Starting phenix.real_space_refine on Mon Sep 23 21:02:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/09_2024/8e27_27827.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3430 2.51 5 N 927 2.21 5 O 984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5371 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5371 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 39, 'TRANS': 636} Chain breaks: 3 Time building chain proxies: 4.04, per 1000 atoms: 0.75 Number of scatterers: 5371 At special positions: 0 Unit cell: (75.24, 83.16, 93.06, 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 30 16.00 O 984 8.00 N 927 7.00 C 3430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 661.8 milliseconds 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1290 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 10 sheets defined 34.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.814A pdb=" N VAL A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 291 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.641A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.542A pdb=" N SER A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.726A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 546 removed outlier: 3.673A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.752A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.772A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 647 removed outlier: 3.679A pdb=" N THR A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 666 removed outlier: 4.329A pdb=" N ALA A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 765 removed outlier: 3.620A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72 removed outlier: 7.598A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 239 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 7.316A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.862A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 469 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.325A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 6.974A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 773 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 804 through 810 231 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.43 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: 1458 1.33 - 1.45: 925 1.45 - 1.57: 3059 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 5487 Sorted by residual: bond pdb=" CB ASN A 391 " pdb=" CG ASN A 391 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CB TRP A 468 " pdb=" CG TRP A 468 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.20e+00 bond pdb=" CG PRO A 702 " pdb=" CD PRO A 702 " ideal model delta sigma weight residual 1.503 1.443 0.060 3.40e-02 8.65e+02 3.16e+00 bond pdb=" CB PRO A 702 " pdb=" CG PRO A 702 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.11e+00 bond pdb=" C ARG A 743 " pdb=" O ARG A 743 " ideal model delta sigma weight residual 1.237 1.216 0.020 1.17e-02 7.31e+03 3.06e+00 ... (remaining 5482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 6956 2.02 - 4.05: 393 4.05 - 6.07: 55 6.07 - 8.10: 19 8.10 - 10.12: 4 Bond angle restraints: 7427 Sorted by residual: angle pdb=" N PHE A 464 " pdb=" CA PHE A 464 " pdb=" C PHE A 464 " ideal model delta sigma weight residual 107.69 100.15 7.54 2.01e+00 2.48e-01 1.41e+01 angle pdb=" N THR A 700 " pdb=" CA THR A 700 " pdb=" C THR A 700 " ideal model delta sigma weight residual 112.92 117.25 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" CA GLN A 538 " pdb=" CB GLN A 538 " pdb=" CG GLN A 538 " ideal model delta sigma weight residual 114.10 107.46 6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" N ARG A 667 " pdb=" CA ARG A 667 " pdb=" C ARG A 667 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.80e+00 angle pdb=" C VAL A 236 " pdb=" N TYR A 237 " pdb=" CA TYR A 237 " ideal model delta sigma weight residual 121.85 116.34 5.51 1.77e+00 3.19e-01 9.69e+00 ... (remaining 7422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3023 17.81 - 35.62: 259 35.62 - 53.43: 67 53.43 - 71.24: 8 71.24 - 89.06: 3 Dihedral angle restraints: 3360 sinusoidal: 1379 harmonic: 1981 Sorted by residual: dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N TYR A 674 " pdb=" CA TYR A 674 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 476 0.050 - 0.099: 248 0.099 - 0.148: 85 0.148 - 0.197: 22 0.197 - 0.247: 6 Chirality restraints: 837 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU A 450 " pdb=" N GLU A 450 " pdb=" C GLU A 450 " pdb=" CB GLU A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 834 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 