Starting phenix.real_space_refine on Fri Dec 27 12:11:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.cif Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.map" model { file = "/net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/12_2024/7the_25893.cif" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2098 2.51 5 N 549 2.21 5 O 641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "B" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "C" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.27, per 1000 atoms: 0.99 Number of scatterers: 3305 At special positions: 0 Unit cell: (65.596, 81.466, 87.814, 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 17 16.00 O 641 8.00 N 549 7.00 C 2098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " 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 601 " - " ASN A 343 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 372.3 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 12.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.981A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.706A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.854A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335 removed outlier: 7.513A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.975A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 34 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.378A pdb=" N GLU B 10 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 102 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.730A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 109 hydrogen bonds defined for protein. 252 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: 0.89 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 928 1.33 - 1.45: 657 1.45 - 1.57: 1781 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3388 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.482 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" CZ ARG B 94 " pdb=" NH2 ARG B 94 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 3383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3171 1.82 - 3.63: 1161 3.63 - 5.45: 247 5.45 - 7.26: 22 7.26 - 9.08: 4 Bond angle restraints: 4605 Sorted by residual: angle pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " pdb=" CG PHE A 347 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" N CYS A 361 " pdb=" CA CYS A 361 " pdb=" C CYS A 361 " ideal model delta sigma weight residual 108.79 117.19 -8.40 1.53e+00 4.27e-01 3.01e+01 angle pdb=" C THR A 393 " pdb=" N ASN A 394 " pdb=" CA ASN A 394 " ideal model delta sigma weight residual 121.75 130.83 -9.08 1.73e+00 3.34e-01 2.75e+01 angle pdb=" CA ASP A 405 " pdb=" CB ASP A 405 " pdb=" CG ASP A 405 " ideal model delta sigma weight residual 112.60 117.25 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA ASP C 70 " pdb=" CB ASP C 70 " pdb=" CG ASP C 70 " ideal model delta sigma weight residual 112.60 117.16 -4.56 1.00e+00 1.00e+00 2.08e+01 ... (remaining 4600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1841 16.95 - 33.89: 139 33.89 - 50.84: 30 50.84 - 67.79: 8 67.79 - 84.73: 4 Dihedral angle restraints: 2022 sinusoidal: 794 harmonic: 1228 Sorted by residual: dihedral pdb=" CA ARG B 83 " pdb=" C ARG B 83 " pdb=" N SER B 84 " pdb=" CA SER B 84 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR B 32 " pdb=" C TYR B 32 " pdb=" N ALA B 33 " pdb=" CA ALA B 33 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N CYS B 92 " pdb=" CA CYS B 92 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 2019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 270 0.076 - 0.152: 164 0.152 - 0.228: 49 0.228 - 0.303: 10 0.303 - 0.379: 6 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA ALA A 520 " pdb=" N ALA A 520 " pdb=" C ALA A 520 " pdb=" CB ALA A 520 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA LEU A 455 " pdb=" N LEU A 455 " pdb=" C LEU A 455 " pdb=" CB LEU A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 496 not shown) Planarity restraints: 595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.113 2.00e-02 2.50e+03 5.99e-02 8.96e+01 pdb=" CG TRP B 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 103 " 0.104 2.00e-02 2.50e+03 