Starting phenix.real_space_refine on Fri Aug 22 16:37:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4q_42975/08_2025/8v4q_42975.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3782 2.51 5 N 1081 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5993 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2048 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 248} Chain breaks: 1 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Time building chain proxies: 1.70, per 1000 atoms: 0.28 Number of scatterers: 5993 At special positions: 0 Unit cell: (117.914, 85.8346, 105.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1104 8.00 N 1081 7.00 C 3782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.44 Conformation dependent library (CDL) restraints added in 239.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 37.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.567A pdb=" N ARG A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.607A pdb=" N ILE A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.734A pdb=" N GLN A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.827A pdb=" N THR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'B' and resid 13 through 30 removed outlier: 3.602A pdb=" N ARG B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 32 No H-bonds generated for 'chain 'B' and resid 31 through 32' Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.575A pdb=" N ALA B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 174 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.694A pdb=" N THR B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'C' and resid 13 through 30 removed outlier: 3.691A pdb=" N ARG C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 32 No H-bonds generated for 'chain 'C' and resid 31 through 32' Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.745A pdb=" N ILE C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 111 through 132 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.755A pdb=" N GLN C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.515A pdb=" N THR C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.600A pdb=" N ALA A 264 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP A 244 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 262 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 246 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG A 260 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA A 248 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.829A pdb=" N LEU A 148 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 227 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 215 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 41 removed outlier: 5.673A pdb=" N LEU B 239 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 268 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL B 241 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 266 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 245 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 262 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 247 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 260 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 249 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 150 removed outlier: 4.332A pdb=" N GLY B 227 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 94 removed outlier: 5.220A pdb=" N ALA C 264 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP C 244 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N LEU C 266 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER C 242 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG C 268 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA C 240 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 148 through 150 removed outlier: 6.878A pdb=" N LEU C 148 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 227 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 215 " --> pdb=" O TYR C 181 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 732 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: 0.83 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1609 1.33 - 1.45: 1074 1.45 - 1.57: 3389 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6118 Sorted by residual: bond pdb=" N LEU B 222 " pdb=" CA LEU B 222 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.88e+00 bond pdb=" N ARG C 36 " pdb=" CA ARG C 36 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.26e+00 bond pdb=" N THR A 104 " pdb=" CA THR A 104 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.90e+00 bond pdb=" N HIS A 105 " pdb=" CA HIS A 105 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.66e+00 bond pdb=" N ILE C 196 " pdb=" CA ILE C 196 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.44e+00 ... (remaining 6113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 7879 1.01 - 2.01: 299 2.01 - 3.02: 78 3.02 - 4.03: 29 4.03 - 5.04: 9 Bond angle restraints: 8294 Sorted by residual: angle pdb=" CA PHE C 178 " pdb=" CB PHE C 178 " pdb=" CG PHE C 178 " ideal model delta sigma weight residual 113.80 117.33 -3.53 1.00e+00 1.00e+00 1.24e+01 angle pdb=" C PHE C 178 " pdb=" CA