Starting phenix.real_space_refine on Wed Mar 5 23:09:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wlv_21843/03_2025/6wlv_21843.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlv_21843/03_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_21843/03_2025/6wlv_21843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2025/6wlv_21843.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_2025/6wlv_21843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlv_21843/03_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-5624/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: 3.11, per 1000 atoms: 0.76 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: 1.05 Conformation dependent library (CDL) restraints added in 501.6 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: 1.38 Time building geometry restraints manager: 1.26 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: 0.230 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.070 Find NCS groups from input model: 0.160 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:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- 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 : 0.420 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: 0.1786 time to fit residues: 17.5672 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 : 0.465 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079579 restraints weight = 10410.104| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.63 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 : 0.412 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: 0.8670 (t80) cc_final: 0.8103 (t80) outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.1411 time to fit residues: 13.4434 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 : 0.439 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.103190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.079883 restraints weight = 10297.610| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.63 r_work: 0.3060 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1770 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= 0.182 Angle : 0.522 5.834 5768 Z= 0.271 Chirality : 0.040 0.126 638 Planarity : 0.004 0.052 706 Dihedral : 3.687 12.855 552 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 1.72 (0.38), residues: 508 helix: 2.08 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.17 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 A 143 *********************** 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 76 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8799 (t0) cc_final: 0.8586 (t0) REVERT: A 195 TYR cc_start: 0.9066 (t80) cc_final: 0.8708 (t80) REVERT: B 190 TYR cc_start: 0.8696 (t80) cc_final: 0.8112 (t80) outliers start: 5 outliers final: 4 residues processed: 74 average time/residue: 0.1390 time to fit residues: 13.4695 Evaluate side-chains 70 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 41 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.104385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081478 restraints weight = 10271.803| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.59 r_work: 0.3091 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2104 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= 0.144 Angle : 0.500 6.100 5768 Z= 0.258 Chirality : 0.039 0.130 638 Planarity : 0.004 0.054 706 Dihedral : 3.519 12.228 552 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.11 % Allowed : 15.96 % Favored : 81.92 % 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: 2.11 (0.38), residues: 508 helix: 2.37 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.06 (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 0.019 0.001 PHE B 147 TYR 0.012 0.001 TYR B 223 ARG 0.001 0.000 ARG A 143 *********************** 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 95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8798 (t0) cc_final: 0.8553 (t0) REVERT: A 195 TYR cc_start: 0.9043 (t80) cc_final: 0.8726 (t80) REVERT: B 44 HIS cc_start: 0.8920 (t-90) cc_final: 0.8630 (t-90) REVERT: B 49 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: B 81 ASN cc_start: 0.8138 (t0) cc_final: 0.7735 (t0) REVERT: B 148 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6338 (mm) REVERT: B 190 TYR cc_start: 0.8688 (t80) cc_final: 0.8211 (t80) outliers start: 9 outliers final: 3 residues processed: 93 average time/residue: 0.1399 time to fit residues: 16.9316 Evaluate side-chains 83 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.103947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080959 restraints weight = 10630.674| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.69 r_work: 0.3084 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2278 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= 0.177 Angle : 0.525 6.338 5768 Z= 0.269 Chirality : 0.039 0.129 638 Planarity : 0.004 0.054 706 Dihedral : 3.492 13.062 552 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.64 % Allowed : 17.14 % Favored : 81.22 % 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: 2.19 (0.38), residues: 508 helix: 2.42 (0.26), residues: 389 sheet: None (None), residues: 0 loop : -2.02 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.020 0.001 PHE A 226 TYR 0.014 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 81 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8840 (t0) cc_final: 0.8570 (t0) REVERT: A 195 TYR cc_start: 0.9098 (t80) cc_final: 0.8766 (t80) REVERT: A 251 GLU cc_start: 0.8316 (pt0) cc_final: 0.8067 (pt0) REVERT: B 44 HIS cc_start: 0.8912 (t-90) cc_final: 0.8595 (t-90) REVERT: B 49 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: B 81 ASN cc_start: 0.8189 (t0) cc_final: 0.7772 (t0) REVERT: B 148 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6332 (mm) REVERT: B 190 TYR cc_start: 0.8704 (t80) cc_final: 0.8206 (t80) outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.1334 time to fit residues: 13.8862 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.8980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.103989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.081007 restraints weight = 10408.318| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.63 r_work: 0.3090 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2404 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 : 0.518 7.347 5768 Z= 0.264 Chirality : 0.039 0.139 638 Planarity : 0.004 0.054 706 Dihedral : 3.447 12.714 552 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.64 % Allowed : 17.61 % Favored : 80.75 % 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: 2.49 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.10 (0.53), residues: 120 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 0.012 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 84 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8833 (t0) cc_final: 0.8562 (t0) REVERT: A 195 TYR cc_start: 0.9067 (t80) cc_final: 0.8725 (t80) REVERT: B 44 HIS cc_start: 0.8871 (t-90) cc_final: 0.8543 (t-90) REVERT: B 49 