Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:27:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unt_26632/11_2022/7unt_26632_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.006 sd= 0.024 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "x ASP 647": "OD1" <-> "OD2" Residue "x PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 727": "OE1" <-> "OE2" Residue "x PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 832": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 3270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3270 Unusual residues: {'GDP': 1} Classifications: {'peptide': 472, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 17, 'TRANS': 454, None: 1} Not linked: pdbres="GLU x 835 " pdbres="GDP x 901 " Chain breaks: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 17, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 222 Time building chain proxies: 2.76, per 1000 atoms: 0.84 Number of scatterers: 3270 At special positions: 0 Unit cell: (79.9, 76.5, 86.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 P 2 15.00 O 602 8.00 N 596 7.00 C 2059 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 - 3.50 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 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 718.4 milliseconds 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 5 sheets defined 26.5% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'x' and resid 355 through 365 Processing helix chain 'x' and resid 399 through 408 removed outlier: 3.787A pdb=" N MET x 405 " --> pdb=" O ALA x 401 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG x 408 " --> pdb=" O ALA x 404 " (cutoff:3.500A) Processing helix chain 'x' and resid 428 through 440 removed outlier: 3.877A pdb=" N ALA x 440 " --> pdb=" O HIS x 436 " (cutoff:3.500A) Processing helix chain 'x' and resid 460 through 468 removed outlier: 4.480A pdb=" N ALA x 467 " --> pdb=" O ASN x 463 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU x 468 " --> pdb=" O GLY x 464 " (cutoff:3.500A) Processing helix chain 'x' and resid 492 through 501 removed outlier: 3.907A pdb=" N LEU x 500 " --> pdb=" O LEU x 496 " (cutoff:3.500A) Processing helix chain 'x' and resid 598 through 622 removed outlier: 3.617A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) Processing helix chain 'x' and resid 625 through 627 No H-bonds generated for 'chain 'x' and resid 625 through 627' Processing helix chain 'x' and resid 649 through 660 removed outlier: 3.580A pdb=" N LEU x 655 " --> pdb=" O SER x 651 " (cutoff:3.500A) Processing helix chain 'x' and resid 681 through 690 Processing helix chain 'x' and resid 703 through 711 Processing helix chain 'x' and resid 722 through 734 removed outlier: 3.730A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'x' and resid 345 through 349 removed outlier: 7.090A pdb=" N ILE x 415 " --> pdb=" O THR x 346 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N MET x 348 " --> pdb=" O ILE x 415 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE x 417 " --> pdb=" O MET x 348 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL x 482 " --> pdb=" O VAL x 446 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'x' and resid 381 through 384 Processing sheet with id= C, first strand: chain 'x' and resid 554 through 556 removed outlier: 6.265A pdb=" N VAL x 519 " --> pdb=" O VAL x 537 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL x 537 " --> pdb=" O VAL x 519 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'x' and resid 642 through 646 removed outlier: 6.151A pdb=" N VAL x 693 " --> pdb=" O VAL x 643 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LYS x 645 " --> pdb=" O VAL x 693 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE x 695 " --> pdb=" O LYS x 645 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG x 717 " --> pdb=" O LEU x 694 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'x' and resid 786 through 791 removed outlier: 6.984A pdb=" N VAL x 781 " --> pdb=" O ILE x 788 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU x 790 " --> pdb=" O ILE x 779 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE x 779 " --> pdb=" O GLU x 790 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP x 826 " --> pdb=" O VAL x 751 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL x 751 " --> pdb=" O ASP x 826 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY x 747 " --> pdb=" O VAL x 830 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU x 832 " --> pdb=" O ILE x 745 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE x 745 " --> pdb=" O GLU x 832 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE x 748 " --> pdb=" O THR x 769 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY x 765 " --> pdb=" O ARG x 752 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL x 754 " --> pdb=" O ILE x 763 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE x 763 " --> pdb=" O VAL x 754 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 351 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: 0.90 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: 1.23 - 1.34: 1123 1.34 - 1.46: 403 1.46 - 1.57: 1762 1.57 - 1.69: 3 1.69 - 1.81: 20 Bond restraints: 3311 Sorted by residual: bond pdb=" N TYR x 719 " pdb=" CA TYR x 719 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.27e-02 6.20e+03 4.82e+00 bond pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C5 GDP x 901 " pdb=" C4 GDP x 901 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" CA VAL x 550 " pdb=" CB VAL x 550 " ideal model delta sigma weight residual 1.531 1.543 -0.012 1.16e-02 7.43e+03 1.05e+00 bond pdb=" CB GLU x 614 " pdb=" CG GLU x 614 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.36e-01 ... (remaining 3306 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.55: 112 107.55 - 114.68: 2014 114.68 - 121.80: 1574 121.80 - 128.92: 797 128.92 - 136.04: 11 Bond angle restraints: 4508 Sorted by residual: angle pdb=" N ILE x 451 " pdb=" CA ILE x 451 " pdb=" C ILE x 451 " ideal model delta sigma weight