Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:36:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x0u_21984/04_2022/6x0u_21984.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 3091 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 933 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain breaks: 4 Chain: "A" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 484 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 454 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Time building chain proxies: 2.34, per 1000 atoms: 0.76 Number of scatterers: 3091 At special positions: 0 Unit cell: (99.456, 83.916, 81.844, 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 18 16.00 O 587 8.00 N 544 7.00 C 1942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 390.9 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 68.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 8 through 21 removed outlier: 3.826A pdb=" N GLN B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 21 " --> pdb=" O CYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.612A pdb=" N ARG B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.870A pdb=" N VAL B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 85 removed outlier: 4.061A pdb=" N SER B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 4.107A pdb=" N ILE B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 removed outlier: 3.684A pdb=" N PHE D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.902A pdb=" N LYS D 39 " --> pdb=" O ARG D 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.578A pdb=" N LEU D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.642A pdb=" N ALA D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 91 " --> pdb=" O ASP D 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 removed outlier: 3.537A pdb=" N ASP D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 183 removed outlier: 4.098A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE D 175 " --> pdb=" O CYS D 171 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN D 176 " --> pdb=" O HIS D 172 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N VAL D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.769A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.654A pdb=" N SER A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 75 removed outlier: 3.833A pdb=" N SER A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.531A pdb=" N MET C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 28 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.808A pdb=" N GLY C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 75 removed outlier: 3.862A pdb=" N LEU C 60 " --> pdb=" O ASN C 56 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER C 62 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.58 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1050 1.34 - 1.46: 519 1.46 - 1.58: 1526 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3121 Sorted by residual: bond pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.60e+00 bond pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.28e-01 bond pdb=" CA VAL B 28 " pdb=" CB VAL B 28 " ideal model delta sigma weight residual 1.530 1.539 -0.009 1.11e-02 8.12e+03 6.79e-01 bond pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 1.525 1.515 0.010 1.29e-02 6.01e+03 6.25e-01 bond pdb=" CG LEU B 96 " pdb=" CD1 LEU B 96 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 ... (remaining 3116 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.00: 71 107.00 - 113.74: 1805 113.74 - 120.47: 1269 120.47 - 127.20: 1040 127.20 - 133.93: 20 Bond angle restraints: 4205 Sorted by residual: angle pdb=" C ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.42 115.77 -5.35 1.99e+00 2.53e-01 7.22e+00 angle pdb=" CA LEU D 82 " pdb=" CB LEU D 82 " pdb=" CG LEU D 82 " ideal model delta sigma weight residual 116.30 125.13 -8.83 3.50e+00 8.16e-02 6.36e+00 angle pdb=" N ARG D 141 " pdb=" CA ARG D 141 " pdb=" C ARG D 141 " ideal model delta sigma weight residual 111.96 108.82 3.14 1.41e+00 5.03e-01 4.94e+00 angle pdb=" N ASN D 135 " pdb=" CA ASN D 135 " pdb=" CB ASN D 135 " ideal model delta sigma weight residual 110.49 106.91 3.58 1.69e+00 3.50e-01 4.49e+00 angle pdb=" N ASP A 26 " pdb=" CA ASP A 26 " pdb=" C ASP A 26 " ideal model delta sigma weight residual 113.41 111.00 2.41 1.22e+00 6.72e-01 3.89e+00 ... (remaining 4200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1738 17.60 - 35.20: 171 35.20 - 52.80: 34 52.80 - 70.39: 5 70.39 - 87.99: 2 Dihedral angle restraints: 1950 sinusoidal: 794 harmonic: 1156 Sorted by residual: dihedral pdb=" CA LEU D 134 " pdb=" C LEU D 134 " pdb=" N ASN D 135 " pdb=" CA ASN D 135 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE D 133 " pdb=" C PHE D 133 " pdb=" N LEU D 134 " pdb=" CA LEU D 134 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ASN D 135 " pdb=" C ASN D 135 " pdb=" N ASN D 136 " pdb=" CA ASN D 136 " ideal model