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: B 81 ASN cc_start: 0.8128 (t0) cc_final: 0.7694 (t0) REVERT: B 148 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6059 (mm) REVERT: B 190 TYR cc_start: 0.8680 (t80) cc_final: 0.8181 (t80) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.1251 time to fit residues: 13.5301 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 : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 4.9990 chunk 38 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.103980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080928 restraints weight = 10437.149| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.63 r_work: 0.3092 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2479 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 : 0.527 7.962 5768 Z= 0.270 Chirality : 0.040 0.141 638 Planarity : 0.004 0.054 706 Dihedral : 3.456 13.059 552 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.88 % Allowed : 17.61 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.38), residues: 508 helix: 2.50 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -2.10 (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 0.002 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 75 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8787 (t0) cc_final: 0.8544 (t0) REVERT: B 44 HIS cc_start: 0.8883 (t-90) cc_final: 0.8602 (t-90) REVERT: B 49 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: B 81 ASN cc_start: 0.8118 (t0) cc_final: 0.7705 (t0) REVERT: B 148 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6011 (mm) REVERT: B 190 TYR cc_start: 0.8671 (t80) cc_final: 0.8221 (t80) outliers start: 8 outliers final: 5 residues processed: 73 average time/residue: 0.1367 time to fit residues: 13.2974 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 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: 4.9990 chunk 48 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.104053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081204 restraints weight = 10295.617| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.60 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: 0.8306 moved from start: 0.2572 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 : 0.537 8.474 5768 Z= 0.277 Chirality : 0.039 0.143 638 Planarity : 0.004 0.054 706 Dihedral : 3.437 12.986 552 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: 2.22 (0.38), residues: 508 helix: 2.42 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 129 HIS 0.002 0.000 HIS A 253 PHE 0.018 0.001 PHE B 147 TYR 0.015 0.002 TYR B 38 ARG 0.001 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 78 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8841 (t0) cc_final: 0.8509 (t0) REVERT: B 44 HIS cc_start: 0.8990 (t-90) cc_final: 0.8641 (t-90) REVERT: B 49 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6941 (m-80) REVERT: B 81 ASN cc_start: 0.8114 (t0) cc_final: 0.7698 (t0) REVERT: B 148 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6007 (mm) REVERT: B 190 TYR cc_start: 0.8673 (t80) cc_final: 0.8216 (t80) outliers start: 9 outliers final: 5 residues processed: 76 average time/residue: 0.1381 time to fit residues: 13.8977 Evaluate side-chains 72 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 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: 0.9990 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.0870 chunk 21 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.104729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081702 restraints weight = 10312.126| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.64 r_work: 0.3098 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2665 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= 0.166 Angle : 0.534 6.654 5768 Z= 0.276 Chirality : 0.040 0.147 638 Planarity : 0.004 0.054 706 Dihedral : 3.406 13.002 552 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.66 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: 2.35 (0.38), residues: 508 helix: 2.52 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.88 (0.53), residues: 120 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 0.017 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 77 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8871 (t0) cc_final: 0.8611 (t0) REVERT: B 44 HIS cc_start: 0.8898 (t-90) cc_final: 0.8637 (t-90) REVERT: B 49 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: B 81 ASN cc_start: 0.8076 (t0) cc_final: 0.7620 (t0) REVERT: B 148 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.5998 (mm) REVERT: B 190 TYR cc_start: 0.8694 (t80) cc_final: 0.8217 (t80) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 0.1318 time to fit residues: 13.1256 Evaluate side-chains 71 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.103284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.080016 restraints weight = 10465.147| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.68 r_work: 0.3062 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4236 Z= 0.229 Angle : 0.576 8.915 5768 Z= 0.299 Chirality : 0.043 0.295 638 Planarity : 0.004 0.054 706 Dihedral : 3.499 13.240 552 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.64 % Allowed : 19.72 % Favored : 78.64 % 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: 2.43 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -1.99 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 129 HIS 0.002 0.001 HIS A 30 PHE 0.018 0.001 PHE B 147 TYR 0.023 0.002 TYR B 223 ARG 0.001 0.000 ARG B 112 ********************** 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 to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8838 (t0) cc_final: 0.8555 (t0) REVERT: B 49 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: B 81 ASN cc_start: 0.8231 (t0) cc_final: 0.7775 (t0) REVERT: B 148 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6039 (mm) REVERT: B 190 TYR cc_start: 0.8691 (t80) cc_final: 0.8126 (t80) REVERT: B 260 ARG cc_start: 0.5547 (ttt180) cc_final: 0.5304 (ttt-90) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.1383 time to fit residues: 13.2571 Evaluate side-chains 73 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.104130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081934 restraints weight = 10274.802| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.61 r_work: 0.3083 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2699 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= 0.179 Angle : 0.589 13.004 5768 Z= 0.298 Chirality : 0.043 0.329 638 Planarity : 0.004 0.054 706 Dihedral : 3.515 12.835 552 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.41 % Allowed : 20.19 % 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: 2.40 (0.38), residues: 508 helix: 2.56 (0.26), residues: 388 sheet: None (None), residues: 0 loop : -1.88 (0.53), residues: 120 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 0.018 0.001 PHE B 147 TYR 0.022 0.002 TYR B 223 ARG 0.001 0.000 ARG B 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.14 seconds wall clock time: 37 minutes 33.27 seconds (2253.27 seconds total)