Starting phenix.real_space_refine on Sun Mar 10 20:30:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_2024/7the_25893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_2024/7the_25893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_2024/7the_25893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_2024/7the_25893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7the_25893/03_2024/7the_25893.pdb" } 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 Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.48, per 1000 atoms: 0.75 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 - 3.50 Amino acid : False - 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: 1.33 Conformation dependent library (CDL) restraints added in 687.5 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: 0.47 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: 0.93 Time building geometry restraints manager: 1.46 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: 98.26 - 105.54: 88 105.54 - 112.83: 1438 112.83 - 120.11: 1594 120.11 - 127.40: 1445 127.40 - 134.68: 40 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 2.440 nonbonded pdb=" OD1 ASP A 467 " pdb=" OG SER A 469 " model vdw 2.565 2.440 nonbonded pdb=" OE2 GLU A 484 " pdb=" OH TYR B 95 " model vdw 2.566 2.440 nonbonded pdb=" OH TYR B 100B" pdb=" OD1 ASN C 34 " model vdw 2.569 2.440 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.588 2.440 ... (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 ========== 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: 1.370 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: 6.720 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.030 Find NCS groups from input model: 0.100 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: 26.270 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.419 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: 0.2093 time to fit residues: 30.8630 Evaluate side-chains 90 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7557 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3388 Z= 0.227 Angle : 0.703 6.191 4605 Z= 0.379 Chirality : 0.047 0.166 499 Planarity : 0.005 0.034 594 Dihedral : 7.430 55.905 489 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.32 % Allowed : 13.30 % Favored : 83.38 % 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: -1.58 (0.39), residues: 417 helix: -3.39 (0.67), residues: 35 sheet: 0.00 (0.44), residues: 138 loop : -1.33 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.018 0.002 PHE C 98 TYR 0.019 0.002 TYR A 365 ARG 0.003 0.001 ARG A 466 *********************** 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 110 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8362 (pt0) cc_final: 0.8152 (pt0) REVERT: A 467 ASP cc_start: 0.7507 (t0) cc_final: 0.6573 (p0) REVERT: A 468 ILE cc_start: 0.9148 (pt) cc_final: 0.8919 (pt) REVERT: A 493 GLN cc_start: 0.8807 (tt0) cc_final: 0.8439 (tt0) REVERT: B 12 LYS cc_start: 0.7019 (mttm) cc_final: 0.6814 (mttm) REVERT: B 36 TRP cc_start: 0.8993 (m100) cc_final: 0.8115 (m-10) REVERT: B 48 MET cc_start: 0.8141 (mtp) cc_final: 0.7563 (mtm) REVERT: B 96 MET cc_start: 0.8076 (mtp) cc_final: 0.7785 (mmm) REVERT: B 105 GLN cc_start: 0.8759 (tt0) cc_final: 0.8184 (pt0) outliers start: 12 outliers final: 11 residues processed: 104 average time/residue: 0.1662 time to fit residues: 20.6686 Evaluate side-chains 99 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 58 ASN 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: 0.8980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3388 Z= 0.201 Angle : 0.629 6.131 4605 Z= 0.334 Chirality : 0.045 0.162 499 Planarity : 0.005 0.043 594 Dihedral : 6.850 55.435 489 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.71 % Allowed : 13.85 % Favored : 81.44 % 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: -1.30 (0.40), residues: 417 helix: -3.13 (0.74), residues: 35 sheet: 0.04 (0.41), residues: 153 loop : -1.09 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 464 TYR 0.012 0.001 TYR A 365 ARG 0.005 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 110 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.7848 (t80) cc_final: 0.7562 (t80) REVERT: A 467 ASP cc_start: 0.7481 (t0) cc_final: 0.6690 (p0) REVERT: A 493 GLN cc_start: 0.8811 (tt0) cc_final: 0.8488 (tt0) REVERT: B 36 TRP cc_start: 0.8978 (m100) cc_final: 0.8170 (m-10) REVERT: B 48 MET cc_start: 0.8182 (mtp) cc_final: 0.7422 (mtm) REVERT: B 61 GLN cc_start: 0.8947 (pm20) cc_final: 0.8352 (pp30) REVERT: B 105 GLN cc_start: 0.8750 (tt0) cc_final: 0.8165 (pt0) REVERT: C 89 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7354 (tm-30) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 0.1629 time to fit residues: 19.6378 Evaluate side-chains 97 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 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 31 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 ILE 