delta harmonic sigma weight residual 180.00 163.43 16.57 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 247 0.024 - 0.048: 175 0.048 - 0.072: 56 0.072 - 0.096: 18 0.096 - 0.120: 9 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA PRO B 123 " pdb=" N PRO B 123 " pdb=" C PRO B 123 " pdb=" CB PRO B 123 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA PRO B 9 " pdb=" N PRO B 9 " pdb=" C PRO B 9 " pdb=" CB PRO B 9 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.09e-01 chirality pdb=" CA VAL D 143 " pdb=" N VAL D 143 " pdb=" C VAL D 143 " pdb=" CB VAL D 143 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 502 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 122 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO B 123 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 185 " -0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO D 186 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 186 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 186 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 8 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.35e-01 pdb=" N PRO B 9 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.014 5.00e-02 4.00e+02 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 872 2.80 - 3.33: 2848 3.33 - 3.85: 4253 3.85 - 4.38: 5348 4.38 - 4.90: 8717 Nonbonded interactions: 22038 Sorted by model distance: nonbonded pdb=" O PRO A 57 " pdb=" OG SER A 61 " model vdw 2.277 2.440 nonbonded pdb=" O ALA C 59 " pdb=" OG SER C 62 " model vdw 2.283 2.440 nonbonded pdb=" OE1 GLN B 84 " pdb=" OG1 THR A 24 " model vdw 2.301 2.440 nonbonded pdb=" O ALA B 115 " pdb=" NE2 GLN B 120 " model vdw 2.310 2.520 nonbonded pdb=" O GLY B 40 " pdb=" OG SER B 41 " model vdw 2.332 2.440 ... (remaining 22033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 75) selection = chain 'C' } 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 18 5.16 5 C 1942 2.51 5 N 544 2.21 5 O 587 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.790 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 13.390 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.024 3121 Z= 0.257 Angle : 0.618 8.827 4205 Z= 0.348 Chirality : 0.037 0.120 505 Planarity : 0.003 0.033 540 Dihedral : 14.498 87.993 1190 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.05 % 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: -5.79 (0.33), residues: 380 helix: -4.35 (0.17), residues: 263 sheet: None (None), residues: 0 loop : -1.86 (0.61), residues: 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2475 time to fit residues: 31.8956 Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN B 82 HIS D 48 ASN D 176 GLN C 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 3121 Z= 0.218 Angle : 0.631 8.800 4205 Z= 0.316 Chirality : 0.037 0.126 505 Planarity : 0.006 0.063 540 Dihedral : 4.475 17.806 423 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.38), residues: 380 helix: -2.37 (0.25), residues: 266 sheet: None (None), residues: 0 loop : -1.77 (0.60), residues: 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.382 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.2333 time to fit residues: 25.2326 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0303 time to fit residues: 0.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.0030 chunk 17 optimal weight: 5.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN B 120 GLN D 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 3121 Z= 0.149 Angle : 0.554 7.172 4205 Z= 0.274 Chirality : 0.034 0.120 505 Planarity : 0.006 0.084 540 Dihedral : 3.940 19.232 423 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.42), residues: 380 helix: -0.77 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -1.79 (0.60), residues: 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.351 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.2386 time to fit residues: 23.9526 Evaluate side-chains 78 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0435 time to fit residues: 0.7425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.084 3121 Z= 0.140 Angle : 0.504 6.743 4205 Z= 0.253 Chirality : 0.035 0.118 505 Planarity : 0.006 0.092 540 Dihedral : 3.749 18.117 423 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 2.34 % 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: -0.99 (0.44), residues: 380 helix: -0.05 (0.33), residues: 271 sheet: None (None), residues: 0 loop : -2.01 (0.56), residues: 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.358 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 85 average time/residue: 0.2587 time to fit residues: 24.6269 Evaluate side-chains 82 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0322 time to fit residues: 0.7433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.0010 chunk 32 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 20 optimal weight: 0.0000 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN D 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 