Starting phenix.real_space_refine on Tue Feb 13 07:33:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlv_21843/02_2024/6wlv_21843.pdb" } resolution = 3.45 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= 1.000 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 14 5.16 5 C 2744 2.51 5 N 668 2.21 5 O 682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ASP 66": "OD1" <-> "OD2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4111 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2054 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.88, per 1000 atoms: 0.70 Number of scatterers: 4111 At special positions: 0 Unit cell: (94.371, 65.946, 78.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 14 16.00 O 682 8.00 N 668 7.00 C 2744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS B 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 734.3 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 48 removed outlier: 3.812A pdb=" N THR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 10 " --> pdb=" O PRO A 6 " (cutoff:3.500A) Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 53 through 70 removed outlier: 3.594A pdb=" N GLN A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 96 Processing helix chain 'A' and resid 108 through 152 removed outlier: 3.686A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.677A pdb=" N ARG A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.602A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.442A pdb=" N MET A 248 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N HIS A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 4.256A pdb=" N LYS A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 259' Processing helix chain 'B' and resid 7 through 49 Proline residue: B 29 - end of helix removed outlier: 3.586A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 68 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.927A pdb=" N ILE B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 152 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.724A pdb=" N VAL B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.710A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 254 Processing helix chain 'B' and resid 255 through 260 292 hydrogen bonds defined for protein. 876 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: 1.18 Time building geometry restraints manager: 1.96 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: 1226 1.34 - 1.46: 886 1.46 - 1.57: 2104 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4236 Sorted by residual: bond pdb=" CB PRO B 179 " pdb=" CG PRO B 179 " ideal model delta sigma weight residual 1.492 1.453 0.039 5.00e-02 4.00e+02 6.15e-01 bond pdb=" CG1 ILE B 12 " pdb=" CD1 ILE B 12 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.85e-01 bond pdb=" CB PRO A 179 " pdb=" CG PRO A 179 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.57e-01 bond pdb=" CB ILE A 199 " pdb=" CG2 ILE A 199 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.28e-01 bond pdb=" C PRO B 178 " pdb=" N PRO B 179 " ideal model delta sigma weight residual 1.333 1.344 -0.010 1.44e-02 4.82e+03 5.14e-01 ... (remaining 4231 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.32: 147 107.32 - 113.99: 2373 113.99 - 120.66: 1894 120.66 - 127.33: 1288 127.33 - 133.99: 66 Bond angle restraints: 5768 Sorted by residual: angle pdb=" N PRO A 178 " pdb=" CA PRO A 178 " pdb=" C PRO A 178 " ideal model delta sigma weight residual 110.70 113.67 -2.97 1.22e+00 6.72e-01 5.93e+00 angle pdb=" N TRP B 85 " pdb=" CA TRP B 85 " pdb=" C TRP B 85 " ideal model delta sigma weight residual 109.81 114.30 -4.49 2.21e+00 2.05e-01 4.13e+00 angle pdb=" N PRO B 178 " pdb=" CA PRO B 178 " pdb=" C PRO B 178 " ideal model delta sigma weight residual 110.70 113.14 -2.44 1.22e+00 6.72e-01 3.98e+00 angle pdb=" C TRP B 244 " pdb=" N LYS B 245 " pdb=" CA LYS B 245 " ideal model delta sigma weight residual 120.79 123.55 -2.76 1.39e+00 5.18e-01 3.95e+00 angle pdb=" CA TRP B 85 " pdb=" C TRP B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 121.55 -3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 5763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 2142 16.04 - 32.08: 197 32.08 - 48.11: 52 48.11 - 64.15: 6 64.15 - 80.19: 2 Dihedral angle restraints: 2399 sinusoidal: 925 harmonic: 1474 Sorted by residual: dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS B 51 " pdb=" CB CYS B 51 " ideal model delta sinusoidal sigma weight residual 93.00 134.32 -41.32 1 1.00e+01 1.00e-02 2.39e+01 dihedral pdb=" CA ASN A 189 " pdb=" C ASN A 189 " pdb=" N TYR A 190 " pdb=" CA TYR A 190 " ideal model delta harmonic sigma weight residual -180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA GLY A 102 " pdb=" C GLY A 102 " pdb=" N ASN A 103 " pdb=" CA ASN A 103 " ideal model delta harmonic sigma weight residual 180.00 164.16 15.84 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 333 0.026 - 0.052: 189 0.052 - 0.079: 77 0.079 - 0.105: 33 0.105 - 0.131: 6 Chirality restraints: 638 Sorted by residual: chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA PRO A 179 " pdb=" N PRO A 179 " pdb=" C PRO A 179 " pdb=" CB PRO A 179 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA THR A 98 " pdb=" N THR A 98 " pdb=" C THR A 98 " pdb=" CB THR A 98 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 635 not shown) Planarity restraints: 706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 178 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A 179 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 178 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO B 179 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 179 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 179 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 177 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 178 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.014 