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 Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN ** C 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3388 Z= 0.268 Angle : 0.640 6.559 4605 Z= 0.343 Chirality : 0.045 0.150 499 Planarity : 0.005 0.047 594 Dihedral : 6.797 56.368 489 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.82 % Allowed : 17.17 % 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: -1.40 (0.40), residues: 417 helix: -3.17 (0.72), residues: 35 sheet: -0.09 (0.40), residues: 156 loop : -1.13 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.004 0.003 HIS A 519 PHE 0.011 0.001 PHE B 54 TYR 0.012 0.002 TYR B 95 ARG 0.006 0.001 ARG A 466 *********************** 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 105 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7641 (m110) cc_final: 0.7261 (m110) REVERT: A 403 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7294 (ttp-110) REVERT: A 406 GLU cc_start: 0.8648 (pt0) cc_final: 0.7965 (pt0) REVERT: A 423 TYR cc_start: 0.7845 (t80) cc_final: 0.7404 (t80) REVERT: A 467 ASP cc_start: 0.7455 (t0) cc_final: 0.6705 (p0) REVERT: A 493 GLN cc_start: 0.8850 (tt0) cc_final: 0.8562 (tt0) REVERT: B 36 TRP cc_start: 0.9140 (m100) cc_final: 0.8380 (m-10) REVERT: B 48 MET cc_start: 0.8163 (mtp) cc_final: 0.7433 (mtm) REVERT: B 61 GLN cc_start: 0.8919 (pm20) cc_final: 0.8296 (pp30) REVERT: B 99 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8599 (tmm-80) REVERT: B 100 GLN cc_start: 0.8609 (mp10) cc_final: 0.8404 (mm-40) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.1555 time to fit residues: 17.9988 Evaluate side-chains 100 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 LEU 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 31 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 THR 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 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 82 ASP Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3388 Z= 0.269 Angle : 0.629 6.478 4605 Z= 0.338 Chirality : 0.045 0.177 499 Planarity : 0.005 0.050 594 Dihedral : 6.735 56.213 489 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 8.31 % Allowed : 16.90 % 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: -1.29 (0.40), residues: 417 helix: -2.75 (0.80), residues: 35 sheet: -0.06 (0.41), residues: 155 loop : -1.09 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 436 HIS 0.006 0.004 HIS A 519 PHE 0.009 0.001 PHE B 54 TYR 0.013 0.002 TYR B 95 ARG 0.005 0.001 ARG A 466 *********************** 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 110 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7765 (m110) cc_final: 0.7388 (m110) REVERT: A 423 TYR cc_start: 0.7822 (t80) cc_final: 0.7492 (t80) REVERT: A 467 ASP cc_start: 0.7423 (t70) cc_final: 0.6752 (p0) REVERT: A 493 GLN cc_start: 0.8921 (tt0) cc_final: 0.8597 (tt0) REVERT: B 12 LYS cc_start: 0.6181 (mmtt) cc_final: 0.5979 (mttm) REVERT: B 36 TRP cc_start: 0.9193 (m100) cc_final: 0.8813 (m100) REVERT: B 61 GLN cc_start: 0.8874 (pm20) cc_final: 0.8214 (pp30) REVERT: B 82 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7231 (pp) REVERT: B 96 MET cc_start: 0.8439 (mmm) cc_final: 0.8212 (mmm) REVERT: B 99 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8665 (tmm-80) outliers start: 30 outliers final: 25 residues processed: 98 average time/residue: 0.1530 time to fit residues: 18.3414 Evaluate side-chains 104 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 87 THR 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 6 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 102 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: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3388 Z= 0.310 Angle : 0.653 6.908 4605 Z= 0.352 Chirality : 0.045 0.185 499 Planarity : 0.005 0.051 594 Dihedral : 6.873 56.580 489 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 9.70 % Allowed : 16.34 % Favored : 73.96 % 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: -1.56 (0.40), residues: 417 helix: -3.18 (0.66), residues: 42 sheet: -0.21 (0.40), residues: 155 loop : -1.16 (0.42), residues: 220 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 0.010 0.002 PHE B 54 TYR 0.014 0.002 TYR B 95 ARG 0.007 0.001 ARG B 83 *********************** 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 113 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 78 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7775 (m110) cc_final: 0.7403 (m110) REVERT: A 403 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7486 (ttp-110) REVERT: A 423 TYR cc_start: 0.7835 (t80) cc_final: 0.7523 (t80) REVERT: A 467 ASP cc_start: 0.7532 (t70) cc_final: 0.6738 (p0) REVERT: A 493 GLN cc_start: 0.8943 (tt0) cc_final: 0.8591 (tt0) REVERT: A 519 HIS cc_start: 0.2246 (OUTLIER) cc_final: 0.1053 (p-80) REVERT: B 45 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7459 (mt) REVERT: B 48 MET cc_start: 0.8357 (mtp) cc_final: 0.8121 (mtp) REVERT: B 61 GLN cc_start: 0.8860 (pm20) cc_final: 0.8282 (pp30) REVERT: B 99 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8734 (tmm-80) outliers start: 35 outliers final: 29 residues processed: 100 average time/residue: 0.1492 time to fit residues: 18.1754 Evaluate side-chains 108 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 401 VAL 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 31 SER 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 64 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR 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 6 GLN Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 102 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: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7610 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3388 Z= 0.224 Angle : 0.604 6.214 4605 Z= 0.324 Chirality : 0.044 0.181 499 Planarity : 0.005 0.054 594 Dihedral : 6.555 55.597 489 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 9.14 % Allowed : 16.90 % Favored : 73.96 % 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: -1.47 (0.41), residues: 417 helix: -3.04 (0.68), residues: 42 sheet: -0.16 (0.40), residues: 155 loop : -1.11 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 47 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE C 62 TYR 0.015 0.001 TYR B 32 ARG 0.006 0.001 ARG B 83 *********************** 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 117 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7697 (m110) cc_final: 0.7332 (m110) REVERT: A 403 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7446 (ttp-110) REVERT: A 423 TYR cc_start: 0.7804 (t80) cc_final: 0.7544 (t80) REVERT: A 467 ASP cc_start: 0.7487 (t70) cc_final: 0.6753 (p0) REVERT: A 493 GLN cc_start: 0.8922 (tt0) cc_final: 0.8553 (tt0) REVERT: B 36 TRP cc_start: 0.9161 (m100) cc_final: 0.8821 (m-10) REVERT: B 45 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7400 (mt) REVERT: B 61 GLN cc_start: 0.8782 (pm20) cc_final: 0.8161 (pp30) REVERT: B 99 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8710 (tmm-80) outliers start: 33 outliers final: 28 residues processed: 102 average time/residue: 0.1535 time to fit residues: 19.1036 Evaluate side-chains 109 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 387 LEU 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 478 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 31 SER 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 64 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 87 THR 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 28 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 104 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- 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: 0.7644 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3388 Z= 0.285 Angle : 0.629 6.861 4605 Z= 0.340 Chirality : 0.045 0.148 499 Planarity : 0.005 0.053 594 Dihedral : 6.762 56.300 489 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 9.42 % Allowed : 18.28 % Favored : 72.30 % 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: -1.57 (0.40), residues: 417 helix: -3.03 (0.69), residues: 42 sheet: -0.14 (0.41), residues: 150 loop : -1.24 (0.42), residues: 225 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 0.009 0.002 PHE B 54 TYR 0.018 0.002 TYR B 32 ARG 0.006 0.001 ARG B 94 *********************** 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 112 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7783 (m110) cc_final: 0.7409 (m110) REVERT: A 403 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7436 (ttp-110) REVERT: A 423 TYR cc_start: 0.7867 (t80) cc_final: 0.7580 (t80) REVERT: A 467 ASP cc_start: 0.7674 (t70) cc_final: 0.6855 (p0) REVERT: A 493 GLN cc_start: 0.8920 (tt0) cc_final: 0.8544 (tt0) REVERT: B 36 TRP cc_start: 0.9194 (m100) cc_final: 0.8815 (m-10) REVERT: B 45 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7318 (mt) REVERT: B 61 GLN cc_start: 0.8797 (pm20) cc_final: 0.8162 (pp30) REVERT: B 99 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8758 (tmm-80) outliers start: 34 outliers final: 29 residues processed: 96 average time/residue: 0.1518 time to fit residues: 17.8949 Evaluate side-chains 108 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 387 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL 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 B residue 5 VAL Chi-restraints excluded: chain B residue 31 SER 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 64 GLN Chi-restraints excluded: chain B residue 68 THR 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 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 28 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 102 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: 5.9990 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.0070 chunk 36 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.7578 moved from start: 