Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:50:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unq_26629/11_2022/7unq_26629_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unq_26629/11_2022/7unq_26629.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/7unq_26629/11_2022/7unq_26629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unq_26629/11_2022/7unq_26629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unq_26629/11_2022/7unq_26629_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unq_26629/11_2022/7unq_26629_updated.pdb" } resolution = 3.4 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= 0.026 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 352": "OD1" <-> "OD2" Residue "x ASP 423": "OD1" <-> "OD2" Residue "x ASP 459": "OD1" <-> "OD2" Residue "x GLU 578": "OE1" <-> "OE2" Residue "x GLU 653": "OE1" <-> "OE2" Residue "x ASP 740": "OD1" <-> "OD2" Residue "x ASP 753": "OD1" <-> "OD2" Residue "x PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 826": "OD1" <-> "OD2" 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: 3528 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3528 Unusual residues: {'GDP': 1} Classifications: {'peptide': 486, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 467, None: 1} Not linked: pdbres="GLU x 835 " pdbres="GDP x 901 " Unresolved chain links: 1 Chain breaks: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 115 Time building chain proxies: 2.63, per 1000 atoms: 0.75 Number of scatterers: 3528 At special positions: 0 Unit cell: (79.05, 79.9, 85, 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 13 16.00 P 2 15.00 O 660 8.00 N 648 7.00 C 2205 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: 1.41 Conformation dependent library (CDL) restraints added in 553.4 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 11 helices and 7 sheets defined 24.1% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.81 Creating SS restraints... Processing helix chain 'x' and resid 355 through 366 removed outlier: 3.593A pdb=" N ILE x 362 " --> pdb=" O LEU x 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG x 363 " --> pdb=" O LEU x 359 " (cutoff:3.500A) Processing helix chain 'x' and resid 401 through 404 No H-bonds generated for 'chain 'x' and resid 401 through 404' Processing helix chain 'x' and resid 430 through 439 Processing helix chain 'x' and resid 459 through 464 Processing helix chain 'x' and resid 466 through 468 No H-bonds generated for 'chain 'x' and resid 466 through 468' Processing helix chain 'x' and resid 492 through 505 removed outlier: 3.792A pdb=" N VAL x 505 " --> pdb=" O LEU x 501 " (cutoff:3.500A) Processing helix chain 'x' and resid 598 through 622 removed outlier: 3.575A pdb=" N LYS x 616 " --> pdb=" O PHE x 612 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU x 617 " --> pdb=" O ARG x 613 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA x 618 " --> pdb=" O GLU x 614 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG x 619 " --> pdb=" O VAL x 615 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA x 620 " --> pdb=" O LYS x 616 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS x 621 " --> pdb=" O LEU x 617 " (cutoff:3.500A) Processing helix chain 'x' and resid 649 through 658 Processing helix chain 'x' and resid 681 through 690 Processing helix chain 'x' and resid 703 through 712 Processing helix chain 'x' and resid 722 through 734 removed outlier: 3.620A pdb=" N ILE x 726 " --> pdb=" O ILE x 722 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'x' and resid 481 through 483 removed outlier: 8.993A pdb=" N VAL x 482 " --> pdb=" O ILE x 444 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL x 446 " --> pdb=" O VAL x 482 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL x 420 " --> pdb=" O ALA x 447 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'x' and resid 553 through 556 removed outlier: 4.427A pdb=" N MET x 547 " --> pdb=" O VAL x 595 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL x 519 " --> pdb=" O VAL x 537 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL x 537 " --> pdb=" O VAL x 519 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'x' and resid 523 through 526 Processing sheet with id= D, first strand: chain 'x' and resid 559 through 561 removed outlier: 3.966A pdb=" N ALA x 559 " --> pdb=" O LEU x 580 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'x' and resid 642 through 645 removed outlier: 6.289A pdb=" N VAL x 693 " --> pdb=" O VAL x 643 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS x 645 " --> pdb=" O VAL x 693 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE x 695 " --> pdb=" O LYS x 645 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG x 717 " --> pdb=" O LEU x 694 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'x' and resid 743 through 745 removed outlier: 3.656A pdb=" N ASN x 744 " --> pdb=" O GLU x 832 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU x 832 " --> pdb=" O ASN x 744 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'x' and resid 786 through 791 removed outlier: 6.983A pdb=" N VAL x 781 " --> pdb=" O ILE x 788 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU x 790 " --> pdb=" O ILE x 779 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE x 779 " --> pdb=" O GLU x 790 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU x 750 " --> pdb=" O VAL x 768 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL x 768 " --> pdb=" O GLU x 750 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 312 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: 1.17 Time building geometry restraints manager: 1.57 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: 800 1.33 - 1.45: 649 1.45 - 1.57: 2095 1.57 - 1.69: 3 1.69 - 1.81: 24 Bond restraints: 3571 Sorted by residual: bond pdb=" N VAL x 426 " pdb=" CA VAL x 426 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.34e+00 bond pdb=" N ASP x 424 " pdb=" CA ASP x 424 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.63e+00 bond pdb=" N SER x 739 " pdb=" CA SER x 739 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.16e-02 7.43e+03 6.45e+00 bond pdb=" N ASP x 740 " pdb=" CA ASP x 740 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.64e+00 bond pdb=" C PRO x 428 " pdb=" O PRO x 428 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.24e+00 ... (remaining 3566 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.95: 93 106.95 - 114.26: 2157 114.26 - 121.57: 1665 121.57 - 128.88: 924 128.88 - 136.19: 12 Bond angle restraints: 4851 Sorted by residual: angle pdb=" N ALA x 422 " pdb=" CA ALA x 422 " pdb=" C ALA x 422 " ideal model delta sigma weight residual 111.02 106.72 4.30 1.22e+00 6.72e-01 1.24e+01 angle pdb=" C MET x 427 " pdb=" N PRO x 428 " pdb=" CA PRO x 428 " ideal model delta sigma weight residual 119.84 123.48 -3.64 1.25e+00 6.40e-01 8.47e+00 angle pdb=" CA ASP x 352 " pdb=" C ASP x 352 " pdb=" O ASP x 352 " ideal model delta sigma weight residual 120.81 117.27 3.54 1.24e+00 6.50e-01 8.14e+00 angle pdb=" CA SER x 739 " pdb=" C SER x 739 " pdb=" O SER x 739 " ideal model delta sigma weight residual 121.38 118.36 3.02 1.06e+00 8.90e-01 8.09e+00 angle pdb=" CA ASP x 423 " pdb=" C ASP x 423 " pdb=" O ASP x 423 " ideal model delta sigma weight residual 120.58 117.30 3.28 1.16e+00 7.43e-01 7.99e+00 ... (remaining 4846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1960 17.98 - 35.95: 162 35.95 - 53.92: 22 53.92 - 71.90: 7 71.90 - 89.87: 2 Dihedral angle restraints: 2153 sinusoidal: 795 harmonic: 1358 Sorted by residual: dihedral pdb=" C VAL x 426 " pdb=" N VAL x 426 " pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" N VAL x 426 " pdb=" C VAL x 426 " pdb=" CA VAL x 426 " pdb=" CB VAL x 426 " ideal model delta harmonic sigma weight residual 123.40 133.87 -10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA ARG x 775 " pdb=" C ARG x 775 " pdb=" N ASN x 776 " pdb=" CA ASN x 776 " ideal model delta harmonic sigma weight residual 180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 2150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 484 0.063 - 0.126: 93 0.126 - 0.189: 6 0.189 - 0.252: 1 0.252 - 0.315: 1 Chirality restraints: 585 Sorted by residual: chirality pdb=" CA VAL x 426 " pdb=" N VAL x 426 " pdb=" C VAL x 426 " pdb=" CB VAL x 426 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL x 426 " pdb=" CA VAL x 426 " pdb=" CG1 VAL x 426 " pdb=" CG2 VAL x 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ALA x 422 " pdb=" N ALA x 422 " pdb=" C ALA x 422 " pdb=" CB ALA x 422 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 582 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA x 342 " -0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO x 343 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO x 343 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO x 343 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL x 442 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO x 443 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO x 443 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO x 443 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA x 421 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ALA x 421 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA x 421 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA x 422 " -0.008 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 555 2.77 - 3.30: 3388 3.30 - 3.83: 5460 3.83 - 4.37: 5978 4.37 - 4.90: 10972 Nonbonded interactions: 26353 Sorted by model distance: nonbonded pdb=" OG1 THR x 376 " pdb=" N GLN x 377 " model vdw 2.233 2.520 nonbonded pdb=" O MET x 427 " pdb=" N GLN x 429 " model vdw 2.315 2.520 nonbonded pdb=" OG1 THR x 386 " pdb=" O GLY x 389 " model vdw 2.325 2.440 nonbonded