Starting phenix.real_space_refine on Tue Feb 11 03:57:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_21843.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_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/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_21843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_21843.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_21843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlv_21843/02_2025/6wlv_21843.cif" } 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. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.10, per 1000 atoms: 0.75 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 - 3.00 Amino acid : True - 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: 1.14 Conformation dependent library (CDL) restraints added in 504.6 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: 0.32 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: 1.02 Time building geometry restraints manager: 1.28 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: 0.00 - 1.08: 5489 1.08 - 2.16: 223 2.16 - 3.24: 33 3.24 - 4.32: 13 4.32 - 5.40: 10 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 3.040 nonbonded pdb=" O LEU A 7 " pdb=" OG SER A 10 " model vdw 2.214 3.040 nonbonded pdb=" O GLU B 33 " pdb=" ND2 ASN B 37 " model vdw 2.284 3.120 nonbonded pdb=" NE2 GLN A 54 " pdb=" OD1 ASP A 58 " model vdw 2.321 3.120 nonbonded pdb=" O ALA B 236 " pdb=" OG SER B 239 " model vdw 2.357 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.200 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.970 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.452 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: 0.1771 time to fit residues: 17.5298 Evaluate side-chains 55 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 0.0670 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 253 HIS B 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.079573 restraints weight = 10410.104| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.64 r_work: 0.3058 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4236 Z= 0.188 Angle : 0.556 6.017 5768 Z= 0.289 Chirality : 0.040 0.129 638 Planarity : 0.004 0.049 706 Dihedral : 3.788 13.855 552 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.17 % Allowed : 11.50 % Favored : 87.32 % 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: 1.19 (0.38), residues: 508 helix: 1.75 (0.26), residues: 382 sheet: None (None), residues: 0 loop : -2.32 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 PHE 0.021 0.001 PHE B 147 TYR 0.018 0.001 TYR B 38 ARG 0.002 0.000 ARG A 156 *********************** 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 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8932 (m-30) cc_final: 0.8519 (m-30) REVERT: B 143 ARG cc_start: 0.7834 (ttp-170) cc_final: 0.7491 (tmm-80) REVERT: B 190 TYR cc_start: 0.8671 (t80) cc_final: 0.8104 (t80) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.1438 time to fit residues: 13.6892 Evaluate side-chains 65 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 optimal weight: 5.9990 chunk 46 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN B 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.102747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.079369 restraints weight = 10316.478| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.66 r_work: 0.3052 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4236 Z= 0.200 Angle : 0.530 5.783 5768 Z= 0.275 Chirality : 0.040 0.126 638 Planarity : 0.004 0.051 706 Dihedral : 3.712 13.127 552 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.17 % Allowed : 13.85 % Favored : 84.98 % 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: 1.69 (0.38), residues: 508 helix: 2.06 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.19 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 223 ARG 0.001 0.000 ARG B 112 *********************** 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 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8797 (t0) cc_final: 0.8589 (t0) REVERT: A 195 TYR cc_start: 0.9080 (t80) cc_final: 0.8727 (t80) REVERT: B 49 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: B 190 TYR cc_start: 0.8683 (t80) cc_final: 0.8096 (t80) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.1361 time to fit residues: 13.1970 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 249 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 0.0470 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081088 restraints weight = 10297.782| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.63 r_work: 0.3085 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4236 Z= 0.146 Angle : 0.507 6.070 5768 Z= 0.261 Chirality : 0.039 0.137 638 Planarity : 0.004 0.054 706 Dihedral : 3.554 12.286 552 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.11 % Allowed : 15.02 % Favored : 82.86 % 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: 2.06 (0.38), residues: 508 helix: 2.33 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.05 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.003 