Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 06:59:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5m_13201/04_2023/7p5m_13201.pdb" } resolution = 3.92 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= 0.005 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4006 2.51 5 N 976 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3018 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain breaks: 1 Chain: "B" Number of atoms: 3018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3018 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 9, 'TRANS': 384} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.84, per 1000 atoms: 0.62 Number of scatterers: 6204 At special positions: 0 Unit cell: (92.442, 70.308, 128.898, 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 46 16.00 O 1176 8.00 N 976 7.00 C 4006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 382 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 367 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 283 " " NAG A 602 " - " ASN A 31 " " NAG B 601 " - " ASN B 283 " " NAG B 602 " - " ASN B 31 " " NAG C 1 " - " ASN A 352 " " NAG D 1 " - " ASN A 129 " " NAG E 1 " - " ASN B 352 " " NAG F 1 " - " ASN B 129 " Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.0 seconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 38 through 70 removed outlier: 3.660A pdb=" N ALA A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 159 removed outlier: 4.199A pdb=" N LEU A 150 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 4.333A pdb=" N ALA A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 237 removed outlier: 3.502A pdb=" N LEU A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 276 removed outlier: 3.654A pdb=" N LEU A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 244 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 308 through 337 removed outlier: 3.971A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Proline residue: A 335 - end of helix Processing helix chain 'A' and resid 341 through 365 Processing helix chain 'A' and resid 366 through 382 removed outlier: 4.426A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 414 removed outlier: 3.682A pdb=" N GLN A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Proline residue: A 411 - end of helix Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 38 through 70 removed outlier: 3.646A pdb=" N ALA B 70 " --> pdb=" O TYR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 159 removed outlier: 4.245A pdb=" N LEU B 150 " --> pdb=" O MET B 146 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 4.284A pdb=" N ALA B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 191 through 237 removed outlier: 3.611A pdb=" N LEU B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 276 removed outlier: 3.739A pdb=" N LEU B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 244 " --> pdb=" O CYS B 240 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 285 Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 308 through 337 removed outlier: 4.127A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Proline residue: B 335 - end of helix Processing helix chain 'B' and resid 341 through 365 Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.418A pdb=" N LEU B 370 " --> pdb=" O ASP B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 409 removed outlier: 3.543A pdb=" N GLN B 387 " --> pdb=" O TYR B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 562 hydrogen bonds defined for protein. 1680 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: 1.81 Time building geometry restraints manager: 2.91 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: 1918 1.34 - 1.46: 1290 1.46 - 1.58: 3062 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6332 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.01e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.78e+00 ... (remaining 6327 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.34: 69 105.34 - 112.52: 3510 112.52 - 119.71: 1969 119.71 - 126.89: 3000 126.89 - 134.07: 82 Bond angle restraints: 8630 Sorted by residual: angle pdb=" C LEU B 282 " pdb=" N ASN B 283 " pdb=" CA ASN B 283 " ideal model delta sigma weight residual 122.65 116.56 6.09 1.60e+00 3.91e-01 1.45e+01 angle pdb=" C ASP B 166 " pdb=" N TYR B 167 " pdb=" CA TYR B 167 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C ASP A 166 " pdb=" N TYR A 167 " pdb=" CA TYR A 167 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C LEU A 282 " pdb=" N ASN A 283 " pdb=" CA ASN A 283 " ideal model delta sigma weight residual 122.38 116.47 5.91 1.81e+00 3.05e-01 1.07e+01 angle pdb=" N VAL B 23 " pdb=" CA VAL B 23 " pdb=" C VAL B 23 " ideal model delta sigma weight residual 113.71 110.95 2.76 9.50e-01 1.11e+00 8.42e+00 ... (remaining 8625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 3193 16.05 - 32.10: 300 32.10 - 48.15: 91 48.15 - 64.20: 6 64.20 - 80.25: 6 Dihedral angle restraints: 3596 sinusoidal: 1310 harmonic: 2286 Sorted by residual: dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 61.58 31.42 1 1.00e+01 1.00e-02 1.41e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 367 " pdb=" CB CYS B 367 " ideal model delta sinusoidal sigma weight residual 93.00 62.60 30.40 1 1.00e+01 1.00e-02 1.32e+01 dihedral pdb=" CA ASN B 283 " pdb=" C ASN B 283 " pdb=" N VAL B 284 " pdb=" CA VAL B 284 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 3593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 901 0.051 - 0.102: 148 0.102 - 0.152: 11 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 1066 Sorted by residual: chirality pdb=" CA ASN A 283 " pdb=" N ASN A 283 " pdb=" C ASN A 283 " pdb=" CB ASN A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1063 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 283 " 0.001 2.00e-02 2.50e+03 3.05e-02 1.16e+01 pdb=" CG ASN A 283 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 283 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 283 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 167 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C TYR B 167 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR B 167 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 168 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 167 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C TYR A 167 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 167 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 168 " -0.019 2.00e-02 2.50e+03 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 823 2.75 - 3.29: 6592 3.29 - 3.82: 10801 3.82 - 4.36: 11266 4.36 - 4.90: 20145 Nonbonded interactions: 49627 Sorted by model distance: nonbonded pdb=" O TYR A 41 " pdb=" OG SER A 44 " model vdw 2.209 2.440 nonbonded pdb=" O LEU A 154 " pdb=" OG SER A 158 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU A 151 " pdb=" NE2 GLN A 175 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN B 31 " pdb=" OG1 THR B 33 " model vdw 2.249 2.440 nonbonded pdb=" OD2 ASP A 38 " pdb=" OG SER A 40 " model vdw 2.259 2.440 ... (remaining 49622 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.950 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 20.150 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6332 Z= 0.225 Angle : 0.597 7.966 8630 Z= 0.297 Chirality : 0.039 0.254 1066 Planarity : 0.004 0.052 1050 Dihedral : 13.681 80.248 2116 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 3.52 (0.30), residues: 780 helix: 2.66 (0.19), residues: 662 sheet: None (None), residues: 0 loop : 0.33 (0.60), residues: 