5.15e-02 6.64e+01 pdb=" CG TRP B 103 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 103 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP B 103 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 103 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TRP B 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 103 " -0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 103 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 103 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 103 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.102 2.00e-02 2.50e+03 5.49e-02 6.03e+01 pdb=" CG TYR A 351 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " -0.031 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.085 2.00e-02 2.50e+03 ... (remaining 592 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1818 3.02 - 3.49: 3232 3.49 - 3.96: 5382 3.96 - 4.43: 5919 4.43 - 4.90: 9826 Nonbonded interactions: 26177 Sorted by model distance: nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.565 3.040 nonbonded pdb=" OE2 GLU A 484 " pdb=" OH TYR B 95 " model vdw 2.566 3.040 nonbonded pdb=" OH TYR B 100B" pdb=" OD1 ASN C 34 " model vdw 2.569 3.040 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.588 3.040 ... (remaining 26172 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 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.013 0.069 3388 Z= 0.844 Angle : 1.877 9.080 4605 Z= 1.234 Chirality : 0.106 0.379 499 Planarity : 0.015 0.104 594 Dihedral : 13.764 84.731 1226 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.01 (0.39), residues: 417 helix: -4.02 (0.48), residues: 40 sheet: 0.21 (0.50), residues: 117 loop : -1.70 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.029 TRP B 47 HIS 0.007 0.004 HIS A 519 PHE 0.062 0.013 PHE B 54 TYR 0.102 0.022 TYR A 351 ARG 0.015 0.002 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90) REVERT: A 484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7878 (pm20) REVERT: A 493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8364 (tt0) REVERT: A 506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0) REVERT: B 36 TRP cc_start: 0.9068 (m100) cc_final: 0.8253 (m-10) REVERT: B 48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm) REVERT: B 56 ILE cc_start: 0.8594 (mt) cc_final: 0.8365 (tt) REVERT: B 105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0) REVERT: C 34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40) REVERT: C 89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7010 (tm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2165 time to fit residues: 31.9816 Evaluate side-chains 90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 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 501 ASN B 58 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3388 Z= 0.246 Angle : 0.723 6.328 4605 Z= 0.391 Chirality : 0.048 0.166 499 Planarity : 0.005 0.036 594 Dihedral : 7.512 55.944 489 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.05 % Allowed : 12.74 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.50 (0.39), residues: 417 helix: -3.35 (0.68), residues: 35 sheet: 0.09 (0.45), residues: 138 loop : -1.30 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.002 PHE C 98 TYR 0.020 0.002 TYR A 365 ARG 0.005 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7131 (ttp-110) REVERT: A 406 GLU cc_start: 0.8371 (pt0) cc_final: 0.7380 (pt0) REVERT: A 467 ASP cc_start: 0.7553 (t0) cc_final: 0.6332 (p0) REVERT: A 468 ILE cc_start: 0.9127 (pt) cc_final: 0.8894 (pt) REVERT: A 484 GLU cc_start: 0.8194 (pm20) cc_final: 0.7900 (pm20) REVERT: B 12 LYS cc_start: 0.6998 (mttm) cc_final: 0.6792 (mttm) REVERT: B 36 TRP cc_start: 0.9020 (m100) cc_final: 0.8105 (m-10) REVERT: B 48 MET cc_start: 0.8115 (mtp) cc_final: 0.7519 (mtm) REVERT: B 96 MET cc_start: 0.8082 (mtp) cc_final: 0.7792 (mmm) REVERT: B 105 GLN cc_start: 0.8668 (tt0) cc_final: 0.8130 (pt0) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.1798 time to fit residues: 22.2047 Evaluate side-chains 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3388 Z= 0.172 Angle : 0.625 7.185 4605 Z= 0.330 Chirality : 0.044 0.164 499 Planarity : 0.005 0.042 594 Dihedral : 6.685 