Starting phenix.real_space_refine (version: dev) on Sun Feb 19 23:54:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/02_2023/7k8a_22724.pdb" } resolution = 3.65 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= 0.000 sd= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5513 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5513 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5513 Classifications: {'peptide': 723} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 685} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 3.81, per 1000 atoms: 0.69 Number of scatterers: 5513 At special positions: 0 Unit cell: (92.22, 99.64, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1002 8.00 N 913 7.00 C 3570 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: 2.21 Conformation dependent library (CDL) restraints added in 845.0 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1324 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 71.1% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.661A pdb=" N TRP A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 12 " --> pdb=" O THR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 31 removed outlier: 4.589A pdb=" N VAL A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 48 through 62 removed outlier: 3.914A pdb=" N ALA A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 4.347A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 83 through 101 removed outlier: 4.169A pdb=" N GLN A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 143 through 160 removed outlier: 3.566A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 170 through 206 removed outlier: 3.734A pdb=" N LEU A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 207 through 233 Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 241 through 271 removed outlier: 3.529A pdb=" N VAL A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.774A pdb=" N SER A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 309 through 342 removed outlier: 4.998A pdb=" N ALA A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 removed outlier: 4.254A pdb=" N ARG A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 415 Proline residue: A 407 - end of helix removed outlier: 3.678A pdb=" N VAL A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 471 through 483 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.503A pdb=" N LYS A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 532 " --> pdb=" O LYS A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 563 Processing helix chain 'A' and resid 563 through 583 removed outlier: 3.530A pdb=" N MET A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 612 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 630 through 660 removed outlier: 3.536A pdb=" N PHE A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 692 removed outlier: 4.275A pdb=" N ALA A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 722 removed outlier: 3.791A pdb=" N ILE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.624A pdb=" N TRP A 737 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 747 removed outlier: 4.402A pdb=" N VAL A 745 " --> pdb=" O TRP A 741 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.967A pdb=" N THR A 133 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 518 removed outlier: 3.523A pdb=" N ILE A 516 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN A 518 " --> pdb=" O LEU A 457 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1053 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: 1.99 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1661 1.34 - 1.46: 864 1.46 - 1.58: 3045 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 5624 Sorted by residual: bond pdb=" N ASP A 78 " pdb=" CA ASP A 78 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.33e-02 5.65e+03 1.16e+01 bond pdb=" CA THR A 74 " pdb=" C THR A 74 " ideal model delta sigma weight residual 1.519 1.558 -0.039 1.28e-02 6.10e+03 9.24e+00 bond pdb=" CA ASP A 78 " pdb=" C ASP A 78 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.43e-02 4.89e+03 8.40e+00 bond pdb=" C THR A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.38e+00 bond pdb=" C VAL A 302 " pdb=" N PRO A 303 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.11e-02 8.12e+03 4.82e+00 ... (remaining 5619 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.18: 167 106.18 - 113.64: 3219 113.64 - 121.10: 2865 121.10 - 128.56: 1356 128.56 - 136.02: 46 Bond angle restraints: 7653 Sorted by residual: angle pdb=" N PRO A 75 " pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 110.70 117.53 -6.83 1.22e+00 6.72e-01 3.13e+01 angle pdb=" N LEU A 73 " pdb=" CA LEU A 73 " pdb=" C LEU A 73 " ideal model delta sigma weight residual 109.46 116.61 -7.15 1.66e+00 3.63e-01 1.86e+01 angle pdb=" C PRO A 75 " pdb=" N PRO A 76 " pdb=" CA PRO A 76 " ideal model delta sigma weight residual 119.84 114.51 5.33 1.25e+00 6.40e-01 1.82e+01 angle pdb=" C ILE A 719 " pdb=" N ARG A 720 " pdb=" CA ARG A 720 " ideal model delta sigma weight residual 122.38 115.10 7.28 1.81e+00 3.05e-01 1.62e+01 angle pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta sigma weight residual 110.28 116.18 -5.90 1.55e+00 4.16e-01 1.45e+01 ... (remaining 7648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3073 17.99 - 35.98: 235 35.98 - 53.97: 45 53.97 - 71.96: 3 71.96 - 89.95: 4 Dihedral angle restraints: 3360 sinusoidal: 1302 harmonic: 2058 