Starting phenix.real_space_refine on Wed Jan 17 17:44:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/01_2024/8i9q_35280_neut.pdb" } resolution = 4.22 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= 0.003 sd= 0.059 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 29 5.16 5 C 3264 2.51 5 N 897 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "Q TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 161": "NH1" <-> "NH2" Residue "Q GLU 171": "OE1" <-> "OE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q GLU 209": "OE1" <-> "OE2" Residue "Q GLU 210": "OE1" <-> "OE2" Residue "Q ARG 225": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 5179 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 14, 'TRANS': 493} Chain: "Q" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1347 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Time building chain proxies: 3.43, per 1000 atoms: 0.66 Number of scatterers: 5179 At special positions: 0 Unit cell: (117.52, 118.65, 110.74, 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 29 16.00 O 989 8.00 N 897 7.00 C 3264 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: 1.98 Conformation dependent library (CDL) restraints added in 1.0 seconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 51.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'D' and resid 27 through 49 removed outlier: 4.035A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.784A pdb=" N ILE D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.543A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.674A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 removed outlier: 3.572A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 209 removed outlier: 4.009A pdb=" N LYS D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.332A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 284 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.888A pdb=" N CYS D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.581A pdb=" N ILE D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 removed outlier: 3.640A pdb=" N LEU D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.454A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.598A pdb=" N THR D 464 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.809A pdb=" N THR D 476 " --> pdb=" O ASN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.101A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 78 removed outlier: 4.581A pdb=" N TYR Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG Q 75 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 Processing helix chain 'Q' and resid 104 through 109 Processing helix chain 'Q' and resid 124 through 141 removed outlier: 3.637A pdb=" N ALA Q 128 " --> pdb=" O ILE Q 124 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU Q 129 " --> pdb=" O PRO Q 125 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN Q 131 " --> pdb=" O CYS Q 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER Q 135 " --> pdb=" O ASN Q 131 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS Q 140 " --> pdb=" O GLY Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 185 Processing helix chain 'Q' and resid 190 through 196 Processing helix chain 'Q' and resid 204 through 208 Processing helix chain 'Q' and resid 220 through 231 removed outlier: 4.348A pdb=" N VAL Q 224 " --> pdb=" O LEU Q 220 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Q 225 " --> pdb=" O LEU Q 221 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER Q 227 " --> pdb=" O SER Q 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.606A pdb=" N LYS D 59 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.590A pdb=" N ARG D 153 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 301 removed outlier: 7.077A pdb=" N ILE D 300 " --> pdb=" O ILE D 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 95 through 96 removed outlier: 7.682A pdb=" N LEU Q 95 " --> pdb=" O LYS Q 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 207 hydrogen bonds defined for protein. 