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1519 time to fit residues: 42.3196 Evaluate side-chains 188 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 6332 Z= 0.200 Angle : 0.563 7.651 8630 Z= 0.284 Chirality : 0.037 0.169 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.723 20.262 838 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.29), residues: 780 helix: 2.75 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.46 (0.60), residues: 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 215 average time/residue: 0.1494 time to fit residues: 43.8328 Evaluate side-chains 206 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0650 time to fit residues: 2.3817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7689 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 6332 Z= 0.253 Angle : 0.591 7.098 8630 Z= 0.294 Chirality : 0.039 0.240 1066 Planarity : 0.004 0.050 1050 Dihedral : 3.728 18.234 838 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.53 % 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 (0.29), residues: 780 helix: 2.66 (0.19), residues: 664 sheet: None (None), residues: 0 loop : 0.39 (0.60), residues: 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 214 average time/residue: 0.1619 time to fit residues: 46.7772 Evaluate side-chains 212 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0630 time to fit residues: 1.8793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7656 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6332 Z= 0.166 Angle : 0.548 7.986 8630 Z= 0.270 Chirality : 0.037 0.234 1066 Planarity : 0.004 0.050 1050 Dihedral : 3.667 16.912 838 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer Outliers : 2.29 % 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: 3.72 (0.29), residues: 780 helix: 2.82 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.17 (0.59), residues: 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 218 average time/residue: 0.1524 time to fit residues: 45.2104 Evaluate side-chains 213 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 203 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0638 time to fit residues: 2.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.7687 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 6332 Z= 0.236 Angle : 0.586 7.052 8630 Z= 0.288 Chirality : 0.038 0.242 1066 Planarity : 0.004 0.050 1050 Dihedral : 3.658 16.458 838 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.68 % 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: 3.70 (0.29), residues: 780 helix: 2.79 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.22 (0.60), residues: 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 212 average time/residue: 0.1420 time to fit residues: 41.3385 Evaluate side-chains 213 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0665 time to fit residues: 1.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6332 Z= 0.174 Angle : 0.564 7.604 8630 Z= 0.274 Chirality : 0.036 0.229 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.649 16.315 838 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.29), residues: 780 helix: 2.89 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.33 (0.61), residues: 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 216 average time/residue: 0.1449 time to fit residues: 43.2034 Evaluate side-chains 218 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 204 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0629 time to fit residues: 2.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7677 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6332 Z= 0.207 Angle : 0.578 7.596 8630 Z= 0.283 Chirality : 0.037 0.229 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.660 17.047 838 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 0.92 % 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: 3.81 (0.29), residues: 780 helix: 2.86 (0.19), residues: 666 sheet: None (None), residues: 0 loop : 0.34 (0.61), residues: 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 211 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 215 average time/residue: 0.1448 time to fit residues: 42.7797 Evaluate side-chains 209 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0626 time to fit residues: 1.4784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 42 optimal weight: 0.1980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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: 0.7643 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 6332 Z= 0.163 Angle : 0.574 8.042 8630 Z= 0.277 Chirality : 0.036 0.218 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.644 15.787 838 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 1.53 % 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: 3.95 (0.29), residues: 780 helix: 2.94 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.37 (0.61), residues: 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 222 average time/residue: 0.1526 time to fit residues: 45.8069 Evaluate side-chains 219 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 211 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0635 time to fit residues: 1.7823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.7650 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6332 Z= 0.176 Angle : 0.603 9.078 8630 Z= 0.288 Chirality : 0.037 0.219 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.689 19.686 838 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.61 % 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: 3.96 (0.29), residues: 780 helix: 2.94 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.43 (0.61), residues: 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 214 average time/residue: 0.1513 time to fit residues: 44.0455 Evaluate side-chains 214 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0642 time to fit residues: 1.4109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 6332 Z= 0.195 Angle : 0.615 8.702 8630 Z= 0.295 Chirality : 0.038 0.219 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.668 17.565 838 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.07 % 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: 3.93 (0.29), residues: 780 helix: 2.91 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.49 (0.62), residues: 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 206 average time/residue: 0.1520 time to fit residues: 42.6997 Evaluate side-chains 209 residues out of total 654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 204 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0593 time to fit residues: 1.5087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.175733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.151213 restraints weight = 8525.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155031 restraints weight = 5101.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.157595 restraints weight = 3551.405| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 6332 Z= 0.192 Angle : 0.611 8.665 8630 Z= 0.292 Chirality : 0.038 0.218 1066 Planarity : 0.004 0.051 1050 Dihedral : 3.684 18.305 838 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.46 % 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: 3.94 (0.29), residues: 780 helix: 2.92 (0.19), residues: 668 sheet: None (None), residues: 0 loop : 0.49 (0.61), residues: 112 =============================================================================== Job complete usr+sys time: 1415.91 seconds wall clock time: 26 minutes 36.38 seconds (1596.38 seconds total)