Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:20:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/11_2022/7pqg_13593.pdb" } resolution = 3.7 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2296 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 2.46, per 1000 atoms: 0.76 Number of scatterers: 3251 At special positions: 0 Unit cell: (61.488, 75.6, 99.792, 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 31 16.00 O 564 8.00 N 522 7.00 C 2134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 445.6 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 67.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.715A pdb=" N ASP B 90 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.610A pdb=" N TYR B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 44 removed outlier: 4.031A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.686A pdb=" N MET A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.970A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 3.785A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.475A pdb=" N ASP A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.590A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.281A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.568A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.535A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.800A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.933A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 98 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 115 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.707A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 598 1.45 - 1.57: 1814 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 3324 Sorted by residual: bond pdb=" CG GLN A 293 " pdb=" CD GLN A 293 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N LYS A 189 " pdb=" CA LYS A 189 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C VAL A 187 " pdb=" N ILE A 188 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.26e-02 6.30e+03 1.21e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.94e-01 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.11: 60 104.11 - 111.58: 1467 111.58 - 119.06: 1210 119.06 - 126.53: 1726 126.53 - 134.00: 43 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.62 114.37 -3.75 1.02e+00 9.61e-01 1.35e+01 angle pdb=" N GLN A 293 " pdb=" CA GLN A 293 " pdb=" CB GLN A 293 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 114.01 -3.39 1.02e+00 9.61e-01 1.10e+01 angle pdb=" N GLN A 261 " pdb=" CA GLN A 261 " pdb=" C GLN A 261 " ideal model delta sigma weight residual 109.96 114.98 -5.02 1.58e+00 4.01e-01 1.01e+01 angle pdb=" N TYR A 186 " pdb=" CA TYR A 186 " pdb=" C TYR A 186 " ideal model delta sigma weight residual 113.50 109.63 3.87 1.23e+00 6.61e-01 9.89e+00 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1809 17.01 - 34.02: 131 34.02 - 51.03: 22 51.03 - 68.04: 3 68.04 - 85.05: 3 Dihedral angle restraints: 1968 sinusoidal: 758 harmonic: 1210 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 164.83 -71.83 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CA LYS A 309 " pdb=" C LYS A 309 " pdb=" N PHE A 310 " pdb=" CA PHE A 310 " ideal model delta harmonic sigma weight residual 180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU B 89 " pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 335 0.037 - 0.074: 120 0.074 - 0.112: 50 0.112 - 0.149: 19 0.149 - 0.186: 3 Chirality restraints: 527 Sorted by residual: chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 524 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 109 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 289 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C TYR A 289 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR A 289 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 290 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.011 2.00e-02 2.50e+03 1.33e-02 3.08e+00 pdb=" CG PHE A 36 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 389 2.74 - 3.28: 3900 3.28 - 3.82: 5577 3.82 - 4.36: 6655 4.36 - 4.90: 10332 Nonbonded interactions: 26853 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG1 THR A 127 " model vdw 2.204 2.440 nonbonded pdb=" O TRP B 53 " pdb=" NH2 ARG B 72 " model vdw 2.223 2.520 nonbonded pdb=" O LYS A 113 " pdb=" NH2 ARG A 249 " model vdw 2.225 2.520 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.247 2.440 nonbonded pdb=" O ILE A 168 " pdb=" OG1 THR A 171 " model vdw 2.252 2.440 ... (remaining 26848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 2134 2.51 5 N 522 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.200 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.030 Process input model: 14.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 3324 Z= 0.271 Angle : 0.880 7.914 4506 Z= 0.481 Chirality : 0.049 0.186 527 Planarity : 0.006 0.049 551 Dihedral : 12.564 85.048 1195 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.41), residues: 419 helix: 0.44 (0.32), residues: 241 sheet: -3.49 (0.73), residues: 34 loop : -1.44 (0.53), residues: 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1578 time to fit residues: 26.7392 Evaluate side-chains 115 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 39 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3324 Z= 0.260 Angle : 0.874 8.230 4506 Z= 0.459 Chirality : 0.052 0.183 527 Planarity : 0.005 0.033 551 Dihedral : 5.688 20.215 454 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -1.06 (0.41), residues: 419 helix: 0.26 (0.31), residues: 253 sheet: -2.68 (0.75), residues: 44 loop : -1.76 (0.58), residues: 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 133 average time/residue: 0.1500 time to fit residues: 23.8939 Evaluate side-chains 117 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0438 time to fit residues: 0.6137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3324 Z= 0.269 Angle : 0.898 9.471 4506 Z= 0.477 Chirality : 0.054 0.320 527 Planarity : 0.005 0.031 551 Dihedral : 5.628 22.797 454 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 31.