Sorted by residual: dihedral pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual 122.80 139.31 -16.51 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" C PHE A 649 " pdb=" N PHE A 649 " pdb=" CA PHE A 649 " pdb=" CB PHE A 649 " ideal model delta harmonic sigma weight residual -122.60 -139.03 16.43 0 2.50e+00 1.60e-01 4.32e+01 dihedral pdb=" CA PHE A 722 " pdb=" C PHE A 722 " pdb=" N LEU A 723 " pdb=" CA LEU A 723 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 905 0.135 - 0.270: 8 0.270 - 0.405: 0 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 914 Sorted by residual: chirality pdb=" CA PHE A 649 " pdb=" N PHE A 649 " pdb=" C PHE A 649 " pdb=" CB PHE A 649 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CB ILE A 137 " pdb=" CA ILE A 137 " pdb=" CG1 ILE A 137 " pdb=" CG2 ILE A 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA ILE A 135 " pdb=" N ILE A 135 " pdb=" C ILE A 135 " pdb=" CB ILE A 135 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 911 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 406 " -0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO A 407 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 407 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 407 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 418 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 649 " 0.016 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE A 649 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 649 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 649 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 649 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 649 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 649 " 0.001 2.00e-02 2.50e+03 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 936 2.76 - 3.30: 5906 3.30 - 3.83: 9048 3.83 - 4.37: 10106 4.37 - 4.90: 16840 Nonbonded interactions: 42836 Sorted by model distance: nonbonded pdb=" N ASP A 142 " pdb=" OE2 GLU A 146 " model vdw 2.226 2.520 nonbonded pdb=" O MET A 610 " pdb=" OH TYR A 622 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR A 61 " pdb=" O VAL A 513 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THR A 680 " pdb=" NH2 ARG A 720 " model vdw 2.305 2.520 nonbonded pdb=" O GLY A 426 " pdb=" OH TYR A 431 " model vdw 2.306 2.440 ... (remaining 42831 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3570 2.51 5 N 913 2.21 5 O 1002 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.090 Process input model: 19.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 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 : 0.004 0.045 5624 Z= 0.265 Angle : 0.918 11.022 7653 Z= 0.501 Chirality : 0.052 0.675 914 Planarity : 0.006 0.075 967 Dihedral : 13.382 89.947 2036 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.15 % 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: -1.30 (0.30), residues: 719 helix: -0.15 (0.24), residues: 457 sheet: -3.15 (0.69), residues: 31 loop : -1.78 (0.41), residues: 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.677 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1501 time to fit residues: 26.0371 Evaluate side-chains 117 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0554 time to fit residues: 0.9841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5624 Z= 0.260 Angle : 0.813 8.042 7653 Z= 0.410 Chirality : 0.046 0.222 914 Planarity : 0.006 0.068 967 Dihedral : 5.457 24.450 767 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.87 % Favored : 94.99 % Rotamer Outliers : 3.23 % 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: -1.28 (0.30), residues: 719 helix: -0.04 (0.24), residues: 458 sheet: -3.31 (0.69), residues: 31 loop : -2.00 (0.40), residues: 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.611 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.1618 time to fit residues: 27.3101 Evaluate side-chains 127 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0603 time to fit residues: 2.3564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 44 optimal weight: 0.0170 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5502 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5624 Z= 0.201 Angle : 0.749 8.295 7653 Z= 0.371 Chirality : 0.044 0.280 914 Planarity : 0.005 0.059 967 Dihedral : 5.227 22.309 767 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer Outliers : 2.21 % 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: -1.00 (0.31), residues: 719 helix: 0.21 (0.24), residues: 460 sheet: -3.10 (0.67), residues: 44 loop : -1.88 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.634 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 0.1743 time to fit residues: 29.9731 Evaluate side-chains 121 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.637 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0584 time to fit residues: 1.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 5624 Z= 0.293 Angle : 0.820 7.259 7653 Z= 0.420 Chirality : 0.046 0.189 914 Planarity : 0.007 0.086 967 Dihedral : 5.602 24.422 767 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.82 % Favored : 93.05 % Rotamer Outliers : 4.25 % 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: -1.34 (0.31), residues: 719 helix: -0.06 (0.24), residues: 462 sheet: -3.35 (0.65), residues: 36 loop : -2.06 (0.40), residues: 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.649 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 0.1772 time to fit residues: 30.6907 Evaluate side-chains 125 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0627 time to fit residues: 2.4832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 17 optimal weight: 7.