0.000 HIS A 253 PHE 0.020 0.001 PHE B 147 TYR 0.014 0.001 TYR B 223 ARG 0.001 0.000 ARG A 151 *********************** 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 93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8760 (t0) cc_final: 0.8533 (t0) REVERT: A 195 TYR cc_start: 0.9040 (t80) cc_final: 0.8720 (t80) REVERT: B 44 HIS cc_start: 0.8938 (t-90) cc_final: 0.8645 (t-90) REVERT: B 49 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: B 81 ASN cc_start: 0.8241 (t0) cc_final: 0.7820 (t0) REVERT: B 148 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6345 (mm) REVERT: B 190 TYR cc_start: 0.8696 (t80) cc_final: 0.8169 (t80) outliers start: 9 outliers final: 3 residues processed: 91 average time/residue: 0.1414 time to fit residues: 16.6501 Evaluate side-chains 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 0.0170 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.0020 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.080753 restraints weight = 10627.225| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.65 r_work: 0.3081 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4236 Z= 0.171 Angle : 0.523 6.179 5768 Z= 0.268 Chirality : 0.039 0.132 638 Planarity : 0.004 0.054 706 Dihedral : 3.500 13.208 552 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.17 % Allowed : 17.84 % Favored : 80.99 % 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: 2.18 (0.38), residues: 508 helix: 2.40 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.00 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 129 HIS 0.003 0.000 HIS A 253 PHE 0.021 0.001 PHE A 226 TYR 0.015 0.002 TYR B 223 ARG 0.001 0.000 ARG B 112 *********************** 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 80 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8822 (t0) cc_final: 0.8551 (t0) REVERT: A 195 TYR cc_start: 0.9080 (t80) cc_final: 0.8766 (t80) REVERT: B 24 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 44 HIS cc_start: 0.8926 (t-90) cc_final: 0.8468 (t-90) REVERT: B 81 ASN cc_start: 0.8139 (t0) cc_final: 0.7723 (t0) REVERT: B 148 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6339 (mm) REVERT: B 190 TYR cc_start: 0.8686 (t80) cc_final: 0.8201 (t80) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.1356 time to fit residues: 13.8818 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.0470 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081544 restraints weight = 10363.225| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.65 r_work: 0.3096 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4236 Z= 0.155 Angle : 0.524 6.975 5768 Z= 0.267 Chirality : 0.039 0.132 638 Planarity : 0.004 0.054 706 Dihedral : 3.431 12.805 552 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 18.08 % 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: 2.24 (0.38), residues: 508 helix: 2.48 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.09 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 129 HIS 0.003 0.000 HIS A 253 PHE 0.018 0.001 PHE B 147 TYR 0.010 0.001 TYR B 38 ARG 0.001 0.000 ARG A 156 *********************** 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 91 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8820 (t0) cc_final: 0.8574 (t0) REVERT: A 195 TYR cc_start: 0.9066 (t80) cc_final: 0.8751 (t80) REVERT: A 251 GLU cc_start: 0.8324 (pt0) cc_final: 0.8075 (pt0) REVERT: B 49 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: B 81 ASN cc_start: 0.8092 (t0) cc_final: 0.7663 (t0) REVERT: B 148 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6043 (mm) REVERT: B 190 TYR cc_start: 0.8685 (t80) cc_final: 0.8234 (t80) outliers start: 8 outliers final: 4 residues processed: 89 average time/residue: 0.1346 time to fit residues: 15.8371 Evaluate side-chains 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 6 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081138 restraints weight = 10395.768| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.62 r_work: 0.3088 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4236 Z= 0.188 Angle : 0.532 6.012 5768 Z= 0.275 Chirality : 0.039 0.138 638 Planarity : 0.004 0.054 706 Dihedral : 3.465 13.333 552 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.11 % Allowed : 18.31 % Favored : 79.58 % 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: 2.23 (0.38), residues: 508 helix: 2.49 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.15 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.018 0.001 PHE B 147 TYR 0.018 0.002 TYR B 223 ARG 0.001 0.000 ARG A 156 *********************** 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 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8819 (t0) cc_final: 0.8506 (t0) REVERT: B 49 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: B 81 ASN cc_start: 0.8149 (t0) cc_final: 0.7727 (t0) REVERT: B 148 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6011 (mm) REVERT: B 190 TYR cc_start: 0.8696 (t80) cc_final: 0.8241 (t80) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.1326 time to fit residues: 12.9686 Evaluate side-chains 72 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 