464 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C PHE A 464 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE A 464 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 465 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 699 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C PHE A 699 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE A 699 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 700 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 508 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ILE A 508 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE A 508 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 509 " -0.016 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1474 2.82 - 3.34: 4320 3.34 - 3.86: 7906 3.86 - 4.38: 8806 4.38 - 4.90: 15989 Nonbonded interactions: 38495 Sorted by model distance: nonbonded pdb=" O SER A 701 " pdb=" OD2 ASP A 708 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 419 " pdb=" NH2 ARG A 722 " model vdw 2.339 3.120 nonbonded pdb=" OD1 ASP A 343 " pdb=" OG SER A 345 " model vdw 2.394 3.040 nonbonded pdb=" N ASP A 633 " pdb=" OD1 ASP A 633 " model vdw 2.402 3.120 nonbonded pdb=" OG SER A 701 " pdb=" OD2 ASP A 708 " model vdw 2.434 3.040 ... (remaining 38490 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.010 0.088 5487 Z= 0.660 Angle : 1.095 10.119 7427 Z= 0.598 Chirality : 0.067 0.247 837 Planarity : 0.008 0.067 958 Dihedral : 14.240 89.056 2070 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.34 % Allowed : 4.05 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.29), residues: 668 helix: -0.31 (0.32), residues: 213 sheet: 0.33 (0.50), residues: 103 loop : -1.05 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 468 HIS 0.011 0.003 HIS A 409 PHE 0.026 0.003 PHE A 95 TYR 0.024 0.003 TYR A 796 ARG 0.013 0.002 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.564 Fit side-chains REVERT: A 79 LYS cc_start: 0.8136 (tttm) cc_final: 0.7791 (tttp) REVERT: A 95 PHE cc_start: 0.7518 (t80) cc_final: 0.7276 (t80) REVERT: A 242 LYS cc_start: 0.8429 (mttt) cc_final: 0.8180 (mttp) REVERT: A 293 PRO cc_start: 0.8341 (Cg_endo) cc_final: 0.8013 (Cg_exo) REVERT: A 309 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8069 (mmtp) REVERT: A 424 ASP cc_start: 0.8355 (t70) cc_final: 0.8085 (t0) REVERT: A 659 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7949 (tp30) REVERT: A 783 ASP cc_start: 0.7875 (m-30) cc_final: 0.7204 (m-30) outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2326 time to fit residues: 25.7249 Evaluate side-chains 57 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 309 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5487 Z= 0.162 Angle : 0.532 5.334 7427 Z= 0.279 Chirality : 0.042 0.144 837 Planarity : 0.005 0.047 958 Dihedral : 4.580 29.912 738 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.52 % Allowed : 8.60 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.31), residues: 668 helix: 0.80 (0.37), residues: 211 sheet: 0.50 (0.50), residues: 112 loop : -0.96 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 PHE 0.017 0.001 PHE A 634 TYR 0.011 0.001 TYR A 340 ARG 0.005 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.645 Fit side-chains REVERT: A 253 LEU cc_start: 0.7553 (mm) cc_final: 0.6897 (tt) REVERT: A 293 PRO cc_start: 0.8303 (Cg_endo) cc_final: 0.7989 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8425 (t70) cc_final: 0.8197 (t0) REVERT: A 634 PHE cc_start: 0.8060 (m-10) cc_final: 0.7738 (m-10) REVERT: A 659 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8037 (tp30) REVERT: A 783 ASP cc_start: 0.7705 (m-30) cc_final: 0.7120 (m-30) REVERT: A 794 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7658 (ttm170) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.1969 time to fit residues: 18.8832 Evaluate side-chains 66 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5487 Z= 0.139 Angle : 0.488 6.445 7427 Z= 0.252 Chirality : 0.041 0.136 837 Planarity : 0.004 0.041 958 Dihedral : 4.031 18.120 732 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.01 % Allowed : 10.96 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.32), residues: 668 helix: 1.02 (0.37), residues: 213 sheet: 0.66 (0.50), residues: 118 loop : -0.87 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 468 HIS 0.003 0.001 HIS A 688 PHE 0.014 0.001 PHE A 837 TYR 0.009 0.001 TYR A 340 ARG 0.006 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.653 Fit side-chains REVERT: A 253 LEU cc_start: 0.7553 (mm) cc_final: 0.7118 (tp) REVERT: A 293 PRO cc_start: 0.8147 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8431 (t70) cc_final: 0.8205 (t0) REVERT: A 783 ASP cc_start: 0.7757 (m-30) cc_final: 0.7275 (m-30) REVERT: A 820 TRP cc_start: 0.7268 (m100) cc_final: 0.6733 (m100) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.2136 time to fit residues: 19.3392 Evaluate side-chains 62 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5487 Z= 0.150 Angle : 0.478 5.413 7427 Z= 0.245 Chirality : 0.041 0.134 837 Planarity : 0.004 0.039 958 Dihedral : 3.869 17.270 732 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.18 % Allowed : 12.65 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.32), residues: 668 helix: 1.13 (0.37), residues: 214 sheet: 0.64 (0.47), residues: 132 loop : -0.73 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 468 HIS 0.007 0.001 HIS A 688 PHE 0.008 0.001 PHE A 634 TYR 0.009 0.001 TYR A 340 ARG 0.004 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.546 Fit side-chains REVERT: A 74 ARG cc_start: 0.6909 (ttp80) cc_final: 0.6519 (mtm110) REVERT: A 253 LEU cc_start: 0.7564 (mm) cc_final: 0.7112 (tp) REVERT: A 293 PRO cc_start: 0.8153 (Cg_endo) cc_final: 0.7748 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8421 (t70) cc_final: 0.8184 (t0) REVERT: A 783 ASP cc_start: 0.7725 (m-30) cc_final: 0.7373 (m-30) REVERT: A 820 TRP cc_start: 0.7337 (m100) cc_final: 0.6712 (m100) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.2282 time to fit residues: 19.1795 Evaluate side-chains 63 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8086 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5487 Z= 0.223 Angle : 0.509 7.177 7427 Z= 0.261 Chirality : 0.042 0.141 837 Planarity : 0.004 0.039 958 Dihedral : 3.938 19.851 732 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 11.80 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.32), residues: 668 helix: 1.08 (0.37), residues: 214 sheet: 0.73 (0.48), residues: 128 loop : -0.56 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.005 0.001 HIS A 526 PHE 0.011 0.001 PHE A 585 TYR 0.010 0.001 TYR A 340 ARG 0.004 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.566 Fit side-chains REVERT: A 74 ARG cc_start: 0.6951 (ttp80) cc_final: 0.6577 (mtm110) REVERT: A 293 PRO cc_start: 0.8151 (Cg_endo) cc_final: 0.7711 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8423 (t70) cc_final: 0.8184 (t0) REVERT: A 820 TRP cc_start: 0.7356 (m100) cc_final: 0.6908 (m100) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.1949 time to fit residues: 16.8669 Evaluate side-chains 68 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS A 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 5487 Z= 0.430 Angle : 0.626 12.040 7427 Z= 0.321 Chirality : 0.046 0.152 837 Planarity : 0.005 0.042 958 Dihedral : 4.308 19.649 732 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.53 % Allowed : 12.31 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.32), residues: 668 helix: 0.70 (0.36), residues: 214 sheet: 0.74 (0.48), residues: 131 loop : -0.78 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 468 HIS 0.007 0.001 HIS A 526 PHE 0.022 0.002 PHE A 95 TYR 0.013 0.001 TYR A 340 ARG 0.003 0.001 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 55 time to evaluate : 0.735 Fit side-chains REVERT: A 74 ARG cc_start: 0.6972 (ttp80) cc_final: 0.6569 (mtm110) REVERT: A 95 PHE cc_start: 0.7198 (t80) cc_final: 0.6839 (t80) REVERT: A 253 LEU cc_start: 0.7676 (mm) cc_final: 0.6950 (tp) REVERT: A 293 PRO cc_start: 0.8237 (Cg_endo) cc_final: 0.7785 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8440 (t70) cc_final: 0.8190 (t0) REVERT: A 820 TRP cc_start: 0.7389 (m100) cc_final: 0.6841 (m100) outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.2017 time to fit residues: 17.6616 Evaluate side-chains 66 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5487 Z= 0.149 Angle : 0.505 7.787 7427 Z= 0.254 Chirality : 0.041 0.198 837 Planarity : 0.004 0.037 958 Dihedral : 3.953 19.972 732 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.52 % Allowed : 14.00 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.33), residues: 668 helix: 1.10 (0.37), residues: 214 sheet: 0.82 (0.49), residues: 121 loop : -0.58 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.003 0.001 HIS A 688 PHE 0.019 0.001 PHE A 95 TYR 0.009 0.001 TYR A 340 ARG 0.005 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.607 Fit side-chains REVERT: A 74 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6655 (mtm110) REVERT: A 95 PHE cc_start: 0.7262 (t80) cc_final: 0.6863 (t80) REVERT: A 253 LEU cc_start: 0.7709 (mm) cc_final: 0.6956 (tp) REVERT: A 293 PRO cc_start: 0.8190 (Cg_endo) cc_final: 0.7744 