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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: 0.5565 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 5624 Z= 0.213 Angle : 0.743 8.637 7653 Z= 0.369 Chirality : 0.045 0.396 914 Planarity : 0.005 0.039 967 Dihedral : 5.303 24.194 767 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.29 % Favored : 94.58 % Rotamer Outliers : 2.38 % 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: -1.05 (0.31), residues: 719 helix: 0.20 (0.24), residues: 461 sheet: -3.23 (0.64), residues: 44 loop : -1.94 (0.41), residues: 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.648 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 0.1714 time to fit residues: 29.2863 Evaluate side-chains 124 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0664 time to fit residues: 1.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 5624 Z= 0.295 Angle : 0.828 7.798 7653 Z= 0.417 Chirality : 0.046 0.213 914 Planarity : 0.006 0.048 967 Dihedral : 5.616 24.301 767 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.79 % Favored : 92.07 % Rotamer Outliers : 3.23 % 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 (0.31), residues: 719 helix: 0.03 (0.24), residues: 456 sheet: -3.43 (0.65), residues: 36 loop : -1.97 (0.40), residues: 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.610 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 128 average time/residue: 0.1803 time to fit residues: 30.1635 Evaluate side-chains 124 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 0.643 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0597 time to fit residues: 2.1882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5514 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5624 Z= 0.203 Angle : 0.747 7.659 7653 Z= 0.366 Chirality : 0.044 0.246 914 Planarity : 0.005 0.043 967 Dihedral : 5.146 21.762 767 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 719 helix: 0.34 (0.24), residues: 460 sheet: -3.30 (0.64), residues: 44 loop : -1.79 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 0.649 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 125 average time/residue: 0.1788 time to fit residues: 29.6768 Evaluate side-chains 121 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0648 time to fit residues: 1.7138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5624 Z= 0.231 Angle : 0.780 9.068 7653 Z= 0.382 Chirality : 0.046 0.357 914 Planarity : 0.006 0.070 967 Dihedral : 5.176 22.088 767 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 719 helix: 0.33 (0.24), residues: 461 sheet: -3.44 (0.63), residues: 44 loop : -1.77 (0.42), residues: 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.604 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.1831 time to fit residues: 27.9486 Evaluate side-chains 122 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0656 time to fit residues: 1.8555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5624 Z= 0.200 Angle : 0.757 8.665 7653 Z= 0.367 Chirality : 0.045 0.288 914 Planarity : 0.005 0.051 967 Dihedral : 5.037 20.477 767 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.71 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 719 helix: 0.45 (0.24), residues: 464 sheet: -3.45 (0.62), residues: 44 loop : -1.92 (0.41), residues: 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 116 average time/residue: 0.1855 time to fit residues: 27.9444 Evaluate side-chains 109 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0567 time to fit residues: 1.0367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 10.0000 chunk 47 optimal weight: 0.0270 chunk 71 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5624 Z= 0.202 Angle : 0.763 8.634 7653 Z= 0.366 Chirality : 0.044 0.244 914 Planarity : 0.006 0.088 967 Dihedral : 5.022 26.699 767 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.87 % Favored : 94.99 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.32), residues: 719 helix: 0.53 (0.25), residues: 467 sheet: -3.45 (0.60), residues: 44 loop : -1.96 (0.41), residues: 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 109 average time/residue: 0.1829 time to fit residues: 26.1549 Evaluate side-chains 109 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0886 time to fit residues: 1.1809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.269808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.253796 restraints weight = 9071.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.256064 restraints weight = 5714.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.258067 restraints weight = 4588.368| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5533 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5624 Z= 0.196 Angle : 0.755 12.118 7653 Z= 0.361 Chirality : 0.044 0.243 914 Planarity : 0.005 0.051 967 Dihedral : 4.852 24.102 767 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.32), residues: 719 helix: 0.59 (0.25), residues: 468 sheet: -3.32 (0.62), residues: 44 loop : -1.78 (0.42), residues: 207 =============================================================================== Job complete usr+sys time: 1255.76 seconds wall clock time: 23 minutes 38.71 seconds (1418.71 seconds total)