0.4516 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= 0.183 Angle : 0.592 7.950 4605 Z= 0.314 Chirality : 0.044 0.151 499 Planarity : 0.005 0.055 594 Dihedral : 6.371 55.070 489 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 6.65 % Allowed : 20.78 % Favored : 72.58 % 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: -1.35 (0.41), residues: 417 helix: -2.95 (0.71), residues: 42 sheet: 0.00 (0.42), residues: 150 loop : -1.08 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE C 62 TYR 0.018 0.001 TYR B 32 ARG 0.004 0.001 ARG A 466 *********************** 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 106 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7680 (m110) cc_final: 0.7315 (m110) REVERT: A 403 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7439 (ttp-110) REVERT: A 423 TYR cc_start: 0.7814 (t80) cc_final: 0.7553 (t80) REVERT: A 467 ASP cc_start: 0.7504 (t70) cc_final: 0.6779 (p0) REVERT: A 493 GLN cc_start: 0.8933 (tt0) cc_final: 0.8544 (tt0) REVERT: A 509 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7681 (mtt90) REVERT: B 36 TRP cc_start: 0.9099 (m100) cc_final: 0.8713 (m-10) REVERT: B 45 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7310 (mt) REVERT: B 48 MET cc_start: 0.8339 (mtp) cc_final: 0.8119 (mtp) REVERT: B 61 GLN cc_start: 0.8689 (pm20) cc_final: 0.8071 (pp30) REVERT: B 99 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8647 (tmm-80) REVERT: C 92 TYR cc_start: 0.7211 (t80) cc_final: 0.6930 (t80) outliers start: 24 outliers final: 21 residues processed: 94 average time/residue: 0.1434 time to fit residues: 16.4789 Evaluate side-chains 103 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 68 THR Chi-restraints excluded: chain B residue 80 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 11 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 102 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: 0.0980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3388 Z= 0.191 Angle : 0.589 6.273 4605 Z= 0.316 Chirality : 0.044 0.152 499 Planarity : 0.005 0.049 594 Dihedral : 6.282 54.948 489 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 6.93 % Allowed : 19.94 % Favored : 73.13 % 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: -1.27 (0.41), residues: 417 helix: -2.97 (0.71), residues: 42 sheet: 0.03 (0.42), residues: 150 loop : -0.98 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 47 HIS 0.001 0.000 HIS A 519 PHE 0.009 0.001 PHE C 62 TYR 0.011 0.001 TYR C 49 ARG 0.005 0.001 ARG B 94 ********************** 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 103 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7684 (m110) cc_final: 0.7329 (m110) REVERT: A 403 ARG cc_start: 0.7920 (ttp80) cc_final: 0.7469 (ttp-110) REVERT: A 423 TYR cc_start: 0.7825 (t80) cc_final: 0.7545 (t80) REVERT: A 467 ASP cc_start: 0.7532 (t70) cc_final: 0.6813 (p0) REVERT: A 493 GLN cc_start: 0.8945 (tt0) cc_final: 0.8560 (tt0) REVERT: A 509 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7798 (mtt90) REVERT: B 36 TRP cc_start: 0.9098 (m100) cc_final: 0.8741 (m-10) REVERT: B 45 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7297 (mt) REVERT: B 48 MET cc_start: 0.8322 (mtp) cc_final: 0.8105 (mtp) REVERT: B 61 GLN cc_start: 0.8674 (pm20) cc_final: 0.8014 (pp30) REVERT: B 99 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8666 (tmm-80) outliers start: 25 outliers final: 22 residues processed: 89 average time/residue: 0.1522 time to fit residues: 16.5115 Evaluate side-chains 101 residues out of total 361 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 387 LEU 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 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 68 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 80 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 11 LEU Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 102 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: 0.5980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.116186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104271 restraints weight = 8766.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.107110 restraints weight = 4555.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108988 restraints weight = 2795.306| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3388 Z= 0.185 Angle : 0.582 6.372 4605 Z= 0.311 Chirality : 0.043 0.151 499 Planarity : 0.005 0.049 594 Dihedral : 6.227 54.857 489 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.65 % Allowed : 20.78 % Favored : 72.58 % 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: -1.23 (0.41), residues: 417 helix: -2.92 (0.72), residues: 42 sheet: 0.08 (0.42), residues: 150 loop : -0.97 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE C 62 TYR 0.011 0.001 TYR C 49 ARG 0.005 0.001 ARG B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1308.88 seconds wall clock time: 24 minutes 1.99 seconds (1441.99 seconds total)