Starting phenix.real_space_refine on Sun Mar 10 22:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/03_2024/6qnt_4608.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/03_2024/6qnt_4608.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/6qnt_4608/03_2024/6qnt_4608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/03_2024/6qnt_4608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/03_2024/6qnt_4608.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qnt_4608/03_2024/6qnt_4608.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3709 2.51 5 N 928 2.21 5 O 1117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5774 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1400 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain breaks: 2 Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 11, 'TRANS': 169} Chain breaks: 2 Chain: "C" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1409 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 2 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1541 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Time building chain proxies: 3.72, per 1000 atoms: 0.64 Number of scatterers: 5774 At special positions: 0 Unit cell: (93.896, 100.298, 91.762, 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 20 16.00 O 1117 8.00 N 928 7.00 C 3709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.0 seconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 16 sheets defined 3.3% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.524A pdb=" N ASN B 186 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 186 removed outlier: 3.671A pdb=" N LYS C 185 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 186 " --> pdb=" O LEU C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 182 through 186' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.754A pdb=" N PHE C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.562A pdb=" N LEU A 160 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 154 through 158 removed outlier: 3.687A pdb=" N THR A 172 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 197 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 197 Processing sheet with id=AA5, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 188 through 197 removed outlier: 3.731A pdb=" N TYR B 284 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 289 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASN B 293 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 215 through 216 removed outlier: 3.990A pdb=" N VAL C 161 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N LEU C 292 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.653A pdb=" N LEU C 292 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ASN C 293 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 120 removed outlier: 6.733A pdb=" N PHE D 115 " --> pdb=" O GLN D 210 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ARG D 212 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY D 117 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU D 214 " --> pdb=" O GLY D 117 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 119 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR D 187 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LEU D 154 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR D 189 " --> pdb=" O VAL D 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.855A pdb=" N ILE D 171 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 230 through 231 removed outlier: 6.641A pdb=" N GLY D 230 " --> pdb=" O LYS D 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 245 removed outlier: 6.839A pdb=" N GLU D 240 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 287 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR D 242 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 285 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 282 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 262 through 265 removed outlier: 7.010A pdb=" N SER D 302 " --> pdb=" O ALA D 264 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 387 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: 1.46 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1788 1.34 - 1.46: 1082 1.46 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.80: 34 Bond restraints: 5899 Sorted by residual: bond pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.53e+00 bond pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.57e+00 bond pdb=" CA LYS A 275 " pdb=" C LYS A 275 