3121 Z= 0.139 Angle : 0.535 9.887 4205 Z= 0.260 Chirality : 0.034 0.118 505 Planarity : 0.006 0.097 540 Dihedral : 3.477 18.074 423 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.45), residues: 380 helix: 0.43 (0.33), residues: 273 sheet: None (None), residues: 0 loop : -1.74 (0.58), residues: 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.398 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 92 average time/residue: 0.2278 time to fit residues: 23.6845 Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0299 time to fit residues: 0.5649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 3121 Z= 0.151 Angle : 0.511 6.756 4205 Z= 0.259 Chirality : 0.035 0.117 505 Planarity : 0.007 0.106 540 Dihedral : 3.460 16.797 423 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 2.63 % 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: 0.14 (0.45), residues: 380 helix: 0.78 (0.33), residues: 278 sheet: None (None), residues: 0 loop : -1.74 (0.59), residues: 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.395 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 86 average time/residue: 0.2467 time to fit residues: 23.9359 Evaluate side-chains 81 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0325 time to fit residues: 0.6759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 3121 Z= 0.158 Angle : 0.562 10.221 4205 Z= 0.276 Chirality : 0.035 0.116 505 Planarity : 0.007 0.111 540 Dihedral : 3.386 17.646 423 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.45), residues: 380 helix: 1.15 (0.33), residues: 276 sheet: None (None), residues: 0 loop : -1.66 (0.57), residues: 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.371 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 85 average time/residue: 0.2409 time to fit residues: 23.1362 Evaluate side-chains 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0341 time to fit residues: 0.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.0670 chunk 14 optimal weight: 0.0670 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 3121 Z= 0.153 Angle : 0.512 7.757 4205 Z= 0.253 Chirality : 0.035 0.116 505 Planarity : 0.006 0.089 540 Dihedral : 3.401 17.152 423 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.45), residues: 380 helix: 1.35 (0.34), residues: 277 sheet: None (None), residues: 0 loop : -1.56 (0.57), residues: 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.340 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 79 average time/residue: 0.2400 time to fit residues: 21.3385 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0323 time to fit residues: 0.6501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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: 0.7801 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.152 3121 Z= 0.191 Angle : 0.619 12.474 4205 Z= 0.314 Chirality : 0.036 0.115 505 Planarity : 0.008 0.130 540 Dihedral : 3.447 17.375 423 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.45), residues: 380 helix: 1.50 (0.34), residues: 275 sheet: None (None), residues: 0 loop : -1.75 (0.56), residues: 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.389 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.2657 time to fit residues: 22.6142 Evaluate side-chains 74 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0372 time to fit residues: 0.5680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.130 3121 Z= 0.203 Angle : 0.598 10.231 4205 Z= 0.298 Chirality : 0.037 0.115 505 Planarity : 0.007 0.110 540 Dihedral : 3.621 16.530 423 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.45), residues: 380 helix: 1.42 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.77 (0.56), residues: 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.600 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.2602 time to fit residues: 23.5850 Evaluate side-chains 75 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0330 time to fit residues: 0.7325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.0030 chunk 21 optimal weight: 0.0270 chunk 33 optimal weight: 0.0040 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.2860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140724 restraints weight = 4166.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141273 restraints weight = 3545.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141290 restraints weight = 3150.349| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.119 3121 Z= 0.158 Angle : 0.570 10.427 4205 Z= 0.278 Chirality : 0.035 0.115 505 Planarity : 0.006 0.098 540 Dihedral : 3.355 17.913 423 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.45), residues: 380 helix: 1.72 (0.33), residues: 277 sheet: None (None), residues: 0 loop : -1.64 (0.58), residues: 103 =============================================================================== Job complete usr+sys time: 1243.61 seconds wall clock time: 23 minutes 1.19 seconds (1381.19 seconds total)