54.873 489 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.32 % Allowed : 16.07 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.40), residues: 417 helix: -3.05 (0.75), residues: 35 sheet: 0.15 (0.41), residues: 155 loop : -0.93 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.007 0.001 PHE C 62 TYR 0.013 0.001 TYR A 365 ARG 0.006 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7488 (m110) cc_final: 0.7056 (m110) REVERT: A 467 ASP cc_start: 0.7162 (t0) cc_final: 0.6359 (p0) REVERT: A 484 GLU cc_start: 0.8020 (pm20) cc_final: 0.7772 (pm20) REVERT: B 36 TRP cc_start: 0.8947 (m100) cc_final: 0.8108 (m-10) REVERT: B 48 MET cc_start: 0.8156 (mtp) cc_final: 0.7439 (mtm) REVERT: B 61 GLN cc_start: 0.8851 (pm20) cc_final: 0.8336 (pp30) REVERT: B 96 MET cc_start: 0.8184 (mtp) cc_final: 0.7984 (mmm) REVERT: B 105 GLN cc_start: 0.8603 (tt0) cc_final: 0.8152 (pt0) REVERT: C 89 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.1786 time to fit residues: 22.0818 Evaluate side-chains 100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3388 Z= 0.194 Angle : 0.623 6.779 4605 Z= 0.329 Chirality : 0.044 0.156 499 Planarity : 0.005 0.047 594 Dihedral : 6.513 55.414 489 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.88 % Allowed : 17.45 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.83 (0.41), residues: 417 helix: -2.70 (0.74), residues: 41 sheet: 0.21 (0.41), residues: 151 loop : -0.59 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 PHE 0.007 0.001 PHE C 62 TYR 0.018 0.002 TYR A 451 ARG 0.008 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7624 (m110) cc_final: 0.7218 (m110) REVERT: A 406 GLU cc_start: 0.8384 (pt0) cc_final: 0.8158 (pt0) REVERT: A 423 TYR cc_start: 0.7768 (t80) cc_final: 0.7541 (t80) REVERT: A 467 ASP cc_start: 0.7243 (t0) cc_final: 0.6337 (p0) REVERT: B 36 TRP cc_start: 0.8969 (m100) cc_final: 0.8179 (m-10) REVERT: B 48 MET cc_start: 0.8164 (mtp) cc_final: 0.7444 (mtm) REVERT: B 99 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8476 (tmm-80) REVERT: B 105 GLN cc_start: 0.8659 (tt0) cc_final: 0.8157 (pt0) REVERT: C 31 ASN cc_start: 0.7872 (m-40) cc_final: 0.7211 (t0) outliers start: 14 outliers final: 13 residues processed: 100 average time/residue: 0.1934 time to fit residues: 22.7249 Evaluate side-chains 93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3388 Z= 0.196 Angle : 0.623 7.136 4605 Z= 0.325 Chirality : 0.044 0.182 499 Planarity : 0.005 0.048 594 Dihedral : 6.386 55.347 489 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.54 % Allowed : 16.62 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.96 (0.41), residues: 417 helix: -2.59 (0.76), residues: 41 sheet: 0.10 (0.41), residues: 152 loop : -0.70 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.002 0.002 HIS A 519 PHE 0.010 0.001 PHE C 62 TYR 0.012 0.001 TYR A 451 ARG 0.008 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7657 (m110) cc_final: 0.7232 (m110) REVERT: A 406 GLU cc_start: 0.8446 (pt0) cc_final: 0.8120 (pt0) REVERT: A 467 ASP cc_start: 0.7086 (t0) cc_final: 0.6319 (p0) REVERT: B 36 TRP cc_start: 0.9016 (m100) cc_final: 0.8278 (m-10) REVERT: B 48 MET cc_start: 0.8103 (mtp) cc_final: 0.7425 (mtm) REVERT: B 82 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7030 (pp) REVERT: B 96 MET cc_start: 0.8402 (mmm) cc_final: 0.8157 (mmm) REVERT: B 99 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8845 (tmm-80) REVERT: B 100 ASP cc_start: 0.8426 (p0) cc_final: 0.8066 (p0) REVERT: B 105 GLN cc_start: 0.8597 (tt0) cc_final: 0.8162 (pt0) REVERT: C 31 ASN cc_start: 0.7721 (m-40) cc_final: 0.7220 (t0) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.1693 time to fit residues: 20.6016 Evaluate side-chains 95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.7564 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3388 Z= 0.208 Angle : 0.618 6.640 4605 Z= 0.326 Chirality : 0.044 0.179 499 Planarity : 0.005 0.049 594 Dihedral : 6.328 55.315 489 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.26 % Allowed : 18.01 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.94 (0.41), residues: 417 helix: -2.65 (0.76), residues: 41 sheet: 0.20 (0.42), residues: 149 loop : -0.74 