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.19e+00 bond pdb=" CA LYS C 275 " pdb=" C LYS C 275 " ideal model delta sigma weight residual 1.523 1.547 -0.024 1.34e-02 5.57e+03 3.16e+00 bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.95e+00 ... (remaining 5894 not shown) Histogram of bond angle deviations from ideal: 100.25 - 107.02: 198 107.02 - 113.78: 3264 113.78 - 120.54: 2175 120.54 - 127.30: 2319 127.30 - 134.07: 62 Bond angle restraints: 8018 Sorted by residual: angle pdb=" C GLU D 234 " pdb=" N ASN D 235 " pdb=" CA ASN D 235 " ideal model delta sigma weight residual 122.82 132.08 -9.26 1.42e+00 4.96e-01 4.25e+01 angle pdb=" N THR B 135 " pdb=" CA THR B 135 " pdb=" C THR B 135 " ideal model delta sigma weight residual 113.89 106.62 7.27 1.58e+00 4.01e-01 2.12e+01 angle pdb=" C ASN A 274 " pdb=" N LYS A 275 " pdb=" CA LYS A 275 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.03e+01 angle pdb=" N ASN D 235 " pdb=" CA ASN D 235 " pdb=" C ASN D 235 " ideal model delta sigma weight residual 111.17 116.92 -5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" CA TYR D 158 " pdb=" CB TYR D 158 " pdb=" CG TYR D 158 " ideal model delta sigma weight residual 113.90 121.08 -7.18 1.80e+00 3.09e-01 1.59e+01 ... (remaining 8013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3116 16.52 - 33.03: 316 33.03 - 49.55: 65 49.55 - 66.07: 9 66.07 - 82.59: 5 Dihedral angle restraints: 3511 sinusoidal: 1368 harmonic: 2143 Sorted by residual: dihedral pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N ASN B 274 " pdb=" CA ASN B 274 " ideal model delta harmonic sigma weight residual -180.00 -132.74 -47.26 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA LEU A 273 " pdb=" C LEU A 273 " pdb=" N ASN A 274 " pdb=" CA ASN A 274 " ideal model delta harmonic sigma weight residual -180.00 -136.92 -43.08 0 5.00e+00 4.00e-02 7.42e+01 dihedral pdb=" CA LEU C 273 " pdb=" C LEU C 273 " pdb=" N ASN C 274 " pdb=" CA ASN C 274 " ideal model delta harmonic sigma weight residual -180.00 -139.58 -40.42 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 3508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 689 0.053 - 0.107: 182 0.107 - 0.160: 48 0.160 - 0.213: 4 0.213 - 0.267: 4 Chirality restraints: 927 Sorted by residual: chirality pdb=" CA ASN D 235 " pdb=" N ASN D 235 " pdb=" C ASN D 235 " pdb=" CB ASN D 235 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA TYR D 158 " pdb=" N TYR D 158 " pdb=" C TYR D 158 " pdb=" CB TYR D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE B 145 " pdb=" CA ILE B 145 " pdb=" CG1 ILE B 145 " pdb=" CG2 ILE B 145 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 924 not shown) Planarity restraints: 1013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 275 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C LYS B 275 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 275 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 276 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 308 " 0.043 5.00e-02 4.00e+02 6.49e-02 6.73e+00 pdb=" N PRO C 309 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 309 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 309 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 273 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C LEU B 273 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU B 273 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 274 " -0.014 2.00e-02 2.50e+03 ... (remaining 1010 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1875 2.84 - 3.36: 4172 3.36 - 3.87: 9369 3.87 - 4.39: 9650 4.39 - 4.90: 18278 Nonbonded interactions: 43344 Sorted by model distance: nonbonded pdb=" OH TYR B 257 " pdb=" OE2 GLU B 299 " model vdw 2.329 2.440 nonbonded pdb=" O LEU B 204 " pdb=" OG SER B 208 " model vdw 2.345 2.440 nonbonded pdb=" OE1 GLU A 194 " pdb=" OH TYR A 196 " model vdw 2.348 2.440 nonbonded pdb=" O VAL D 305 " pdb=" OH TYR D 319 " model vdw 2.349 2.440 nonbonded pdb=" O LEU A 204 " pdb=" OG SER A 208 " model vdw 2.366 2.440 ... (remaining 43339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 130 through 218 or resid 225 through 239 or resid 245 thro \ ugh 318)) selection = (chain 'C' and (resid 130 through 218 or resid 225 through 318)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.090 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.940 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 0.040 5899 Z= 0.279 Angle : 0.852 12.128 8018 Z= 0.460 Chirality : 0.054 0.267 927 Planarity : 0.007 