5.00e-02 4.00e+02 ... (remaining 703 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 1122 2.80 - 3.38: 4936 3.38 - 3.97: 7710 3.97 - 4.55: 10811 4.55 - 5.14: 15422 Nonbonded interactions: 40001 Sorted by model distance: nonbonded pdb=" O ALA A 93 " pdb=" OG1 THR A 97 " model vdw 2.211 2.440 nonbonded pdb=" O LEU A 7 " pdb=" OG SER A 10 " model vdw 2.214 2.440 nonbonded pdb=" O GLU B 33 " pdb=" ND2 ASN B 37 " model vdw 2.284 2.520 nonbonded pdb=" NE2 GLN A 54 " pdb=" OD1 ASP A 58 " model vdw 2.321 2.520 nonbonded pdb=" O ALA B 236 " pdb=" OG SER B 239 " model vdw 2.357 2.440 ... (remaining 39996 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' and resid 5 through 260) selection = chain 'B' } 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 individual isotropic 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: 0.280 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: 1.100 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.680 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 0.039 4236 Z= 0.250 Angle : 0.558 5.404 5768 Z= 0.318 Chirality : 0.040 0.131 638 Planarity : 0.003 0.040 706 Dihedral : 13.212 80.190 1456 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.36), residues: 508 helix: 0.28 (0.25), residues: 372 sheet: None (None), residues: 0 loop : -2.17 (0.54), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 31 HIS 0.003 0.001 HIS A 30 PHE 0.010 0.001 PHE B 241 TYR 0.016 0.001 TYR B 195 ARG 0.002 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: B 143 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7402 (tmm-80) REVERT: B 190 TYR cc_start: 0.8255 (t80) cc_final: 0.7818 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1775 time to fit residues: 17.5263 Evaluate side-chains 55 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.0020 chunk 20 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 218 ASN A 253 HIS B 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.192 Angle : 0.534 5.722 5768 Z= 0.278 Chirality : 0.040 0.122 638 Planarity : 0.004 0.049 706 Dihedral : 3.752 14.373 552 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.17 % Allowed : 12.44 % Favored : 86.38 % 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: 1.07 (0.38), residues: 508 helix: 1.65 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.61 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 PHE 0.020 0.001 PHE B 147 TYR 0.016 0.001 TYR B 38 ARG 0.002 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8189 (m-30) cc_final: 0.7771 (m-30) REVERT: B 190 TYR cc_start: 0.8153 (t80) cc_final: 0.7756 (t80) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.1358 time to fit residues: 12.7102 Evaluate side-chains 66 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 162 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 189 ASN ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4236 Z= 0.163 Angle : 0.502 5.812 5768 Z= 0.260 Chirality : 0.039 0.127 638 Planarity : 0.004 0.052 706 Dihedral : 3.610 12.902 552 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.64 % Allowed : 14.55 % Favored : 83.80 % 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: 1.80 (0.39), residues: 508 helix: 2.19 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -2.34 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 129 HIS 0.003 0.001 HIS A 253 PHE 0.019 0.001 PHE B 147 TYR 0.012 0.001 TYR B 38 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.8740 (t80) cc_final: 0.8409 (t80) REVERT: B 190 TYR cc_start: 0.8165 (t80) cc_final: 0.7830 (t80) outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.1449 time to fit residues: 14.4388 Evaluate side-chains 70 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.179 Angle : 0.498 5.912 5768 Z= 0.259 Chirality : 0.039 0.136 638 Planarity : 0.004 0.053 706 Dihedral : 3.560 12.748 552 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 15.73 % Favored : 82.16 % 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: 2.10 (0.39), residues: 508 helix: 2.41 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -2.26 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 129 HIS 0.002 0.001 HIS A 253 PHE 0.018 0.001 PHE B 147 TYR 0.013 0.001 TYR B 223 ARG 0.001 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8074 (t0) cc_final: 0.7799 (t0) REVERT: B 49 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: B 66 ASP cc_start: 0.8128 (m-30) cc_final: 0.7899 (m-30) REVERT: B 148 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6465 (mm) REVERT: B 190 TYR cc_start: 0.8135 (t80) cc_final: 0.7782 (t80) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.1225 time to fit residues: 12.3385 Evaluate side-chains 71 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.0870 chunk 19 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4236 Z= 0.164 Angle : 0.512 6.781 5768 Z= 0.263 Chirality : 0.039 0.142 638 Planarity : 0.004 0.054 706 Dihedral : 3.544 13.090 552 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.11 % Allowed : 17.84 % Favored : 80.05 % 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: 2.27 (0.39), residues: 508 helix: 2.55 (0.27), residues: 388 sheet: None (None), residues: 0 loop : -2.27 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.017 0.001 PHE B 147 TYR 0.014 0.001 TYR B 223 ARG 0.004 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8066 (t0) cc_final: 0.7748 (t0) REVERT: A 251 GLU cc_start: 0.8313 (pt0) cc_final: 0.8065 (pt0) REVERT: B 49 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: B 148 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6455 (mm) REVERT: B 190 TYR cc_start: 0.8116 (t80) cc_final: 0.7795 (t80) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1157 time to fit residues: 13.0281 Evaluate side-chains 72 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4236 Z= 0.192 Angle : 0.521 6.036 5768 Z= 0.269 Chirality : 0.039 0.131 