Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:19:50 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/12_2021/6xi8_22191_updated.pdb" } resolution = 3.64 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 5022 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 269, 'PCIS': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.64 Number of scatterers: 5022 At special positions: 0 Unit cell: (96.28, 85.49, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 926 8.00 N 836 7.00 C 3229 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 715.5 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 1 sheets defined 43.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.510A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.320A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 184 through 200 removed outlier: 3.967A pdb=" N ASP A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 200 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 62 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 109 through 130 removed outlier: 5.504A pdb=" N LEU B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.810A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 228' Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.685A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.612A pdb=" N LYS B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 358 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.884A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 132 hydrogen bonds defined for protein. 363 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: 1.08 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 823 1.31 - 1.44: 1360 1.44 - 1.56: 2900 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 5136 Sorted by residual: bond pdb=" C THR B 351 " pdb=" N GLU B 352 " ideal model delta sigma weight residual 1.333 1.554 -0.222 1.45e-02 4.76e+03 2.34e+02 bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.629 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.27e-02 6.20e+03 8.97e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5131 not shown) Histogram of bond angle deviations from ideal: 78.53 - 91.43: 6 91.43 - 104.34: 96 104.34 - 117.25: 3486 117.25 - 130.16: 3349 130.16 - 143.07: 37 Bond angle restraints: 6974 Sorted by residual: angle pdb=" O GLU B 344 " pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 122.43 85.70 36.73 1.46e+00 4.69e-01 6.33e+02 angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.07 -31.03 1.44e+00 4.82e-01 4.64e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.88 -16.96 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.32 22.24 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 109.49 78.53 30.96 3.00e+00 1.11e-01 1.07e+02 ... (remaining 6969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 3033 35.19 - 70.38: 54 70.38 - 105.56: 4 105.56 - 140.75: 0 140.75 - 175.94: 2 Dihedral angle restraints: 3093 sinusoidal: 1203 harmonic: 1890 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.25 -44.45 0 2.50e+00 1.60e-01 3.16e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.09 43.49 0 2.50e+00 1.60e-01 3.03e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.92 163.08 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 3090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 785 0.402 - 0.803: 4 0.803 - 1.205: 0 1.205 - 1.607: 0 1.607 - 2.008: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA TYR B 362 " pdb=" N TYR B 362 " pdb=" C TYR B 362 " pdb=" CB TYR B 362 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 787 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 344 " -0.123 2.00e-02 2.50e+03 1.90e-01 3.61e+02 pdb=" C GLU B 344 " 0.328 2.00e-02 2.50e+03 pdb=" O GLU B 344 " -0.112 2.00e-02 2.50e+03 pdb=" N ASP B 345 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.061 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C THR B 351 " 0.183 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.069 2.00e-02 2.50e+03 pdb=" N GLU B 352 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 1 2.05 - 2.76: 686 2.76 - 3.47: 6755 3.47 - 4.19: 11420 4.19 - 4.90: 19696 Nonbonded interactions: 38558 Sorted by model distance: nonbonded pdb=" O CYS B 364 " pdb=" CG PRO B 367 " model vdw 1.333 3.440 nonbonded pdb=" C CYS B 364 " pdb=" CG PRO B 367 " model vdw 2.113 3.670 nonbonded pdb=" O CYS B 364 " pdb=" CD PRO B 367 " model vdw 2.160 3.440 nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O GLU B 344 " pdb=" N CYS B 346 " model vdw 2.215 2.520 ... (remaining 38553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3229 2.51 5 N 836 2.21 5 O 926 1.98 5 F 3 1.80 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=0.77 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 Write .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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.690 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 16.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 22.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 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 : 0.010 0.223 5136 Z= 0.698 Angle : 1.688 36.730 6974 Z= 0.897 Chirality : 0.111 2.008 790 Planarity : 0.012 0.190 881 Dihedral : 15.712 175.938 1861 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 3.03 % 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: -4.62 (0.27), residues: 621 helix: -3.24 (0.21), residues: 289 sheet: -3.17 (0.77), residues: 35 loop : -2.79 (0.31), residues: 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.1959 time to fit residues: 44.3961 Evaluate side-chains 165 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 GLN B 212 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 5136 Z= 0.233 Angle : 1.113 30.113 6974 Z= 0.471 Chirality : 0.049 0.233 790 Planarity : 0.009 0.131 881 Dihedral : 11.357 178.913 699 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.27 (0.30), residues: 621 helix: -1.95 (0.27), residues: 273 sheet: -2.35 (1.06), residues: 24 loop : -2.36 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 172 average time/residue: 0.1996 time to fit residues: 42.0432 Evaluate side-chains 172 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0850 time to fit residues: 2.0784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 142 GLN A 213 GLN A 239 ASN B 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 5136 Z= 0.286 Angle : 1.118 30.171 6974 Z= 0.484 Chirality : 0.049 0.174 790 Planarity : 0.008 0.095 881 Dihedral : 