residual 111.77 107.72 4.05 1.04e+00 9.25e-01 1.52e+01 angle pdb=" C GLY x 425 " pdb=" N VAL x 426 " pdb=" CA VAL x 426 " ideal model delta sigma weight residual 121.97 126.13 -4.16 1.80e+00 3.09e-01 5.35e+00 angle pdb=" C ASP x 423 " pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 121.54 125.85 -4.31 1.91e+00 2.74e-01 5.09e+00 angle pdb=" CA TYR x 719 " pdb=" C TYR x 719 " pdb=" O TYR x 719 " ideal model delta sigma weight residual 121.33 118.99 2.34 1.08e+00 8.57e-01 4.70e+00 angle pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " pdb=" CG1 VAL x 426 " ideal model delta sigma weight residual 110.40 113.80 -3.40 1.70e+00 3.46e-01 4.00e+00 ... (remaining 4503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 1767 16.68 - 33.37: 160 33.37 - 50.05: 42 50.05 - 66.74: 6 66.74 - 83.42: 2 Dihedral angle restraints: 1977 sinusoidal: 657 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ARG x 742 " pdb=" C ARG x 742 " pdb=" N GLU x 743 " pdb=" CA GLU x 743 " ideal model delta harmonic sigma weight residual 180.00 164.61 15.39 0 5.00e+00 4.00e-02 9.48e+00 dihedral pdb=" CB GLU x 473 " pdb=" CG GLU x 473 " pdb=" CD GLU x 473 " pdb=" OE1 GLU x 473 " ideal model delta sinusoidal sigma weight residual 0.00 83.42 -83.42 1 3.00e+01 1.11e-03 9.44e+00 dihedral pdb=" CB LYS x 731 " pdb=" CG LYS x 731 " pdb=" CD LYS x 731 " pdb=" CE LYS x 731 " ideal model delta sinusoidal sigma weight residual 60.00 113.54 -53.54 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 322 0.030 - 0.060: 128 0.060 - 0.089: 64 0.089 - 0.119: 32 0.119 - 0.149: 7 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA VAL x 442 " pdb=" N VAL x 442 " pdb=" C VAL x 442 " pdb=" CB VAL x 442 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE x 471 " pdb=" N ILE x 471 " pdb=" C ILE x 471 " pdb=" CB ILE x 471 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA TYR x 719 " pdb=" N TYR x 719 " pdb=" C TYR x 719 " pdb=" CB TYR x 719 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 550 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL x 482 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO x 483 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO x 483 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO x 483 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET x 427 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO x 428 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO x 428 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO x 428 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS x 453 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO x 454 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO x 454 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO x 454 " -0.019 5.00e-02 4.00e+02 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1158 2.86 - 3.37: 3004 3.37 - 3.88: 5015 3.88 - 4.39: 5208 4.39 - 4.90: 9551 Nonbonded interactions: 23936 Sorted by model distance: nonbonded pdb=" ND2 ASN x 553 " pdb=" OD1 ASP x 583 " model vdw 2.356 2.520 nonbonded pdb=" OE1 GLU x 727 " pdb=" NH2 ARG x 742 " model vdw 2.378 2.520 nonbonded pdb=" NH2 ARG x 775 " pdb=" O GLU x 794 " model vdw 2.451 2.520 nonbonded pdb=" O VAL x 420 " pdb=" N ASN x 449 " model vdw 2.451 2.520 nonbonded pdb=" O TYR x 382 " pdb=" OG1 THR x 392 " model vdw 2.474 2.440 ... (remaining 23931 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 11 5.16 5 C 2059 2.51 5 N 596 2.21 5 O 602 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.650 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 29.220 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.050 Process input model: 14.220 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 3311 Z= 0.174 Angle : 0.603 5.552 4508 Z= 0.326 Chirality : 0.045 0.149 553 Planarity : 0.004 0.047 585 Dihedral : 14.275 83.420 1131 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.05 % Favored : 90.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.39), residues: 464 helix: 1.62 (0.47), residues: 121 sheet: -0.65 (0.51), residues: 106 loop : -2.84 (0.36), residues: 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.324 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1634 time to fit residues: 14.0158 Evaluate side-chains 43 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 431 GLN x 774 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 3311 Z= 0.284 Angle : 0.601 5.209 4508 Z= 0.312 Chirality : 0.045 0.144 553 Planarity : 0.004 0.043 585 Dihedral : 5.728 37.083 505 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.34 % Favored : 89.22 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.39), residues: 464 helix: 1.75 (0.48), residues: 121 sheet: -0.82 (0.49), residues: 110 loop : -2.61 (0.37), residues: 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.373 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 52 average time/residue: 0.1223 time to fit residues: 8.2412 Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0352 time to fit residues: 0.9827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 3311 Z= 0.223 Angle : 0.575 7.644 4508 Z= 0.296 Chirality : 0.045 0.144 553 Planarity : 0.004 0.042 585 Dihedral : 5.642 36.006 505 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.05 % Favored : 90.52 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.39), residues: 464 helix: 1.92 (0.48), residues: 122 sheet: -0.92 (0.47), residues: 116 loop : -2.60 (0.39), residues: 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.392 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 0.1600 time to fit residues: 9.7795 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0370 time to fit residues: 0.7047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 12 optimal weight: 0.0970 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 399 HIS x 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3311 Z= 0.191 Angle : 0.550 5.915 4508 Z= 0.285 Chirality : 0.045 0.144 553 Planarity : 0.004 0.039 585 Dihedral : 5.469 35.408 505 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.27 % Favored : 90.30 