57 LEU 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 15 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.104315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.081282 restraints weight = 10296.281| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.61 r_work: 0.3086 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4236 Z= 0.188 Angle : 0.553 8.609 5768 Z= 0.282 Chirality : 0.040 0.174 638 Planarity : 0.004 0.054 706 Dihedral : 3.454 13.103 552 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.64 % Allowed : 19.48 % 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: 2.20 (0.38), residues: 508 helix: 2.43 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.05 (0.53), residues: 119 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 0.017 0.001 PHE B 147 TYR 0.013 0.001 TYR B 223 ARG 0.002 0.000 ARG A 156 *********************** 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 74 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8841 (t0) cc_final: 0.8507 (t0) REVERT: B 44 HIS cc_start: 0.8905 (t-90) cc_final: 0.8662 (t-90) REVERT: B 49 PHE cc_start: 0.7667 (OUTLIER) cc_final: 0.6900 (m-80) REVERT: B 81 ASN cc_start: 0.8145 (t0) cc_final: 0.7726 (t0) REVERT: B 148 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6007 (mm) REVERT: B 190 TYR cc_start: 0.8680 (t80) cc_final: 0.8218 (t80) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.1215 time to fit residues: 11.8631 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 57 LEU 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 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081639 restraints weight = 10317.353| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.63 r_work: 0.3099 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2678 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= 0.169 Angle : 0.545 9.296 5768 Z= 0.277 Chirality : 0.040 0.200 638 Planarity : 0.004 0.054 706 Dihedral : 3.410 13.263 552 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 2.23 (0.38), residues: 508 helix: 2.44 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.00 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.017 0.001 PHE B 147 TYR 0.012 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 79 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8859 (t0) cc_final: 0.8497 (t0) REVERT: B 44 HIS cc_start: 0.8854 (t-90) cc_final: 0.8585 (t-90) REVERT: B 49 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: B 81 ASN cc_start: 0.8094 (t0) cc_final: 0.7645 (t0) REVERT: B 148 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5984 (mm) REVERT: B 190 TYR cc_start: 0.8671 (t80) cc_final: 0.8200 (t80) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.1307 time to fit residues: 13.3157 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 57 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082765 restraints weight = 10344.370| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.60 r_work: 0.3104 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2746 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= 0.163 Angle : 0.558 10.431 5768 Z= 0.282 Chirality : 0.042 0.273 638 Planarity : 0.004 0.054 706 Dihedral : 3.384 13.025 552 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.64 % Allowed : 19.95 % 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: 2.30 (0.38), residues: 508 helix: 2.48 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.94 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.016 0.001 PHE B 147 TYR 0.024 0.002 TYR B 223 ARG 0.001 0.000 ARG B 150 ********************** 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 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8829 (t0) cc_final: 0.8584 (t0) REVERT: B 44 HIS cc_start: 0.8864 (t-90) cc_final: 0.8590 (t-90) REVERT: B 49 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: B 81 ASN cc_start: 0.8068 (t0) cc_final: 0.7612 (t0) REVERT: B 148 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.5982 (mm) REVERT: B 190 TYR cc_start: 0.8671 (t80) cc_final: 0.8238 (t80) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.1289 time to fit residues: 13.0213 Evaluate side-chains 82 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 57 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.082354 restraints weight = 10274.645| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.61 r_work: 0.3092 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2765 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 : 0.577 10.193 5768 Z= 0.294 Chirality : 0.041 0.238 638 Planarity : 0.004 0.054 706 Dihedral : 3.446 13.317 552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.35 % Allowed : 19.95 % Favored : 77.70 % 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: 2.29 (0.38), residues: 508 helix: 2.48 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -1.96 (0.53), residues: 119 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 0.016 0.001 PHE B 147 TYR 0.021 0.002 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: 2029.57 seconds wall clock time: 36 minutes 46.56 seconds (2206.56 seconds total)