597 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: 1.34 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1640 1.34 - 1.46: 540 1.46 - 1.57: 3009 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5236 Sorted by residual: bond pdb=" C ILE Q 155 " pdb=" N PRO Q 156 " ideal model delta sigma weight residual 1.335 1.498 -0.162 1.36e-02 5.41e+03 1.43e+02 bond pdb=" C TYR Q 158 " pdb=" N PRO Q 159 " ideal model delta sigma weight residual 1.333 1.497 -0.164 1.44e-02 4.82e+03 1.29e+02 bond pdb=" N ARG Q 161 " pdb=" CA ARG Q 161 " ideal model delta sigma weight residual 1.457 1.518 -0.061 1.33e-02 5.65e+03 2.09e+01 bond pdb=" N CYS Q 154 " pdb=" CA CYS Q 154 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" N ILE Q 155 " pdb=" CA ILE Q 155 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.04e+01 ... (remaining 5231 not shown) Histogram of bond angle deviations from ideal: 94.78 - 103.85: 70 103.85 - 112.91: 3006 112.91 - 121.97: 2989 121.97 - 131.03: 985 131.03 - 140.09: 14 Bond angle restraints: 7064 Sorted by residual: angle pdb=" C TYR Q 158 " pdb=" N PRO Q 159 " pdb=" CA PRO Q 159 " ideal model delta sigma weight residual 119.47 140.09 -20.62 1.16e+00 7.43e-01 3.16e+02 angle pdb=" C ILE Q 155 " pdb=" N PRO Q 156 " pdb=" CA PRO Q 156 " ideal model delta sigma weight residual 119.05 137.20 -18.15 1.11e+00 8.12e-01 2.67e+02 angle pdb=" C PRO Q 159 " pdb=" CA PRO Q 159 " pdb=" CB PRO Q 159 " ideal model delta sigma weight residual 112.26 102.02 10.24 1.67e+00 3.59e-01 3.76e+01 angle pdb=" N PRO Q 159 " pdb=" CD PRO Q 159 " pdb=" CG PRO Q 159 " ideal model delta sigma weight residual 103.20 94.78 8.42 1.50e+00 4.44e-01 3.15e+01 angle pdb=" N PRO Q 156 " pdb=" CA PRO Q 156 " pdb=" C PRO Q 156 " ideal model delta sigma weight residual 113.53 121.08 -7.55 1.39e+00 5.18e-01 2.95e+01 ... (remaining 7059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2925 17.46 - 34.92: 281 34.92 - 52.38: 52 52.38 - 69.84: 11 69.84 - 87.30: 6 Dihedral angle restraints: 3275 sinusoidal: 1328 harmonic: 1947 Sorted by residual: dihedral pdb=" CA CYS D 221 " pdb=" C CYS D 221 " pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE Q 216 " pdb=" C ILE Q 216 " pdb=" N GLU Q 217 " pdb=" CA GLU Q 217 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C PRO Q 159 " pdb=" N PRO Q 159 " pdb=" CA PRO Q 159 " pdb=" CB PRO Q 159 " ideal model delta harmonic sigma weight residual -120.70 -109.29 -11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 3272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 620 0.048 - 0.095: 173 0.095 - 0.143: 53 0.143 - 0.190: 9 0.190 - 0.238: 6 Chirality restraints: 861 Sorted by residual: chirality pdb=" CA PRO Q 156 " pdb=" N PRO Q 156 " pdb=" C PRO Q 156 " pdb=" CB PRO Q 156 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE Q 155 " pdb=" N ILE Q 155 " pdb=" C ILE Q 155 " pdb=" CB ILE Q 155 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL Q 94 " pdb=" N VAL Q 94 " pdb=" C VAL Q 94 " pdb=" CB VAL Q 94 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 858 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 147 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE Q 147 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE Q 147 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS Q 148 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 214 " -0.058 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO Q 215 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO Q 215 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO Q 215 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 64 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLY D 64 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY D 64 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS D 65 " 0.018 2.00e-02 2.50e+03 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 17 2.34 - 2.98: 2777 2.98 - 3.62: 7797 3.62 - 4.26: 10534 4.26 - 4.90: 16543 Nonbonded interactions: 37668 Sorted by model distance: nonbonded pdb=" CE LYS Q 121 " pdb=" O PRO Q 159 " model vdw 1.697 3.440 nonbonded pdb=" CG1 VAL Q 94 " pdb=" NZ LYS Q 148 " model vdw 1.954 3.540 nonbonded pdb=" CE1 TYR Q 158 " pdb=" OD1 ASN Q 162 " model vdw 1.969 3.340 nonbonded pdb=" OG1 THR Q 190 " pdb=" OD1 ASP Q 192 " model vdw 2.153 2.440 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.161 2.520 ... (remaining 37663 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 6.580 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 18.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.007 0.164 5236 Z= 0.465 Angle : 0.984 20.623 7064 Z= 0.599 Chirality : 0.052 0.238 861 Planarity : 0.005 0.089 894 Dihedral : 14.664 87.297 2011 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.86 % Allowed : 10.17 % Favored : 88.97 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.28), residues: 671 helix: -1.30 (0.28), residues: 275 sheet: -3.77 (0.58), residues: 49 loop : -3.68 (0.27), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 196 HIS 0.003 0.001 HIS D 315 PHE 0.011 0.001 PHE D 335 TYR 0.017 0.002 TYR D 269 ARG 0.009 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7996 (tmm) cc_final: 0.7286 (tmm) REVERT: D 279 GLU cc_start: 0.7575 (pt0) cc_final: 0.6811 (mm-30) REVERT: D 391 ARG cc_start: 0.6703 (ptm-80) cc_final: 0.6404 (ptm-80) REVERT: Q 69 ARG cc_start: 0.9642 (mtm180) cc_final: 0.9107 (ptp90) REVERT: Q 160 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6019 (p0) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.2548 time to fit residues: 22.8914 Evaluate side-chains 57 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN D 318 ASN D 350 GLN D 484 HIS ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5236 Z= 0.169 Angle : 0.673 10.107 7064 Z= 0.336 Chirality : 0.045 0.200 861 Planarity : 0.004 0.058 894 Dihedral : 5.512 20.280 718 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.17 % Allowed : 7.76 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.31), residues: 671 helix: -0.01 (0.31), residues: 288 sheet: -2.64 (0.73), residues: 40 loop : -3.40 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 82 HIS 0.005 0.001 HIS D 484 PHE 0.010 0.001 PHE Q 91 TYR 0.012 0.001 TYR Q 169 ARG 0.004 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7831 (tmm) cc_final: 0.7326 (tmm) REVERT: D 279 GLU cc_start: 0.7631 (pt0) cc_final: 0.6784 (mm-30) REVERT: D 283 ILE cc_start: 0.9042 (mt) cc_final: 0.8681 (tp) REVERT: D 391 ARG cc_start: 0.6319 (ptm-80) cc_final: 0.6001 (ptm-80) REVERT: Q 73 MET cc_start: 0.8897 (mmt) cc_final: 0.8681 (mmt) REVERT: Q 139 ARG cc_start: 0.7698 (mmp-170) cc_final: 0.7401 (mmm160) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.2411 time to fit residues: 24.7704 Evaluate side-chains 60 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 30.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 GLN ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5236 Z= 0.160 Angle : 0.644 9.769 7064 Z= 0.320 Chirality : 0.044 0.177 861 Planarity : 0.004 0.047 894 Dihedral : 5.278 20.069 718 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.31), residues: 671 helix: 0.24 (0.31), residues: 308 sheet: -2.72 (0.64), residues: 55 loop : -3.35 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 196 HIS 0.001 0.000 HIS D 129 PHE 0.016 0.001 PHE D 137 TYR 0.006 0.001 TYR D 269 ARG 0.003 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 GLU cc_start: 0.7616 (pt0) cc_final: 0.6878 (mm-30) REVERT: D 320 MET cc_start: 0.8287 (tpt) cc_final: 0.8016 (tpp) REVERT: Q 210 GLU cc_start: 0.5796 (mp0) cc_final: 0.5427 (mp0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2094 time to fit residues: 19.4108 Evaluate side-chains 56 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5236 Z= 0.148 Angle : 0.621 9.764 7064 Z= 0.308 Chirality : 0.043 0.185 861 Planarity : 0.004 0.040 894 Dihedral : 4.972 17.883 718 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 671 helix: 0.50 (0.31), residues: 303 sheet: -2.28 (0.67), residues: 55 loop : -3.13 (0.30), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 196 HIS 0.001 0.000 HIS D 484 PHE 0.013 0.001 PHE Q 91 TYR 0.010 0.001 TYR Q 169 ARG 0.002 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 LEU cc_start: 0.7682 (mt) cc_final: 0.6839 (pp) REVERT: D 279 GLU cc_start: 0.7482 (pt0) cc_final: 0.6822 (mm-30) REVERT: D 320 MET cc_start: 0.8097 (tpt) cc_final: 0.7879 (tpt) REVERT: Q 160 ASP cc_start: 0.6099 (p0) cc_final: 0.5883 (p0) REVERT: Q 210 GLU cc_start: 0.5723 (mp0) cc_final: 0.5369 (mp0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2122 time to fit residues: 19.5651 Evaluate side-chains 54 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 50.0000 chunk 26 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 40.0000 chunk 32 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5236 Z= 0.217 Angle : 0.681 9.496 7064 Z= 0.339 Chirality : 0.044 0.182 861 Planarity : 0.004 0.043 894 Dihedral : 5.205 18.708 718 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.32), residues: 671 helix: 0.47 (0.31), residues: 311 sheet: -3.20 (0.78), residues: 35 loop : -3.14 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 114 HIS 0.003 0.001 HIS D 347 PHE 0.034 0.002 PHE D 137 TYR 0.022 0.002 TYR Q 169 ARG 0.006 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 LEU cc_start: 0.7745 (mt) cc_final: 0.6963 (pp) REVERT: D 279 GLU cc_start: 0.7510 (pt0) cc_final: 0.6859 (mm-30) REVERT: Q 69 ARG cc_start: 0.9478 (tmt170) cc_final: 0.9017 (ttp80) REVERT: Q 139 ARG cc_start: 0.7442 (mmp-170) cc_final: 0.6969 (mmm160) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2295 time to fit residues: 19.1079 Evaluate side-chains 55 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 0.0030 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5236 Z= 0.147 Angle : 0.625 9.651 7064 Z= 0.305 Chirality : 0.043 0.185 861 Planarity : 0.003 0.033 894 Dihedral : 4.839 18.645 718 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.33), residues: 671 helix: 0.79 (0.32), residues: 301 sheet: -1.69 (0.72), residues: 53 loop : -2.96 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP Q 196 HIS 0.002 0.000 HIS Q 118 PHE 0.017 0.001 PHE Q 91 TYR 