Starting phenix.real_space_refine (version: dev) on Tue Apr 5 04:49:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/04_2022/7k8a_22724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/04_2022/7k8a_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_22724/04_2022/7k8a_22724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/04_2022/7k8a_22724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/04_2022/7k8a_22724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8a_22724/04_2022/7k8a_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 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 "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-4553/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: 3.78, 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: 2.25 Conformation dependent library (CDL) restraints added in 860.1 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: 0.26 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: 1.54 Time building geometry restraints manager: 2.43 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: 0.080 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: 0.800 Check model and map are aligned: 0.090 Convert atoms to be neutral: 0.050 Process input model: 18.830 Find NCS groups from input model: 0.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- 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 : 16.00 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 : 0.610 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.1561 time to fit residues: 26.9912 Evaluate side-chains 114 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0570 time to fit residues: 0.9818 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 0.1980 chunk 42 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- 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: 0.5613 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 5624 Z= 0.303 Angle : 0.880 12.288 7653 Z= 0.448 Chirality : 0.047 0.208 914 Planarity : 0.007 0.070 967 Dihedral : 5.595 25.141 767 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer Outliers : 3.40 % 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: -1.45 (0.30), residues: 719 helix: -0.18 (0.23), residues: 457 sheet: -3.20 (0.70), residues: 30 loop : -2.08 (0.40), residues: 232 *********************** 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 138 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 118 time to evaluate : 0.603 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 0.1511 time to fit residues: 25.9061 Evaluate side-chains 126 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0571 time to fit residues: 2.4767 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 0.0010 chunk 64 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- 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: 0.5570 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 5624 Z= 0.237 Angle : 0.796 8.279 7653 Z= 0.397 Chirality : 0.045 0.311 914 Planarity : 0.006 0.061 967 Dihedral : 5.439 26.296 767 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.71 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.31), residues: 719 helix: 0.04 (0.24), residues: 460 sheet: -3.21 (0.65), residues: 44 loop : -2.01 (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: 15 poor density : 120 time to evaluate : 0.625 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 129 average time/residue: 0.1708 time to fit residues: 28.9094 Evaluate side-chains 117 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 0.594 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0616 time to fit residues: 1.4832 ------------------------------------------------------------------------------- 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: 0.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** A 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.124 5624 Z= 0.219 Angle : 0.788 15.326 7653 Z= 0.389 Chirality : 0.043 0.180 914 Planarity : 0.006 0.051 967 Dihedral : 5.159 22.232 767 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.01 % Favored : 94.85 % Rotamer Outliers : 3.06 % 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: -0.93 (0.31), residues: 719 helix: 0.35 (0.24), residues: 460 sheet: -3.13 (0.66), residues: 44 loop : -2.05 (0.40), residues: 215 *********************** 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 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.642 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 128 average time/residue: 0.1700 time to fit residues: 28.8421 Evaluate side-chains 122 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.625 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0690 time to fit residues: 2.1726 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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: 0.5509 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 5624 Z= 0.239 Angle : 0.763 8.650 7653 Z= 0.379 Chirality : 0.044 0.365 914 Planarity : 0.006 0.079 967 Dihedral : 5.103 21.930 767 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % 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: -0.83 (0.32), residues: 719 helix: 0.41 (0.24), residues: 463 sheet: -3.01 (0.67), residues: 44 loop : -2.02 (0.41), residues: 212 *********************** 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 135 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 126 average time/residue: 0.1656 time to fit residues: 27.5029 Evaluate side-chains 120 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0592 time to fit residues: 1.7965 ------------------------------------------------------------------------------- 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: 0.4980 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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: 0.5567 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 5624 Z= 0.245 Angle : 0.771 9.837 7653 Z= 0.385 Chirality : 0.043 0.184 914 Planarity : 0.006 0.065 967 Dihedral : 5.189 23.297 767 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer Outliers : 2.04 % 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: -0.91 (0.31), residues: 719 helix: 0.36 (0.24), residues: 463 sheet: -3.13 (0.65), residues: 44 loop : -2.05 (0.41), residues: 212 *********************** 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 132 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 124 average time/residue: 0.1798 time to fit residues: 29.0771 Evaluate side-chains 122 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 113 time to evaluate : 0.640 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0632 time to fit residues: 1.8587 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5492 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.141 5624 Z= 0.231 Angle : 0.771 9.984 7653 Z= 0.375 Chirality : 0.043 0.211 914 Planarity : 0.006 0.073 967 Dihedral : 5.025 21.868 767 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer Outliers : 1.02 % 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: -0.65 (0.32), residues: 719 helix: 0.57 (0.25), residues: 463 sheet: -3.04 (0.64), residues: 44 loop : -1.99 (0.41), residues: 212 *********************** 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 118 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 115 average time/residue: 0.1704 time to fit residues: 26.2170 Evaluate side-chains 113 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0805 time to fit residues: 1.4994 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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: 0.5595 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.160 5624 Z= 0.269 Angle : 0.818 11.330 7653 Z= 0.408 Chirality : 0.046 0.479 914 Planarity : 0.006 0.055 967 Dihedral : 5.249 23.460 767 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.51 % Favored : 92.35 % 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: -0.90 (0.32), residues: 719 helix: 0.37 (0.25), residues: 465 sheet: -3.29 (0.63), residues: 44 loop : -2.04 (0.41), residues: 210 *********************** 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 120 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.1700 time to fit residues: 25.9320 Evaluate side-chains 115 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0605 time to fit residues: 1.5377 ------------------------------------------------------------------------------- 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: 9.9990 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5539 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.167 5624 Z= 0.261 Angle : 0.833 13.501 7653 Z= 0.416 Chirality : 0.045 0.366 914 Planarity : 0.007 0.100 967 Dihedral : 5.177 22.718 767 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % Rotamer Outliers : 1.02 % 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: -0.82 (0.32), residues: 719 helix: 0.47 (0.25), residues: 463 sheet: -3.42 (0.61), residues: 44 loop : -2.05 (0.41), residues: 212 *********************** 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: 6 poor density : 112 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 114 average time/residue: 0.1825 time to fit residues: 27.2166 Evaluate side-chains 113 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.651 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0660 time to fit residues: 1.3243 ------------------------------------------------------------------------------- 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: 7.9990 chunk 71 optimal weight: 0.0570 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.0370 chunk 5 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.185 5624 Z= 0.270 Angle : 0.857 18.421 7653 Z= 0.435 Chirality : 0.044 0.297 914 Planarity : 0.007 0.081 967 Dihedral : 5.221 26.991 767 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.40 % Favored : 93.46 % 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: -0.82 (0.32), residues: 719 helix: 0.48 (0.25), residues: 463 sheet: -3.46 (0.61), residues: 44 loop : -2.08 (0.41), residues: 212 ********************** 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 110 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1785 time to fit residues: 26.0211 Evaluate side-chains 107 residues out of total 591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9191 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.0270 chunk 23 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.271258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.255038 restraints weight = 9382.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.260545 restraints weight = 7928.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.262757 restraints weight = 3684.362| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.165 5624 Z= 0.232 Angle : 0.820 18.003 7653 Z= 0.404 Chirality : 0.043 0.278 914 Planarity : 0.006 0.074 967 Dihedral : 4.909 26.132 767 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -0.51 (0.32), residues: 719 helix: 0.69 (0.25), residues: 468 sheet: -3.28 (0.61), residues: 44 loop : -1.93 (0.42), residues: 207 =============================================================================== Job complete usr+sys time: 1227.65 seconds wall clock time: 23 minutes 0.51 seconds (1380.51 seconds total)