Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 14:10:53 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kue_23036/12_2021/7kue_23036_updated.pdb" } resolution = 3.5 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= 0.032 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: 4726 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: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1854 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 2.94, per 1000 atoms: 0.62 Number of scatterers: 4726 At special positions: 0 Unit cell: (76.36, 83.83, 89.64, 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 866 8.00 N 780 7.00 C 3049 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: 1.95 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 1 sheets defined 42.1% alpha, 0.7% 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: 4.509A 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: 4.321A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.881A 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: 3.965A pdb=" N ASP A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.994A 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 112 through 130 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: 3.809A 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: 4.503A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.691A 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 274 removed outlier: 3.685A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU B 274 " --> pdb=" O THR B 270 " (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 343 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.883A 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 117 hydrogen bonds defined for protein. 324 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: 1.01 Time building geometry restraints manager: 2.11 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: 764 1.31 - 1.44: 1302 1.44 - 1.56: 2719 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 4838 Sorted by residual: bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.302 0.222 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 1.628 -0.202 2.00e-02 2.50e+03 1.03e+02 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 5.50e+01 bond pdb=" O3P TPO A 162 " pdb=" P TPO A 162 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" O1P TPO A 162 " pdb=" P TPO A 162 " ideal model delta sigma weight residual 1.480 1.607 -0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 4833 not shown) Histogram of bond angle deviations from ideal: 78.50 - 91.42: 5 91.42 - 104.34: 89 104.34 - 117.26: 3281 117.26 - 130.18: 3145 130.18 - 143.10: 33 Bond angle restraints: 6553 Sorted by residual: angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.10 -31.06 1.44e+00 4.82e-01 4.65e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.85 -16.93 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 88.28 22.28 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 78.50 30.99 3.00e+00 1.11e-01 1.07e+02 angle pdb=" O1P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 109.48 80.11 29.37 3.00e+00 1.11e-01 9.58e+01 ... (remaining 6548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 2854 35.19 - 70.37: 54 70.37 - 105.56: 4 105.56 - 140.74: 0 140.74 - 175.93: 2 Dihedral angle restraints: 2914 sinusoidal: 1202 harmonic: 1712 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 122.80 167.36 -44.56 0 2.50e+00 1.60e-01 3.18e+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 -166.19 43.59 0 2.50e+00 1.60e-01 3.04e+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 300.00 136.91 163.09 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 2911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 724 0.402 - 0.805: 4 0.805 - 1.207: 0 1.207 - 1.609: 0 1.609 - 2.012: 1 Chirality restraints: 729 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 1.72 0.79 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.67e+00 ... (remaining 726 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.07e-02 4.15e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.061 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 delta sigma weight rms_deltas residual plane pdb=" CA THR A 223 " -0.019 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C THR A 223 " 0.069 2.00e-02 2.50e+03 pdb=" O THR A 223 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 224 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 102 " 0.063 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO A 103 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.053 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 418 2.74 - 3.28: 4377 3.28 - 3.82: 7767 3.82 - 4.36: 8987 4.36 - 4.90: 15076 Nonbonded interactions: 36625 Sorted by model distance: nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O SER A 287 " pdb=" OG SER A 287 " model vdw 2.328 2.440 nonbonded pdb=" OG1 THR A 88 " pdb=" O LEU A 135 " model vdw 2.342 2.440 nonbonded pdb=" OG SER B 153 " pdb=" OE1 GLN B 156 " model vdw 2.358 2.440 nonbonded pdb=" OD2 ASP B 224 " pdb=" OH TYR B 282 " model vdw 2.358 2.440 ... (remaining 36620 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 3049 2.51 5 N 780 2.21 5 O 866 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: 0.420 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: 2.590 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.120 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:2.310 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 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 0.222 4838 Z= 0.623 Angle : 1.621 31.062 6553 Z= 0.815 Chirality : 0.110 2.012 729 Planarity : 0.010 0.095 821 Dihedral : 15.975 175.927 1800 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.54 % Peptide Plane: Cis-proline : 3.45 % 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: -4.55 (0.28), residues: 560 helix: -3.26 (0.22), residues: 258 sheet: -3.17 (0.78), residues: 35 loop : -2.66 (0.33), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.515 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 145 average time/residue: 0.1922 time to fit residues: 34.1177 Evaluate side-chains 136 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.528 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0571 time to fit residues: 1.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 132 ASN B 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 4838 Z= 0.316 Angle : 1.118 31.256 6553 Z= 0.480 Chirality : 0.051 0.218 729 Planarity : 0.008 0.089 821 Dihedral : 11.729 176.065 640 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.31), residues: 560 helix: -2.16 (0.27), residues: 273 sheet: -2.56 (0.90), residues: 29 loop : -2.47 (0.36), residues: 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 157 average time/residue: 0.1998 time to fit residues: 38.2671 Evaluate side-chains 149 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0480 time to fit residues: 1.