0.009 0.001 TYR Q 169 ARG 0.003 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7939 (tpt) cc_final: 0.7681 (mmm) REVERT: D 163 LEU cc_start: 0.7735 (mt) cc_final: 0.7027 (pp) REVERT: D 279 GLU cc_start: 0.7423 (pt0) cc_final: 0.6748 (mm-30) REVERT: Q 210 GLU cc_start: 0.5590 (mp0) cc_final: 0.5228 (mp0) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2565 time to fit residues: 22.3194 Evaluate side-chains 56 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5236 Z= 0.214 Angle : 0.696 9.746 7064 Z= 0.339 Chirality : 0.044 0.211 861 Planarity : 0.004 0.038 894 Dihedral : 5.068 18.830 718 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.33), residues: 671 helix: 0.99 (0.32), residues: 292 sheet: -2.82 (0.81), residues: 35 loop : -2.79 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 82 HIS 0.003 0.001 HIS D 347 PHE 0.016 0.002 PHE Q 91 TYR 0.020 0.002 TYR Q 169 ARG 0.005 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.8033 (tpt) cc_final: 0.7825 (mmm) REVERT: D 163 LEU cc_start: 0.7753 (mt) cc_final: 0.7033 (pp) REVERT: D 279 GLU cc_start: 0.7432 (pt0) cc_final: 0.6739 (mm-30) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2462 time to fit residues: 19.8353 Evaluate side-chains 56 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 50 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5236 Z= 0.165 Angle : 0.671 9.517 7064 Z= 0.324 Chirality : 0.043 0.190 861 Planarity : 0.004 0.046 894 Dihedral : 4.893 19.466 718 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.33), residues: 671 helix: 1.06 (0.32), residues: 292 sheet: -1.48 (0.74), residues: 54 loop : -2.72 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 196 HIS 0.002 0.001 HIS D 347 PHE 0.021 0.002 PHE D 137 TYR 0.008 0.001 TYR Q 169 ARG 0.011 0.000 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 LEU cc_start: 0.7771 (mt) cc_final: 0.6978 (pp) REVERT: D 279 GLU cc_start: 0.7393 (pt0) cc_final: 0.6720 (mm-30) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2305 time to fit residues: 20.7840 Evaluate side-chains 58 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 0.0270 chunk 56 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5236 Z= 0.172 Angle : 0.691 9.451 7064 Z= 0.334 Chirality : 0.044 0.223 861 Planarity : 0.003 0.031 894 Dihedral : 4.891 19.104 718 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.34), residues: 671 helix: 1.03 (0.32), residues: 297 sheet: -0.91 (0.86), residues: 46 loop : -2.78 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 196 HIS 0.002 0.000 HIS D 347 PHE 0.020 0.002 PHE Q 91 TYR 0.013 0.001 TYR Q 169 ARG 0.007 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 163 LEU cc_start: 0.7775 (mt) cc_final: 0.7064 (pp) REVERT: D 279 GLU cc_start: 0.7383 (pt0) cc_final: 0.6668 (mm-30) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.2129 time to fit residues: 18.6873 Evaluate side-chains 59 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5236 Z= 0.181 Angle : 0.693 9.394 7064 Z= 0.335 Chirality : 0.044 0.223 861 Planarity : 0.003 0.032 894 Dihedral : 4.942 20.508 718 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.34), residues: 671 helix: 0.88 (0.32), residues: 303 sheet: -0.32 (0.94), residues: 40 loop : -2.79 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 82 HIS 0.003 0.000 HIS D 347 PHE 0.021 0.002 PHE D 137 TYR 0.015 0.001 TYR Q 169 ARG 0.007 0.000 ARG Q 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 163 LEU cc_start: 0.7768 (mt) cc_final: 0.7061 (pp) REVERT: D 279 GLU cc_start: 0.7436 (pt0) cc_final: 0.6680 (mm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2249 time to fit residues: 18.6182 Evaluate side-chains 55 residues out of total 580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 172 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 = 0.4502 r_free = 0.4502 target = 0.181011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.161748 restraints weight = 13661.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.160718 restraints weight = 21881.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.159912 restraints weight = 20555.117| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5236 Z= 0.266 Angle : 0.769 9.658 7064 Z= 0.376 Chirality : 0.046 0.208 861 Planarity : 0.004 0.037 894 Dihedral : 5.410 23.545 718 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.34), residues: 671 helix: 0.94 (0.32), residues: 300 sheet: -1.05 (0.83), residues: 46 loop : -2.83 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 82 HIS 0.004 0.001 HIS D 347 PHE 0.018 0.002 PHE Q 91 TYR 0.018 0.002 TYR Q 169 ARG 0.006 0.000 ARG Q 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1445.42 seconds wall clock time: 26 minutes 53.52 seconds (1613.52 seconds total)