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 436 HIS 0.003 0.002 HIS A 519 PHE 0.007 0.001 PHE B 54 TYR 0.012 0.001 TYR A 451 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7647 (m110) cc_final: 0.7225 (m110) REVERT: A 406 GLU cc_start: 0.8442 (pt0) cc_final: 0.8115 (pt0) REVERT: A 423 TYR cc_start: 0.7709 (t80) cc_final: 0.6828 (t80) REVERT: A 467 ASP cc_start: 0.7246 (t0) cc_final: 0.6431 (p0) REVERT: A 493 GLN cc_start: 0.8766 (tt0) cc_final: 0.8553 (tt0) REVERT: B 36 TRP cc_start: 0.9079 (m100) cc_final: 0.8352 (m-10) REVERT: B 48 MET cc_start: 0.8117 (mtp) cc_final: 0.7403 (mtm) REVERT: B 82 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7121 (pp) REVERT: B 96 MET cc_start: 0.8417 (mmm) cc_final: 0.8215 (mmm) REVERT: B 99 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8775 (tmm-80) REVERT: B 100 ASP cc_start: 0.8340 (p0) cc_final: 0.8040 (p0) REVERT: B 105 GLN cc_start: 0.8605 (tt0) cc_final: 0.8150 (pt0) REVERT: C 31 ASN cc_start: 0.7611 (m-40) cc_final: 0.7116 (t0) outliers start: 19 outliers final: 17 residues processed: 99 average time/residue: 0.1304 time to fit residues: 16.2768 Evaluate side-chains 103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.0170 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7525 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3388 Z= 0.167 Angle : 0.592 6.832 4605 Z= 0.312 Chirality : 0.043 0.153 499 Planarity : 0.005 0.050 594 Dihedral : 6.078 54.412 489 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.16 % Allowed : 18.84 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.91 (0.41), residues: 417 helix: -2.70 (0.70), residues: 47 sheet: 0.25 (0.42), residues: 148 loop : -0.65 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE C 62 TYR 0.010 0.001 TYR B 100C ARG 0.007 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7582 (m110) cc_final: 0.7162 (m110) REVERT: A 406 GLU cc_start: 0.8423 (pt0) cc_final: 0.8133 (pt0) REVERT: A 423 TYR cc_start: 0.7645 (t80) cc_final: 0.7011 (t80) REVERT: A 467 ASP cc_start: 0.7178 (t0) cc_final: 0.6226 (p0) REVERT: A 493 GLN cc_start: 0.8794 (tt0) cc_final: 0.8536 (tt0) REVERT: B 36 TRP cc_start: 0.9024 (m100) cc_final: 0.8374 (m-10) REVERT: B 48 MET cc_start: 0.8149 (mtp) cc_final: 0.7457 (mtm) REVERT: B 82 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7181 (pp) REVERT: B 96 MET cc_start: 0.8474 (mmm) cc_final: 0.8227 (mmm) REVERT: B 99 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8768 (tmm-80) REVERT: B 100 ASP cc_start: 0.8182 (p0) cc_final: 0.7871 (p0) REVERT: B 105 GLN cc_start: 0.8637 (tt0) cc_final: 0.8194 (pt0) REVERT: C 31 ASN cc_start: 0.7573 (m-40) cc_final: 0.7048 (t0) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.1445 time to fit residues: 17.8357 Evaluate side-chains 99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 37 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7594 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3388 Z= 0.259 Angle : 0.630 6.434 4605 Z= 0.339 Chirality : 0.044 0.152 499 Planarity : 0.005 0.050 594 Dihedral : 6.469 56.062 489 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.09 % Allowed : 17.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.11 (0.41), residues: 417 helix: -2.85 (0.65), residues: 47 sheet: 0.09 (0.41), residues: 155 loop : -0.79 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.005 0.003 HIS A 519 PHE 0.009 0.001 PHE B 54 TYR 0.011 0.002 TYR B 95 ARG 0.006 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7691 (m110) cc_final: 0.7291 (m110) REVERT: A 406 GLU cc_start: 0.8592 (pt0) cc_final: 0.8123 (pt0) REVERT: A 423 TYR cc_start: 0.7687 (t80) cc_final: 0.7043 (t80) REVERT: A 467 ASP cc_start: 0.7175 (t0) cc_final: 0.6373 (p0) REVERT: B 36 TRP cc_start: 0.9169 (m100) cc_final: 0.8840 (m100) REVERT: B 45 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7259 (mt) REVERT: B 82 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7130 (pp) REVERT: B 99 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8783 (tmm-80) REVERT: B 100 ASP cc_start: 0.8231 (p0) cc_final: 0.7923 (p0) REVERT: B 105 GLN cc_start: 0.8653 (tt0) cc_final: 0.8195 (pt0) REVERT: C 31 ASN cc_start: 0.7649 (m-40) cc_final: 