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.29 % Allowed : 7.54 % Favored : 91.16 % 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: 0.86 (0.37), residues: 548 helix: 2.18 (0.40), residues: 189 sheet: 0.13 (0.47), residues: 126 loop : -0.48 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.001 0.001 HIS A 224 PHE 0.018 0.001 PHE A 283 TYR 0.006 0.001 TYR A 519 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.542 Fit side-chains REVERT: A 248 ASP cc_start: 0.8487 (t0) cc_final: 0.8164 (t0) outliers start: 6 outliers final: 5 residues processed: 44 average time/residue: 0.1357 time to fit residues: 8.5084 Evaluate side-chains 46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4455 Z= 0.212 Angle : 0.486 6.401 6036 Z= 0.255 Chirality : 0.042 0.152 662 Planarity : 0.003 0.037 813 Dihedral : 3.576 13.449 602 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.72 % Allowed : 7.97 % Favored : 90.30 % 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: 0.86 (0.37), residues: 548 helix: 2.21 (0.40), residues: 187 sheet: 0.18 (0.47), residues: 126 loop : -0.52 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.002 0.001 HIS A 224 PHE 0.009 0.001 PHE A 399 TYR 0.007 0.001 TYR A 570 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.572 Fit side-chains REVERT: A 248 ASP cc_start: 0.8489 (t0) cc_final: 0.8177 (t0) REVERT: A 283 PHE cc_start: 0.7999 (m-80) cc_final: 0.7768 (m-80) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.1656 time to fit residues: 10.0590 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4455 Z= 0.173 Angle : 0.477 6.744 6036 Z= 0.248 Chirality : 0.042 0.150 662 Planarity : 0.003 0.036 813 Dihedral : 3.464 13.161 602 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.94 % Allowed : 7.97 % Favored : 90.09 % 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: 0.95 (0.38), residues: 548 helix: 2.25 (0.40), residues: 188 sheet: 0.26 (0.47), residues: 126 loop : -0.48 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.010 0.001 PHE A 296 TYR 0.006 0.001 TYR A 570 ARG 0.002 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.521 Fit side-chains REVERT: A 248 ASP cc_start: 0.8479 (t0) cc_final: 0.8170 (t0) REVERT: A 283 PHE cc_start: 0.8019 (m-80) cc_final: 0.7782 (m-80) outliers start: 9 outliers final: 8 residues processed: 46 average time/residue: 0.1439 time to fit residues: 9.0983 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0060 chunk 24 optimal weight: 0.1980 chunk 20 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4455 Z= 0.130 Angle : 0.465 6.434 6036 Z= 0.238 Chirality : 0.041 0.146 662 Planarity : 0.003 0.034 813 Dihedral : 3.166 12.359 602 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.29 % Allowed : 9.91 % Favored : 88.79 % 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: 1.12 (0.38), residues: 548 helix: 2.41 (0.40), residues: 188 sheet: 0.37 (0.47), residues: 126 loop : -0.41 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 105 HIS 0.002 0.000 HIS A 358 PHE 0.010 0.001 PHE A 296 TYR 0.005 0.000 TYR A 570 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.527 Fit side-chains REVERT: A 283 PHE cc_start: 0.7944 (m-80) cc_final: 0.7711 (m-80) outliers start: 6 outliers final: 6 residues processed: 43 average time/residue: 0.1333 time to fit residues: 8.0942 Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4455 Z= 0.216 Angle : 0.489 6.320 6036 Z= 0.253 Chirality : 0.042 0.149 662 Planarity : 0.003 0.034 813 Dihedral : 3.412 12.464 602 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.29 % Allowed : 9.91 % Favored : 88.79 % 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: 1.00 (0.37), residues: 548 helix: 2.31 (0.41), residues: 187 sheet: 0.33 (0.47), residues: 126 loop : -0.48 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 487 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.013 0.001 TYR A 166 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.519 Fit side-chains REVERT: A 248 ASP cc_start: 0.8455 (t0) cc_final: 0.8140 (t0) REVERT: A 283 PHE cc_start: 0.7974 (m-80) cc_final: 0.7736 (m-80) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.1338 time to fit residues: 8.6433 Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 547 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4455 Z= 0.139 Angle : 0.463 6.191 6036 Z= 0.238 Chirality : 0.041 0.148 662 Planarity : 0.003 0.033 813 Dihedral : 3.230 12.000 602 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.51 % Allowed : 9.70 % Favored : 88.79 % 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: 1.06 (0.38), residues: 548 helix: 2.37 (0.40), residues: 188 sheet: 0.35 (0.47), residues: 126 loop : -0.45 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.002 0.000 HIS A 358 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR A 570 ARG 0.001 0.000 ARG A 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.536 Fit side-chains REVERT: A 248 ASP cc_start: 0.8442 (t0) cc_final: 0.8134 (t0) REVERT: A 283 PHE cc_start: 0.7984 (m-80) cc_final: 0.7739 (m-80) outliers start: 7 outliers final: 7 residues processed: 46 average time/residue: 0.1376 time to fit residues: 9.0853 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 547 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.0870 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4455 Z= 0.165 Angle : 0.507 11.298 6036 Z= 0.265 Chirality : 0.042 0.147 662 Planarity : 0.003 0.033 813 Dihedral : 3.263 12.102 602 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.94 % Allowed : 9.05 % Favored : 89.01 % 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: 1.02 (0.37), residues: 548 helix: 2.30 (0.40), residues: 188 sheet: 0.35 (0.47), residues: 126 loop : -0.46 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 105 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR A 570 ARG 0.002 0.000 ARG A 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.533 Fit side-chains REVERT: A 248 ASP cc_start: 0.8444 (t0) cc_final: 0.8131 (t0) REVERT: A 283 PHE cc_start: 0.7922 (m-80) cc_final: 0.7674 (m-80) REVERT: A 408 MET cc_start: 0.8310 (tpp) cc_final: 0.8093 (tpp) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.1330 time to fit residues: 8.8390 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 604 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.084768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.070511 restraints weight = 10263.532| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.33 r_work: 0.2949 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4455 Z= 0.154 Angle : 0.493 10.371 6036 Z= 0.255 Chirality : 0.041 0.147 662 Planarity : 0.003 0.033 813 Dihedral : 3.231 12.071 602 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.51 % Allowed : 9.27 % Favored : 89.22 % 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: 1.05 (0.37), residues: 548 helix: 2.33 (0.40), residues: 188 sheet: 0.36 (0.47), residues: 126 loop : -0.44 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 105 HIS 0.001 0.000 HIS A 358 PHE 0.009 0.001 PHE A 296 TYR 0.005 0.001 TYR A 570 ARG 0.002 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.55 seconds wall clock time: 24 minutes 41.85 seconds (1481.85 seconds total)