0.065 1013 Dihedral : 13.952 82.587 2127 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -4.25 (0.25), residues: 705 helix: -4.46 (0.22), residues: 32 sheet: -2.09 (0.28), residues: 284 loop : -3.34 (0.23), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 134 HIS 0.006 0.001 HIS B 246 PHE 0.016 0.002 PHE A 312 TYR 0.012 0.002 TYR A 314 ARG 0.002 0.000 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 246 HIS cc_start: 0.7775 (m-70) cc_final: 0.7574 (m-70) REVERT: B 256 TYR cc_start: 0.8851 (m-80) cc_final: 0.8453 (m-80) REVERT: B 315 ILE cc_start: 0.9085 (mt) cc_final: 0.8854 (mt) REVERT: D 260 ASN cc_start: 0.8346 (t0) cc_final: 0.8102 (t0) REVERT: D 282 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7622 (mt-10) REVERT: D 320 LYS cc_start: 0.8706 (mttm) cc_final: 0.8381 (ttmm) outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2211 time to fit residues: 41.6157 Evaluate side-chains 111 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 188 ASN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN D 217 ASN D 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5899 Z= 0.331 Angle : 0.635 8.111 8018 Z= 0.325 Chirality : 0.046 0.151 927 Planarity : 0.004 0.039 1013 Dihedral : 5.754 36.907 778 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.91 % Rotamer: Outliers : 1.54 % Allowed : 13.56 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % 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: -3.63 (0.27), residues: 705 helix: -4.09 (0.29), residues: 32 sheet: -1.71 (0.29), residues: 284 loop : -2.88 (0.25), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 134 HIS 0.002 0.001 HIS D 183 PHE 0.023 0.002 PHE D 247 TYR 0.017 0.001 TYR A 256 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.6046 (p0) cc_final: 0.5700 (p0) REVERT: A 149 LYS cc_start: 0.8455 (tmtt) cc_final: 0.7669 (tmtt) REVERT: A 246 HIS cc_start: 0.7849 (m-70) cc_final: 0.7641 (m-70) REVERT: B 256 TYR cc_start: 0.8947 (m-80) cc_final: 0.8622 (m-80) REVERT: B 315 ILE cc_start: 0.8993 (mt) cc_final: 0.8720 (mt) REVERT: C 206 ASP cc_start: 0.7852 (p0) cc_final: 0.7640 (p0) REVERT: C 272 MET cc_start: 0.8127 (tmm) cc_final: 0.7428 (tmm) REVERT: D 282 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7709 (mt-10) REVERT: D 284 ILE cc_start: 0.7498 (mm) cc_final: 0.7290 (tt) REVERT: D 320 LYS cc_start: 0.8729 (mttm) cc_final: 0.8356 (ttmm) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.1891 time to fit residues: 27.2579 Evaluate side-chains 103 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 190 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 69 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 5899 Z= 0.144 Angle : 0.528 7.010 8018 Z= 0.266 Chirality : 0.043 0.136 927 Planarity : 0.003 0.031 1013 Dihedral : 4.977 32.365 778 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.69 % Allowed : 16.02 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -3.13 (0.28), residues: 705 helix: -3.65 (0.37), residues: 32 sheet: -1.39 (0.30), residues: 284 loop : -2.53 (0.26), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 134 HIS 0.001 0.000 HIS D 126 PHE 0.019 0.001 PHE D 247 TYR 0.011 0.001 TYR A 256 ARG 0.005 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.686 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.5940 (p0) cc_final: 0.5475 (p0) REVERT: A 230 MET cc_start: 0.7876 (mmt) cc_final: 0.7640 (mmt) REVERT: B 256 TYR cc_start: 0.8814 (m-80) cc_final: 0.8436 (m-80) REVERT: B 315 ILE cc_start: 0.8886 (mt) cc_final: 0.8626 (mt) REVERT: C 206 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7658 (p0) REVERT: C 272 MET cc_start: 0.7871 (tmm) cc_final: 0.7153 (tmm) REVERT: D 188 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7445 (pp) REVERT: D 282 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7641 (mt-10) REVERT: D 320 LYS cc_start: 0.8737 (mttm) cc_final: 0.8426 (ttmm) outliers start: 11 outliers final: 4 residues processed: 120 average time/residue: 0.1900 time to fit residues: 29.4940 Evaluate side-chains 106 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.0970 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 61 optimal weight: 0.0030 chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 HIS A 249 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5899 Z= 0.178 Angle : 0.522 6.182 8018 Z= 0.264 Chirality : 0.043 0.131 927 Planarity : 0.003 0.030 1013 Dihedral : 4.842 35.604 778 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.16 % Allowed : 17.41 