pdb=" OH TYR x 719 " pdb=" OD2 ASP x 728 " model vdw 2.351 2.440 nonbonded pdb=" NE2 GLN x 377 " pdb=" O GLU x 563 " model vdw 2.374 2.520 ... (remaining 26348 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 13 5.16 5 C 2205 2.51 5 N 648 2.21 5 O 660 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 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: 4.610 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: 29.890 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.060 Process input model: 14.650 Find NCS groups from input model: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.036 3571 Z= 0.201 Angle : 0.634 6.490 4851 Z= 0.348 Chirality : 0.048 0.315 585 Planarity : 0.004 0.037 633 Dihedral : 13.875 89.872 1285 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 1.04 % Allowed : 8.96 % Favored : 90.00 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.23 % 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: -1.44 (0.38), residues: 480 helix: 1.97 (0.49), residues: 113 sheet: -0.94 (0.48), residues: 114 loop : -2.48 (0.34), residues: 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.1817 time to fit residues: 17.2194 Evaluate side-chains 53 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0409 time to fit residues: 0.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 435 GLN x 656 GLN x 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 3571 Z= 0.358 Angle : 0.674 11.784 4851 Z= 0.331 Chirality : 0.046 0.131 585 Planarity : 0.004 0.039 633 Dihedral : 4.971 21.633 532 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.38 % Favored : 90.00 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.38), residues: 480 helix: 2.02 (0.49), residues: 114 sheet: -1.11 (0.48), residues: 117 loop : -2.37 (0.35), residues: 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.449 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1479 time to fit residues: 10.2411 Evaluate side-chains 51 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0374 time to fit residues: 1.0844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 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 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 3571 Z= 0.215 Angle : 0.612 13.187 4851 Z= 0.297 Chirality : 0.045 0.128 585 Planarity : 0.004 0.037 633 Dihedral : 4.681 21.210 532 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.58 % Favored : 89.79 % Rotamer Outliers : 1.17 % 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: -1.21 (0.38), residues: 480 helix: 2.26 (0.50), residues: 114 sheet: -0.99 (0.48), residues: 117 loop : -2.29 (0.35), residues: 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.450 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1432 time to fit residues: 9.0671 Evaluate side-chains 43 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0488 time to fit residues: 0.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 3571 Z= 0.260 Angle : 0.587 5.585 4851 Z= 0.294 Chirality : 0.045 0.128 585 Planarity : 0.004 0.039 633 Dihedral : 4.738 21.402 532 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.75 % Favored : 90.62 % 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: -1.13 (0.38), residues: 480 helix: 2.36 (0.51), residues: 113 sheet: -0.99 (0.48), residues: 117 loop : -2.22 (0.35), residues: 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.443 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 47 average time/residue: 0.1501 time to fit residues: 9.1828 Evaluate side-chains 42 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0406 time to fit residues: 0.6895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.0570 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3571 Z= 0.159 Angle : 0.574 7.921 4851 Z= 0.285 Chirality : 0.045 0.136 585 Planarity : 0.003 0.035 633 Dihedral : 4.468 21.234 532 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.54 % Favored : 90.83 % Rotamer Outliers : 1.17 % 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: -1.14 (0.39), residues: 480 helix: 2.01 (0.51), residues: 120 sheet: -0.76 (0.49), residues: 116 loop : -2.29 (0.36), residues: 244 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.433 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.1475 time to fit residues: 9.6063 Evaluate side-chains 48 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0357 time to fit residues: 0.