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.39), residues: 464 helix: 1.75 (0.47), residues: 127 sheet: -0.79 (0.49), residues: 109 loop : -2.68 (0.38), residues: 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.390 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.1302 time to fit residues: 7.3609 Evaluate side-chains 47 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0337 time to fit residues: 0.7579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 411 GLN x 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3311 Z= 0.284 Angle : 0.607 6.237 4508 Z= 0.316 Chirality : 0.045 0.154 553 Planarity : 0.004 0.039 585 Dihedral : 5.850 40.303 505 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.99 % Favored : 88.58 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.40), residues: 464 helix: 2.12 (0.47), residues: 122 sheet: -0.95 (0.48), residues: 115 loop : -2.54 (0.39), residues: 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.360 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 0.1138 time to fit residues: 6.7344 Evaluate side-chains 43 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0492 time to fit residues: 0.6641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 691 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 3311 Z= 0.204 Angle : 0.577 6.479 4508 Z= 0.299 Chirality : 0.045 0.146 553 Planarity : 0.004 0.039 585 Dihedral : 5.694 39.428 505 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.48 % Favored : 90.09 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.40), residues: 464 helix: 2.07 (0.48), residues: 125 sheet: -1.02 (0.47), residues: 116 loop : -2.48 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.406 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.1371 time to fit residues: 8.2019 Evaluate side-chains 43 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0417 time to fit residues: 0.8239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.0370 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0030 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 overall best weight: 0.4468 ------------------------------------------------------------------------------- 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: 0.7445 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3311 Z= 0.154 Angle : 0.581 6.798 4508 Z= 0.295 Chirality : 0.045 0.140 553 Planarity : 0.004 0.041 585 Dihedral : 5.329 35.004 505 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.27 % Favored : 90.30 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.40), residues: 464 helix: 2.33 (0.49), residues: 121 sheet: -0.83 (0.49), residues: 116 loop : -2.38 (0.39), residues: 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.369 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 44 average time/residue: 0.1106 time to fit residues: 6.5595 Evaluate side-chains 42 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0394 time to fit residues: 0.6799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 3311 Z= 0.257 Angle : 0.612 7.192 4508 Z= 0.311 Chirality : 0.045 0.153 553 Planarity : 0.004 0.036 585 Dihedral : 5.697 39.837 505 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.13 % Favored : 89.44 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.40), residues: 464 helix: 1.93 (0.47), residues: 127 sheet: -1.01 (0.48), residues: 116 loop : -2.46 (0.40), residues: 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.391 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.1150 time to fit residues: 6.6932 Evaluate side-chains 45 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.380 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0346 time to fit residues: 0.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.0030 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 3311 Z= 0.223 Angle : 0.610 7.297 4508 Z= 0.313 Chirality : 0.045 0.153 553 Planarity : 0.004 0.037 585 Dihedral : 5.648 39.431 505 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.70 % Favored : 90.09 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.40), residues: 464 helix: 2.01 (0.48), residues: 125 sheet: -1.07 (0.48), residues: 116 loop : -2.40 (0.40), residues: 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1412 time to fit residues: 7.5437 Evaluate side-chains 41 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0502 time to fit residues: 0.6802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- 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: 0.7480 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3311 Z= 0.178 Angle : 0.587 7.480 4508 Z= 0.299 Chirality : 0.045 0.146 553 Planarity : 0.004 0.036 585 Dihedral : 5.490 37.381 505 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.91 % Favored : 89.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.40), residues: 464 helix: 2.12 (0.48), residues: 125 sheet: -1.03 (0.48), residues: 116 loop : -2.38 (0.39), residues: 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.399 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1167 time to fit residues: 6.4290 Evaluate side-chains 39 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.087465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.069422 restraints weight = 11092.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071418 restraints weight = 5985.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072738 restraints weight = 4060.753| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 3311 Z= 0.252 Angle : 0.612 7.479 4508 Z= 0.313 Chirality : 0.046 0.153 553 Planarity : 0.004 0.036 585 Dihedral : 5.806 41.025 505 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.13 % Favored : 89.44 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.40), residues: 464 helix: 2.07 (0.47), residues: 125 sheet: -1.20 (0.47), residues: 116 loop : -2.39 (0.40), residues: 223 =============================================================================== Job complete usr+sys time: 1303.05 seconds wall clock time: 24 minutes 11.75 seconds (1451.75 seconds total)