11.113 178.761 699 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.79 (0.31), residues: 621 helix: -1.33 (0.28), residues: 268 sheet: -2.98 (0.84), residues: 30 loop : -2.20 (0.33), residues: 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 190 average time/residue: 0.1921 time to fit residues: 45.1176 Evaluate side-chains 182 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 0.572 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0986 time to fit residues: 2.1985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 0.0170 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 213 GLN A 239 ASN A 276 GLN A 283 GLN B 219 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 5136 Z= 0.203 Angle : 1.068 29.682 6974 Z= 0.443 Chirality : 0.047 0.175 790 Planarity : 0.007 0.091 881 Dihedral : 10.566 178.005 699 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.51 (0.31), residues: 621 helix: -0.95 (0.30), residues: 266 sheet: -2.76 (0.90), residues: 30 loop : -2.21 (0.32), residues: 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 178 average time/residue: 0.1822 time to fit residues: 40.5572 Evaluate side-chains 177 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 0.529 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0525 time to fit residues: 1.7558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 212 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 5136 Z= 0.205 Angle : 1.076 29.771 6974 Z= 0.446 Chirality : 0.046 0.186 790 Planarity : 0.006 0.086 881 Dihedral : 10.281 179.924 699 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.36 (0.32), residues: 621 helix: -0.82 (0.31), residues: 268 sheet: -2.78 (0.87), residues: 30 loop : -2.13 (0.33), residues: 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 182 average time/residue: 0.1758 time to fit residues: 40.0411 Evaluate side-chains 181 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 0.573 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0565 time to fit residues: 1.5889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.5842 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.118 5136 Z= 0.208 Angle : 1.092 29.646 6974 Z= 0.452 Chirality : 0.046 0.167 790 Planarity : 0.006 0.084 881 Dihedral : 10.092 179.883 699 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.48 (0.32), residues: 621 helix: -0.87 (0.30), residues: 279 sheet: -2.75 (0.88), residues: 30 loop : -2.28 (0.33), residues: 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 183 average time/residue: 0.1816 time to fit residues: 41.5132 Evaluate side-chains 187 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0814 time to fit residues: 1.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 0.0170 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.128 5136 Z= 0.226 Angle : 1.109 29.687 6974 Z= 0.467 Chirality : 0.046 0.174 790 Planarity : 0.007 0.089 881 Dihedral : 9.964 179.747 699 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.39 (0.32), residues: 621 helix: -0.78 (0.30), residues: 280 sheet: -2.64 (0.95), residues: 30 loop : -2.26 (0.33), residues: 311 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 180 average time/residue: 0.1763 time to fit residues: 39.7470 Evaluate side-chains 183 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 176 time to evaluate : 0.565 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0555 time to fit residues: 1.4716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.2980 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 53 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5822 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 5136 Z= 0.210 Angle : 1.108 29.617 6974 Z= 0.461 Chirality : 0.047 0.174 790 Planarity : 0.006 0.080 881 Dihedral : 9.838 179.620 699 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.33 (0.32), residues: 621 helix: -0.72 (0.31), residues: 272 sheet: -2.53 (0.96), residues: 30 loop : -2.22 (0.33), residues: 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 177 average time/residue: 0.1837 time to fit residues: 40.6423 Evaluate side-chains 175 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0456 time to fit residues: 0.9833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 5136 Z= 0.235 Angle : 1.134 29.665 6974 Z= 0.478 Chirality : 0.049 0.175 790 Planarity : 0.006 0.078 881 Dihedral : 9.826 179.404 699 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.30 (0.32), residues: 621 helix: -0.75 (0.30), residues: 272 sheet: -2.42 (1.00), residues: 30 loop : -2.16 (0.34), residues: 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 174 average time/residue: 0.1957 time to fit residues: 42.4063 Evaluate side-chains 179 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 0.558 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1550 time to fit residues: 2.4468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 0.0010 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 46 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 5136 Z= 0.231 Angle : 1.138 29.642 6974 Z= 0.479 Chirality : 0.049 0.202 790 Planarity : 0.006 0.077 881 Dihedral : 9.790 178.994 699 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.34 (0.32), residues: 621 helix: -0.85 (0.30), residues: 276 sheet: -2.42 (1.00), residues: 30 loop : -2.12 (0.34), residues: 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1960 time to fit residues: 42.5293 Evaluate side-chains 174 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 33 optimal weight: 0.0000 overall best weight: 0.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.155244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.132702 restraints weight = 10662.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136822 restraints weight = 6421.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.139608 restraints weight = 4393.536| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4324 r_free = 0.4324 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 5136 Z= 0.228 Angle : 1.137 29.657 6974 Z= 0.481 Chirality : 0.049 0.267 790 Planarity : 0.006 0.072 881 Dihedral : 9.778 178.826 699 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.29 (0.33), residues: 621 helix: -0.81 (0.30), residues: 276 sheet: -2.37 (1.02), residues: 30 loop : -2.10 (0.34), residues: 315 =============================================================================== Job complete usr+sys time: 1544.44 seconds wall clock time: 28 minutes 27.45 seconds (1707.45 seconds total)