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 3571 Z= 0.338 Angle : 0.642 7.773 4851 Z= 0.322 Chirality : 0.045 0.130 585 Planarity : 0.004 0.039 633 Dihedral : 4.881 21.952 532 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.17 % Favored : 90.21 % Rotamer Outliers : 1.46 % 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: -1.27 (0.38), residues: 480 helix: 1.95 (0.50), residues: 120 sheet: -0.87 (0.48), residues: 114 loop : -2.37 (0.36), residues: 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.440 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 0.1576 time to fit residues: 9.4448 Evaluate side-chains 45 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.439 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0435 time to fit residues: 0.8752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8170 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 3571 Z= 0.158 Angle : 0.594 7.775 4851 Z= 0.294 Chirality : 0.045 0.137 585 Planarity : 0.003 0.035 633 Dihedral : 4.512 21.724 532 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.29 % Favored : 92.08 % Rotamer Outliers : 1.17 % 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: -1.08 (0.38), residues: 480 helix: 2.10 (0.50), residues: 120 sheet: -0.77 (0.48), residues: 111 loop : -2.23 (0.36), residues: 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.451 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.1574 time to fit residues: 10.6497 Evaluate side-chains 48 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0387 time to fit residues: 0.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8207 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3571 Z= 0.242 Angle : 0.607 7.600 4851 Z= 0.302 Chirality : 0.045 0.141 585 Planarity : 0.003 0.035 633 Dihedral : 4.587 21.586 532 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % Rotamer Outliers : 0.88 % 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: -1.08 (0.39), residues: 480 helix: 1.90 (0.50), residues: 126 sheet: -0.78 (0.48), residues: 114 loop : -2.22 (0.37), residues: 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.436 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.1344 time to fit residues: 8.2705 Evaluate side-chains 45 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0348 time to fit residues: 0.7591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 28 optimal weight: 0.0070 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- 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: 0.8216 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3571 Z= 0.277 Angle : 0.618 7.395 4851 Z= 0.311 Chirality : 0.045 0.135 585 Planarity : 0.004 0.036 633 Dihedral : 4.734 21.991 532 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.54 % Favored : 90.83 % Rotamer Outliers : 0.58 % 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: -1.21 (0.38), residues: 480 helix: 1.83 (0.49), residues: 126 sheet: -0.73 (0.48), residues: 111 loop : -2.40 (0.36), residues: 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.445 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 0.1462 time to fit residues: 8.4255 Evaluate side-chains 42 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3571 Z= 0.183 Angle : 0.612 7.608 4851 Z= 0.302 Chirality : 0.045 0.141 585 Planarity : 0.004 0.034 633 Dihedral : 4.526 21.597 532 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.12 % Favored : 91.25 % 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: -1.17 (0.38), residues: 480 helix: 1.85 (0.49), residues: 126 sheet: -0.91 (0.48), residues: 111 loop : -2.25 (0.36), residues: 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.436 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1442 time to fit residues: 8.2769 Evaluate side-chains 44 residues out of total 383 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.431 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5462 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.078214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.061677 restraints weight = 11279.233| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 4.47 r_work: 0.2867 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work: 0.2851 rms_B_bonded: 4.18 restraints_weight: 0.1250 r_work: 0.2844 rms_B_bonded: 4.21 restraints_weight: 0.0625 r_work: 0.2836 rms_B_bonded: 4.26 restraints_weight: 0.0312 r_work: 0.2828 rms_B_bonded: 4.33 restraints_weight: 0.0156 r_work: 0.2819 rms_B_bonded: 4.42 restraints_weight: 0.0078 r_work: 0.2811 rms_B_bonded: 4.52 restraints_weight: 0.0039 r_work: 0.2802 rms_B_bonded: 4.63 restraints_weight: 0.0020 r_work: 0.2794 rms_B_bonded: 4.76 restraints_weight: 0.0010 r_work: 0.2785 rms_B_bonded: 4.90 restraints_weight: 0.0005 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3571 Z= 0.253 Angle : 0.621 7.472 4851 Z= 0.309 Chirality : 0.045 0.140 585 Planarity : 0.004 0.035 633 Dihedral : 4.655 21.603 532 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.96 % Favored : 90.62 % Rotamer Outliers : 0.29 % 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 (0.39), residues: 480 helix: 1.86 (0.49), residues: 126 sheet: -1.14 (0.46), residues: 118 loop : -2.21 (0.37), residues: 236 =============================================================================== Job complete usr+sys time: 1372.12 seconds wall clock time: 26 minutes 10.70 seconds (1570.70 seconds total)