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.40), residues: 419 helix: 0.01 (0.31), residues: 255 sheet: -2.46 (0.79), residues: 44 loop : -1.94 (0.59), residues: 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 125 average time/residue: 0.1515 time to fit residues: 22.7649 Evaluate side-chains 114 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1479 time to fit residues: 1.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3324 Z= 0.273 Angle : 0.930 10.011 4506 Z= 0.478 Chirality : 0.053 0.336 527 Planarity : 0.008 0.142 551 Dihedral : 5.616 20.640 454 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.40), residues: 419 helix: 0.03 (0.30), residues: 255 sheet: -2.46 (0.79), residues: 44 loop : -1.91 (0.59), residues: 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 122 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 125 average time/residue: 0.1621 time to fit residues: 24.0403 Evaluate side-chains 109 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0348 time to fit residues: 0.6596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3324 Z= 0.268 Angle : 0.939 10.884 4506 Z= 0.480 Chirality : 0.054 0.360 527 Planarity : 0.005 0.036 551 Dihedral : 5.538 23.550 454 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 32.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % 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: -1.18 (0.40), residues: 419 helix: 0.05 (0.31), residues: 250 sheet: -2.55 (0.79), residues: 44 loop : -1.57 (0.59), residues: 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.1513 time to fit residues: 23.1149 Evaluate side-chains 119 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0450 time to fit residues: 0.7461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3324 Z= 0.255 Angle : 0.961 12.057 4506 Z= 0.488 Chirality : 0.055 0.384 527 Planarity : 0.005 0.044 551 Dihedral : 5.518 22.221 454 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.40), residues: 419 helix: 0.09 (0.31), residues: 250 sheet: -2.58 (0.77), residues: 44 loop : -1.59 (0.58), residues: 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 120 average time/residue: 0.1506 time to fit residues: 21.7709 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0421 time to fit residues: 0.8087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.258 Angle : 0.964 12.527 4506 Z= 0.488 Chirality : 0.056 0.367 527 Planarity : 0.005 0.034 551 Dihedral : 5.452 23.105 454 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.40), residues: 419 helix: 0.04 (0.31), residues: 250 sheet: -2.44 (0.77), residues: 44 loop : -1.45 (0.59), residues: 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 118 average time/residue: 0.1541 time to fit residues: 21.8340 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0333 time to fit residues: 0.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.0000 chunk 28 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.259 Angle : 1.001 12.817 4506 Z= 0.505 Chirality : 0.057 0.383 527 Planarity : 0.005 0.035 551 Dihedral : 5.476 23.606 454 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 34.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.40), residues: 419 helix: -0.07 (0.30), residues: 254 sheet: -2.13 (0.71), residues: 52 loop : -1.82 (0.60), residues: 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 120 average time/residue: 0.1559 time to fit residues: 22.4660 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0612 time to fit residues: 0.5863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3324 Z= 0.280 Angle : 1.058 12.783 4506 Z= 0.528 Chirality : 0.057 0.365 527 Planarity : 0.005 0.047 551 Dihedral : 5.441 23.435 454 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 36.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.40), residues: 419 helix: -0.16 (0.30), residues: 254 sheet: -1.98 (0.73), residues: 52 loop : -1.82 (0.60), residues: 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 117 average time/residue: 0.1577 time to fit residues: 22.1385 Evaluate side-chains 115 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0392 time to fit residues: 0.6425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 3324 Z= 0.279 Angle : 1.064 12.712 4506 Z= 0.531 Chirality : 0.059 0.381 527 Planarity : 0.005 0.037 551 Dihedral : 5.503 23.747 454 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 36.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.40), residues: 419 helix: -0.22 (0.30), residues: 254 sheet: -1.98 (0.73), residues: 52 loop : -1.69 (0.60), residues: 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.1633 time to fit residues: 22.0181 Evaluate side-chains 108 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0657 time to fit residues: 0.6001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** 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 = 0.3762 r_free = 0.3762 target = 0.079401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.066981 restraints weight = 14251.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.068911 restraints weight = 9914.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.070307 restraints weight = 7397.578| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 3324 Z= 0.275 Angle : 1.124 12.540 4506 Z= 0.558 Chirality : 0.060 0.379 527 Planarity : 0.005 0.045 551 Dihedral : 5.534 24.823 454 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 33.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.40), residues: 419 helix: -0.23 (0.31), residues: 254 sheet: -1.97 (0.72), residues: 52 loop : -1.73 (0.59), residues: 113 =============================================================================== Job complete usr+sys time: 1151.60 seconds wall clock time: 21 minutes 43.64 seconds (1303.64 seconds total)