638 Planarity : 0.004 0.054 706 Dihedral : 3.521 13.048 552 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.58 % Allowed : 18.54 % Favored : 78.87 % 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: 2.33 (0.39), residues: 508 helix: 2.58 (0.27), residues: 389 sheet: None (None), residues: 0 loop : -2.22 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 129 HIS 0.003 0.001 HIS A 30 PHE 0.019 0.001 PHE B 147 TYR 0.011 0.001 TYR B 38 ARG 0.001 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8077 (t0) cc_final: 0.7784 (t0) REVERT: B 49 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: B 148 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6387 (mm) REVERT: B 190 TYR cc_start: 0.8142 (t80) cc_final: 0.7795 (t80) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.1261 time to fit residues: 13.0420 Evaluate side-chains 72 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4236 Z= 0.151 Angle : 0.513 6.187 5768 Z= 0.263 Chirality : 0.038 0.138 638 Planarity : 0.004 0.054 706 Dihedral : 3.443 12.654 552 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.35 % Allowed : 18.78 % Favored : 78.87 % 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: 2.39 (0.39), residues: 508 helix: 2.60 (0.27), residues: 391 sheet: None (None), residues: 0 loop : -2.20 (0.52), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.018 0.001 PHE B 147 TYR 0.018 0.001 TYR B 223 ARG 0.001 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8037 (t0) cc_final: 0.7714 (t0) REVERT: B 49 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6310 (m-80) REVERT: B 148 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6186 (mm) REVERT: B 190 TYR cc_start: 0.8113 (t80) cc_final: 0.7828 (t80) outliers start: 10 outliers final: 7 residues processed: 79 average time/residue: 0.1196 time to fit residues: 12.8161 Evaluate side-chains 73 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4236 Z= 0.171 Angle : 0.513 6.164 5768 Z= 0.267 Chirality : 0.039 0.141 638 Planarity : 0.004 0.054 706 Dihedral : 3.441 12.684 552 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.58 % Allowed : 19.48 % Favored : 77.93 % 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: 2.36 (0.39), residues: 508 helix: 2.53 (0.26), residues: 392 sheet: None (None), residues: 0 loop : -2.08 (0.53), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.025 0.001 PHE A 226 TYR 0.019 0.001 TYR B 223 ARG 0.001 0.000 ARG B 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8019 (t0) cc_final: 0.7707 (t0) REVERT: B 49 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: B 148 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6110 (mm) REVERT: B 190 TYR cc_start: 0.8126 (t80) cc_final: 0.7849 (t80) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1184 time to fit residues: 12.3506 Evaluate side-chains 72 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4236 Z= 0.177 Angle : 0.521 6.118 5768 Z= 0.272 Chirality : 0.039 0.147 638 Planarity : 0.004 0.054 706 Dihedral : 3.440 12.561 552 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.11 % Allowed : 19.48 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.38), residues: 508 helix: 2.56 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -2.10 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.024 0.001 PHE A 226 TYR 0.016 0.001 TYR B 223 ARG 0.001 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8110 (t0) cc_final: 0.7746 (t0) REVERT: A 251 GLU cc_start: 0.8318 (pt0) cc_final: 0.8034 (pt0) REVERT: B 49 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: B 148 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6114 (mm) REVERT: B 190 TYR cc_start: 0.8135 (t80) cc_final: 0.7849 (t80) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.1037 time to fit residues: 10.5336 Evaluate side-chains 72 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4236 Z= 0.219 Angle : 0.562 7.636 5768 Z= 0.294 Chirality : 0.040 0.148 638 Planarity : 0.004 0.054 706 Dihedral : 3.511 12.833 552 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.11 % Allowed : 19.95 % Favored : 77.93 % 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: 2.37 (0.38), residues: 508 helix: 2.55 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -2.07 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 PHE 0.023 0.001 PHE A 226 TYR 0.015 0.001 TYR B 223 ARG 0.001 0.000 ARG A 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8142 (t0) cc_final: 0.7737 (t0) REVERT: B 49 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6323 (m-80) REVERT: B 148 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6136 (mm) REVERT: B 190 TYR cc_start: 0.8132 (t80) cc_final: 0.7791 (t80) outliers start: 9 outliers final: 7 residues processed: 73 average time/residue: 0.1290 time to fit residues: 12.5968 Evaluate side-chains 75 residues out of total 426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 249 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 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 = 0.3634 r_free = 0.3634 target = 0.103530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.080133 restraints weight = 10300.135| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.60 r_work: 0.3064 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4236 Z= 0.204 Angle : 0.590 11.344 5768 Z= 0.300 Chirality : 0.041 0.284 638 Planarity : 0.004 0.054 706 Dihedral : 3.598 15.030 552 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.11 % Allowed : 20.42 % Favored : 77.46 % 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: 2.39 (0.38), residues: 508 helix: 2.56 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -2.07 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 PHE 0.023 0.001 PHE A 226 TYR 0.015 0.001 TYR B 223 ARG 0.001 0.000 ARG A 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1167.25 seconds wall clock time: 21 minutes 52.25 seconds (1312.25 seconds total)