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.83 (0.28), residues: 705 helix: -3.39 (0.44), residues: 32 sheet: -1.20 (0.30), residues: 284 loop : -2.31 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 134 HIS 0.005 0.001 HIS A 246 PHE 0.020 0.001 PHE D 247 TYR 0.008 0.001 TYR D 158 ARG 0.005 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASN cc_start: 0.6008 (p0) cc_final: 0.5570 (p0) REVERT: B 256 TYR cc_start: 0.8843 (m-80) cc_final: 0.8460 (m-80) REVERT: B 315 ILE cc_start: 0.8890 (mt) cc_final: 0.8625 (mt) REVERT: C 272 MET cc_start: 0.7884 (tmm) cc_final: 0.7178 (tmm) REVERT: D 320 LYS cc_start: 0.8746 (mttm) cc_final: 0.8422 (ttmm) outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 0.1987 time to fit residues: 28.2208 Evaluate side-chains 109 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5899 Z= 0.472 Angle : 0.672 8.264 8018 Z= 0.342 Chirality : 0.047 0.141 927 Planarity : 0.004 0.035 1013 Dihedral : 5.666 38.121 778 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 4.01 % Allowed : 17.10 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.88 (0.28), residues: 705 helix: -2.90 (0.59), residues: 26 sheet: -1.27 (0.31), residues: 266 loop : -2.36 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.003 0.001 HIS D 183 PHE 0.029 0.002 PHE D 247 TYR 0.016 0.002 TYR B 170 ARG 0.006 0.001 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6523 (p0) REVERT: A 230 MET cc_start: 0.8145 (mmt) cc_final: 0.7866 (mmt) REVERT: B 218 TYR cc_start: 0.7518 (m-10) cc_final: 0.7291 (m-10) REVERT: B 315 ILE cc_start: 0.9017 (mt) cc_final: 0.8701 (mt) REVERT: C 272 MET cc_start: 0.8155 (tmm) cc_final: 0.7474 (tmm) REVERT: D 188 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7522 (pp) REVERT: D 320 LYS cc_start: 0.8775 (mttm) cc_final: 0.8449 (ttmm) outliers start: 26 outliers final: 16 residues processed: 111 average time/residue: 0.1922 time to fit residues: 27.7323 Evaluate side-chains 110 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5899 Z= 0.279 Angle : 0.585 7.211 8018 Z= 0.298 Chirality : 0.045 0.139 927 Planarity : 0.004 0.031 1013 Dihedral : 5.412 37.519 778 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.54 % Allowed : 18.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.67 (0.29), residues: 705 helix: -2.74 (0.64), residues: 26 sheet: -1.07 (0.31), residues: 273 loop : -2.27 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 134 HIS 0.002 0.001 HIS D 312 PHE 0.024 0.001 PHE D 247 TYR 0.011 0.001 TYR B 170 ARG 0.009 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 130 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.6005 (p0) REVERT: A 230 MET cc_start: 0.8142 (mmt) cc_final: 0.7866 (mmt) REVERT: B 218 TYR cc_start: 0.7574 (m-10) cc_final: 0.7368 (m-10) REVERT: B 315 ILE cc_start: 0.8959 (mt) cc_final: 0.8672 (mt) REVERT: C 272 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: D 188 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7348 (pp) REVERT: D 320 LYS cc_start: 0.8716 (mttm) cc_final: 0.8417 (ttmm) outliers start: 23 outliers final: 14 residues processed: 112 average time/residue: 0.1830 time to fit residues: 26.8127 Evaluate side-chains 112 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5899 Z= 0.190 Angle : 0.551 7.329 8018 Z= 0.277 Chirality : 0.044 0.135 927 Planarity : 0.003 0.033 1013 Dihedral : 5.112 36.435 778 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.24 % Allowed : 19.26 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.29), residues: 705 helix: -2.59 (0.66), residues: 26 sheet: -0.95 (0.31), residues: 273 loop : -2.13 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 134 HIS 0.001 0.000 HIS B 246 PHE 0.022 0.001 PHE D 247 TYR 0.008 0.001 TYR D 158 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: B 315 ILE cc_start: 0.8927 (mt) cc_final: 0.8646 (mt) REVERT: C 272 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7126 (tmm) REVERT: D 188 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7367 (pp) REVERT: D 320 LYS cc_start: 0.8708 (mttm) cc_final: 0.8403 (ttmm) outliers start: 21 outliers final: 17 residues processed: 109 average time/residue: 0.1819 time to fit residues: 26.0517 Evaluate side-chains 114 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 277 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5899 Z= 0.200 Angle : 0.541 6.852 8018 Z= 0.273 Chirality : 0.044 0.134 927 Planarity : 0.003 0.032 1013 Dihedral : 4.990 35.017 778 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.39 % Allowed : 19.26 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.41 (0.29), residues: 705 helix: -2.86 (0.60), residues: 32 sheet: -0.85 (0.32), residues: 273 loop : -2.08 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 134 HIS 0.002 0.000 HIS B 246 PHE 0.023 0.001 PHE D 247 TYR 0.008 0.001 TYR B 170 ARG 0.008 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: B 256 TYR cc_start: 0.8860 (m-80) cc_final: 0.8426 (m-80) REVERT: B 315 ILE cc_start: 0.8916 (mt) cc_final: 0.8639 (mt) REVERT: C 272 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7141 (tmm) REVERT: D 130 MET cc_start: 0.8435 (mmm) cc_final: 0.7954 (mtt) REVERT: D 188 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7336 (pp) REVERT: D 320 LYS cc_start: 0.8708 (mttm) cc_final: 0.8364 (ttmm) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.1848 time to fit residues: 26.5830 Evaluate side-chains 110 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 277 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5899 Z= 0.413 Angle : 0.644 7.162 8018 Z= 0.327 Chirality : 0.047 0.136 927 Planarity : 0.004 0.028 1013 Dihedral : 5.546 36.635 778 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 3.54 % Allowed : 18.80 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.44 % 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: -2.52 (0.29), residues: 705 helix: -2.45 (0.70), residues: 26 sheet: -0.97 (0.31), residues: 273 loop : -2.18 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 134 HIS 0.003 0.001 HIS B 246 PHE 0.029 0.002 PHE D 247 TYR 0.015 0.002 TYR B 170 ARG 0.007 0.001 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 315 ILE cc_start: 0.8996 (mt) cc_final: 0.8712 (mt) REVERT: C 230 MET cc_start: 0.8155 (mmp) cc_final: 0.7771 (mmp) REVERT: C 272 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7420 (tmm) REVERT: D 188 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7439 (pp) REVERT: D 320 LYS cc_start: 0.8770 (mttm) cc_final: 0.8445 (ttmm) outliers start: 23 outliers final: 17 residues processed: 104 average time/residue: 0.1925 time to fit residues: 26.2816 Evaluate side-chains 109 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 5899 Z= 0.161 Angle : 0.542 6.839 8018 Z= 0.274 Chirality : 0.044 0.138 927 Planarity : 0.003 0.029 1013 Dihedral : 4.943 36.196 778 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.62 % Allowed : 19.88 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.23 (0.30), residues: 705 helix: -1.49 (0.95), residues: 20 sheet: -0.86 (0.31), residues: 274 loop : -1.98 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 134 HIS 0.001 0.000 HIS B 246 PHE 0.021 0.001 PHE D 247 TYR 0.011 0.001 TYR D 186 ARG 0.008 0.001 ARG B 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: B 315 ILE cc_start: 0.8915 (mt) cc_final: 0.8627 (mt) REVERT: C 230 MET cc_start: 0.7983 (mmp) cc_final: 0.7635 (mmp) REVERT: C 272 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7106 (tmm) REVERT: D 183 HIS cc_start: 0.6648 (OUTLIER) cc_final: 0.5877 (m-70) REVERT: D 188 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7363 (pp) REVERT: D 277 ASP cc_start: 0.8272 (t70) cc_final: 0.7924 (m-30) REVERT: D 320 LYS cc_start: 0.8758 (mttm) cc_final: 0.8444 (ttmm) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.1764 time to fit residues: 25.7004 Evaluate side-chains 114 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 206 ASP Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 208 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 284 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112911 restraints weight = 7990.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115943 restraints weight = 4418.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117964 restraints weight = 2912.866| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5899 Z= 0.294 Angle : 0.591 7.233 8018 Z= 0.299 Chirality : 0.045 0.134 927 Planarity : 0.004 0.028 1013 Dihedral : 5.198 37.555 778 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.31 % Allowed : 20.34 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.30), residues: 705 helix: -2.18 (0.78), residues: 26 sheet: -0.84 (0.32), residues: 273 loop : -2.03 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 134 HIS 0.002 0.001 HIS D 312 PHE 0.023 0.002 PHE D 247 TYR 0.011 0.001 TYR B 170 ARG 0.007 0.001 ARG B 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.60 seconds wall clock time: 27 minutes 30.16 seconds (1650.16 seconds total)