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8401 (t70) cc_final: 0.8152 (t0) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 0.2081 time to fit residues: 17.2151 Evaluate side-chains 61 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5487 Z= 0.233 Angle : 0.532 9.276 7427 Z= 0.270 Chirality : 0.042 0.169 837 Planarity : 0.004 0.038 958 Dihedral : 3.973 19.845 732 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 14.00 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.33), residues: 668 helix: 0.92 (0.37), residues: 220 sheet: 0.77 (0.49), residues: 121 loop : -0.60 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 468 HIS 0.004 0.001 HIS A 526 PHE 0.018 0.001 PHE A 95 TYR 0.011 0.001 TYR A 340 ARG 0.004 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.643 Fit side-chains REVERT: A 74 ARG cc_start: 0.7007 (ttp80) cc_final: 0.6651 (mtm110) REVERT: A 95 PHE cc_start: 0.7242 (t80) cc_final: 0.6846 (t80) REVERT: A 253 LEU cc_start: 0.7718 (mm) cc_final: 0.6977 (tp) REVERT: A 293 PRO cc_start: 0.8236 (Cg_endo) cc_final: 0.7781 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8410 (t70) cc_final: 0.8159 (t0) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1762 time to fit residues: 14.5641 Evaluate side-chains 62 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5487 Z= 0.199 Angle : 0.517 7.938 7427 Z= 0.261 Chirality : 0.042 0.219 837 Planarity : 0.004 0.037 958 Dihedral : 3.924 20.176 732 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.19 % Allowed : 14.00 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.33), residues: 668 helix: 0.97 (0.37), residues: 220 sheet: 0.81 (0.49), residues: 121 loop : -0.56 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.018 0.001 PHE A 95 TYR 0.010 0.001 TYR A 340 ARG 0.004 0.000 ARG A 724 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.608 Fit side-chains REVERT: A 74 ARG cc_start: 0.7001 (ttp80) cc_final: 0.6646 (mtm110) REVERT: A 95 PHE cc_start: 0.7260 (t80) cc_final: 0.6838 (t80) REVERT: A 253 LEU cc_start: 0.7669 (mm) cc_final: 0.6969 (tp) REVERT: A 293 PRO cc_start: 0.8238 (Cg_endo) cc_final: 0.7786 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8401 (t70) cc_final: 0.8151 (t0) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.1995 time to fit residues: 16.4974 Evaluate side-chains 62 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5487 Z= 0.145 Angle : 0.497 7.297 7427 Z= 0.248 Chirality : 0.041 0.206 837 Planarity : 0.003 0.036 958 Dihedral : 3.759 20.133 732 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.35 % Allowed : 14.67 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.33), residues: 668 helix: 1.14 (0.37), residues: 220 sheet: 0.92 (0.47), residues: 129 loop : -0.52 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 468 HIS 0.003 0.001 HIS A 688 PHE 0.017 0.001 PHE A 95 TYR 0.008 0.001 TYR A 340 ARG 0.005 0.000 ARG A 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.570 Fit side-chains REVERT: A 74 ARG cc_start: 0.6979 (ttp80) cc_final: 0.6639 (mtm110) REVERT: A 95 PHE cc_start: 0.7203 (t80) cc_final: 0.6760 (t80) REVERT: A 253 LEU cc_start: 0.7675 (mm) cc_final: 0.6973 (tp) REVERT: A 293 PRO cc_start: 0.8165 (Cg_endo) cc_final: 0.7683 (Cg_exo) REVERT: A 424 ASP cc_start: 0.8391 (t70) cc_final: 0.8156 (t0) REVERT: A 692 ASN cc_start: 0.7665 (t0) cc_final: 0.7156 (t0) outliers start: 8 outliers final: 7 residues processed: 63 average time/residue: 0.1796 time to fit residues: 14.8054 Evaluate side-chains 62 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 805 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 38 optimal weight: 0.0060 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.1200 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.145717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100565 restraints weight = 7418.029| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.06 r_work: 0.3077 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5487 Z= 0.181 Angle : 0.509 7.872 7427 Z= 0.255 Chirality : 0.042 0.205 837 Planarity : 0.004 0.036 958 Dihedral : 3.782 19.592 732 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.69 % Allowed : 14.84 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.33), residues: 668 helix: 1.11 (0.37), residues: 220 sheet: 0.92 (0.47), residues: 129 loop : -0.50 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 468 HIS 0.003 0.001 HIS A 526 PHE 0.017 0.001 PHE A 95 TYR 0.010 0.001 TYR A 340 ARG 0.006 0.000 ARG A 724 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1476.50 seconds wall clock time: 26 minutes 56.93 seconds (1616.93 seconds total)