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 26 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 283 GLN B 164 HIS B 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 4838 Z= 0.239 Angle : 1.064 30.602 6553 Z= 0.443 Chirality : 0.049 0.272 729 Planarity : 0.009 0.118 821 Dihedral : 11.412 176.232 640 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.25 (0.33), residues: 560 helix: -1.68 (0.29), residues: 272 sheet: -3.00 (0.79), residues: 34 loop : -2.50 (0.37), residues: 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 149 average time/residue: 0.1911 time to fit residues: 34.9301 Evaluate side-chains 140 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 0.468 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1006 time to fit residues: 1.3649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 4838 Z= 0.314 Angle : 1.091 31.335 6553 Z= 0.460 Chirality : 0.051 0.303 729 Planarity : 0.008 0.122 821 Dihedral : 11.190 176.160 640 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.02 (0.33), residues: 560 helix: -1.37 (0.30), residues: 266 sheet: -3.17 (0.80), residues: 36 loop : -2.47 (0.37), residues: 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.2065 time to fit residues: 36.6163 Evaluate side-chains 142 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0521 time to fit residues: 1.8963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 4838 Z= 0.242 Angle : 1.080 30.691 6553 Z= 0.446 Chirality : 0.049 0.199 729 Planarity : 0.008 0.081 821 Dihedral : 10.809 175.370 640 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.78 (0.34), residues: 560 helix: -1.17 (0.31), residues: 267 sheet: -3.15 (0.79), residues: 36 loop : -2.34 (0.38), residues: 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.511 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 141 average time/residue: 0.1948 time to fit residues: 33.4979 Evaluate side-chains 139 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0516 time to fit residues: 1.3165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.0000 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 4838 Z= 0.204 Angle : 1.059 30.207 6553 Z= 0.435 Chirality : 0.047 0.204 729 Planarity : 0.007 0.092 821 Dihedral : 10.437 175.541 640 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.47 (0.35), residues: 560 helix: -0.92 (0.31), residues: 264 sheet: -2.81 (0.97), residues: 24 loop : -2.26 (0.38), residues: 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.2140 time to fit residues: 35.7468 Evaluate side-chains 140 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0907 time to fit residues: 1.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 chunk 21 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 4838 Z= 0.205 Angle : 1.061 30.077 6553 Z= 0.439 Chirality : 0.047 0.204 729 Planarity : 0.008 0.098 821 Dihedral : 10.198 175.686 640 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.46 (0.35), residues: 560 helix: -0.92 (0.31), residues: 268 sheet: -2.90 (1.15), residues: 17 loop : -2.30 (0.38), residues: 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 0.503 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 135 average time/residue: 0.1997 time to fit residues: 33.1042 Evaluate side-chains 135 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0578 time to fit residues: 1.3740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 48 optimal weight: 0.0070 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.1980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 4838 Z= 0.197 Angle : 1.057 30.077 6553 Z= 0.437 Chirality : 0.047 0.200 729 Planarity : 0.008 0.097 821 Dihedral : 9.999 175.759 640 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.35), residues: 560 helix: -0.75 (0.32), residues: 268 sheet: -2.74 (0.99), residues: 24 loop : -2.22 (0.39), residues: 268 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 0.553 Fit side-chains outliers start: 8 outliers final: 1 residues processed: 140 average time/residue: 0.1922 time to fit residues: 33.1822 Evaluate side-chains 136 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3183 time to fit residues: 1.1639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.492 4838 Z= 0.427 Angle : 1.500 73.893 6553 Z= 0.611 Chirality : 0.049 0.215 729 Planarity : 0.008 0.087 821 Dihedral : 10.006 175.802 640 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.32 (0.35), residues: 560 helix: -0.76 (0.32), residues: 268 sheet: -2.74 (0.99), residues: 24 loop : -2.23 (0.38), residues: 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 137 average time/residue: 0.2087 time to fit residues: 34.9194 Evaluate side-chains 144 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0577 time to fit residues: 1.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.136 4838 Z= 0.211 Angle : 1.071 30.262 6553 Z= 0.442 Chirality : 0.048 0.227 729 Planarity : 0.008 0.075 821 Dihedral : 9.883 175.901 640 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.35), residues: 560 helix: -0.77 (0.31), residues: 273 sheet: -2.71 (0.99), residues: 24 loop : -2.26 (0.39), residues: 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.650 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2141 time to fit residues: 33.4766 Evaluate side-chains 137 residues out of total 519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0571 time to fit residues: 0.8797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** 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 = 0.3927 r_free = 0.3927 target = 0.148776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133996 restraints weight = 8144.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.137878 restraints weight = 4054.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140387 restraints weight = 2434.224| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.369 4838 Z= 0.518 Angle : 1.519 73.899 6553 Z= 0.632 Chirality : 0.051 0.335 729 Planarity : 0.008 0.125 821 Dihedral : 9.927 175.877 640 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -2.26 (0.35), residues: 560 helix: -0.73 (0.31), residues: 273 sheet: -2.66 (1.00), residues: 24 loop : -2.22 (0.39), residues: 263 =============================================================================== Job complete usr+sys time: 1421.98 seconds wall clock time: 26 minutes 11.97 seconds (1571.97 seconds total)