0.7133 (t0) outliers start: 22 outliers final: 19 residues processed: 93 average time/residue: 0.1322 time to fit residues: 15.4390 Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3388 Z= 0.187 Angle : 0.613 6.188 4605 Z= 0.326 Chirality : 0.044 0.153 499 Planarity : 0.005 0.051 594 Dihedral : 6.208 54.805 489 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.54 % Allowed : 18.84 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -2.72 (0.68), residues: 47 sheet: 0.14 (0.42), residues: 148 loop : -0.68 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.003 0.002 HIS A 519 PHE 0.008 0.001 PHE C 62 TYR 0.011 0.001 TYR B 95 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7655 (m110) cc_final: 0.7262 (m110) REVERT: A 403 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7640 (ttp80) REVERT: A 406 GLU cc_start: 0.8357 (pt0) cc_final: 0.7969 (pt0) REVERT: A 423 TYR cc_start: 0.7637 (t80) cc_final: 0.7186 (t80) REVERT: A 467 ASP cc_start: 0.7287 (t0) cc_final: 0.6413 (p0) REVERT: B 36 TRP cc_start: 0.9100 (m100) cc_final: 0.8764 (m100) REVERT: B 45 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7212 (mt) REVERT: B 82 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7207 (pp) REVERT: B 99 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8808 (tmm-80) REVERT: B 100 ASP cc_start: 0.8082 (p0) cc_final: 0.7766 (p0) REVERT: B 105 GLN cc_start: 0.8636 (tt0) cc_final: 0.8191 (pt0) REVERT: C 31 ASN cc_start: 0.7651 (m-40) cc_final: 0.7081 (t0) outliers start: 20 outliers final: 17 residues processed: 96 average time/residue: 0.1306 time to fit residues: 15.7666 Evaluate side-chains 102 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7572 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3388 Z= 0.231 Angle : 0.627 6.060 4605 Z= 0.334 Chirality : 0.044 0.153 499 Planarity : 0.005 0.051 594 Dihedral : 6.364 55.213 489 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.54 % Allowed : 19.67 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.08 (0.41), residues: 417 helix: -2.83 (0.66), residues: 47 sheet: 0.06 (0.42), residues: 146 loop : -0.69 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 47 HIS 0.004 0.003 HIS A 519 PHE 0.008 0.001 PHE A 464 TYR 0.021 0.002 TYR A 380 ARG 0.009 0.001 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7703 (m110) cc_final: 0.7335 (m110) REVERT: A 403 ARG cc_start: 0.8011 (ttp80) cc_final: 0.7585 (ttp80) REVERT: A 406 GLU cc_start: 0.8552 (pt0) cc_final: 0.8044 (pt0) REVERT: A 423 TYR cc_start: 0.7674 (t80) cc_final: 0.7211 (t80) REVERT: A 467 ASP cc_start: 0.7396 (t0) cc_final: 0.6479 (p0) REVERT: B 36 TRP cc_start: 0.9174 (m100) cc_final: 0.8815 (m100) REVERT: B 45 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7234 (mt) REVERT: B 82 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7162 (pp) REVERT: B 99 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8794 (tmm-80) REVERT: B 100 ASP cc_start: 0.8114 (p0) cc_final: 0.7786 (p0) REVERT: B 105 GLN cc_start: 0.8649 (tt0) cc_final: 0.8207 (pt0) REVERT: C 31 ASN cc_start: 0.7710 (m-40) cc_final: 0.7115 (t0) outliers start: 20 outliers final: 17 residues processed: 91 average time/residue: 0.1497 time to fit residues: 16.8039 Evaluate side-chains 97 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103980 restraints weight = 8680.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.106793 restraints weight = 4511.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108692 restraints weight = 2784.732| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3388 Z= 0.220 Angle : 0.622 6.695 4605 Z= 0.332 Chirality : 0.044 0.156 499 Planarity : 0.005 0.051 594 Dihedral : 6.325 55.101 489 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.26 % Allowed : 19.94 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.41), residues: 417 helix: -2.87 (0.66), residues: 47 sheet: 0.05 (0.41), residues: 152 loop : -0.75 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 47 HIS 0.004 0.002 HIS A 519 PHE 0.009 0.001 PHE A 464 TYR 0.018 0.001 TYR A 380 ARG 0.009 0.001 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.11 seconds wall clock time: 24 minutes 25.44 seconds (1465.44 seconds total)