PHE C 178 " pdb=" CB PHE C 178 " ideal model delta sigma weight residual 111.82 107.18 4.64 1.38e+00 5.25e-01 1.13e+01 angle pdb=" CA HIS A 105 " pdb=" C HIS A 105 " pdb=" O HIS A 105 " ideal model delta sigma weight residual 120.55 117.11 3.44 1.06e+00 8.90e-01 1.05e+01 angle pdb=" N TRP B 17 " pdb=" CA TRP B 17 " pdb=" C TRP B 17 " ideal model delta sigma weight residual 111.36 107.87 3.49 1.09e+00 8.42e-01 1.02e+01 angle pdb=" N ARG B 223 " pdb=" CA ARG B 223 " pdb=" CB ARG B 223 " ideal model delta sigma weight residual 110.69 105.73 4.96 1.61e+00 3.86e-01 9.51e+00 ... (remaining 8289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3328 17.75 - 35.50: 266 35.50 - 53.25: 42 53.25 - 71.00: 14 71.00 - 88.75: 5 Dihedral angle restraints: 3655 sinusoidal: 1471 harmonic: 2184 Sorted by residual: dihedral pdb=" CA ASP A 154 " pdb=" CB ASP A 154 " pdb=" CG ASP A 154 " pdb=" OD1 ASP A 154 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual 180.00 -137.45 -42.55 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" N ARG C 19 " pdb=" CA ARG C 19 " pdb=" CB ARG C 19 " pdb=" CG ARG C 19 " ideal model delta sinusoidal sigma weight residual -180.00 -126.41 -53.59 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 3652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 667 0.042 - 0.084: 173 0.084 - 0.127: 63 0.127 - 0.169: 11 0.169 - 0.211: 3 Chirality restraints: 917 Sorted by residual: chirality pdb=" CA MET A 107 " pdb=" N MET A 107 " pdb=" C MET A 107 " pdb=" CB MET A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ARG C 36 " pdb=" N ARG C 36 " pdb=" C ARG C 36 " pdb=" CB ARG C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE C 196 " pdb=" N ILE C 196 " pdb=" C ILE C 196 " pdb=" CB ILE C 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 914 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 257 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO B 258 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 257 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 258 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 16 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C GLU B 16 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU B 16 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 377 2.74 - 3.28: 5390 3.28 - 3.82: 9209 3.82 - 4.36: 11042 4.36 - 4.90: 19448 Nonbonded interactions: 45466 Sorted by model distance: nonbonded pdb=" NH1 ARG B 170 " pdb=" OE2 GLU B 174 " model vdw 2.201 3.120 nonbonded pdb=" O THR C 84 " pdb=" OH TYR C 138 " model vdw 2.218 3.040 nonbonded pdb=" NH1 ARG A 170 " pdb=" OE2 GLU A 174 " model vdw 2.285 3.120 nonbonded pdb=" OE2 GLU B 167 " pdb=" NH2 ARG B 170 " model vdw 2.365 3.120 nonbonded pdb=" OE2 GLU A 22 " pdb=" NE2 GLN A 26 " model vdw 2.399 3.120 ... (remaining 45461 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 9 through 44 or resid 83 through 279)) selection = (chain 'B' and (resid 9 through 44 or resid 83 through 279)) selection = (chain 'C' and resid 9 through 279) } 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: 3.670 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.190 Find NCS groups from input model: 0.100 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.003 0.036 6118 Z= 0.163 Angle : 0.525 5.035 8294 Z= 0.318 Chirality : 0.045 0.211 917 Planarity : 0.004 0.062 1087 Dihedral : 13.530 88.754 2255 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.48 % Allowed : 0.96 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.30), residues: 749 helix: 2.23 (0.33), residues: 247 sheet: -0.62 (0.38), residues: 184 loop : -0.97 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 223 TYR 0.006 0.001 TYR C 197 PHE 0.015 0.001 PHE C 178 TRP 0.009 0.001 TRP B 96 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6118) covalent geometry : angle 0.52512 ( 8294) hydrogen bonds : bond 0.13064 ( 253) hydrogen bonds : angle 5.99520 ( 732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.252 Fit side-chains REVERT: A 170 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7877 (ttp80) REVERT: B 171 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7987 (mttt) REVERT: C 178 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6167 (m-80) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.8405 time to fit residues: 108.2943 Evaluate side-chains 93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 220 ASN C 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124094 restraints weight = 6559.062| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.16 r_work: 0.3148 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6118 Z= 0.100 Angle : 0.447 3.297 8294 Z= 0.241 Chirality : 0.043 0.136 917 Planarity : 0.004 0.050 1087 Dihedral : 4.199 52.223 850 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.93 % Allowed : 10.91 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.30), residues: 749 helix: 2.46 (0.33), residues: 254 sheet: -0.31 (0.39), residues: 174 loop : -0.95 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.017 0.001 TYR C 41 PHE 0.011 0.001 PHE C 92 TRP 0.007 0.001 TRP B 96 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6118) covalent geometry : angle 0.44658 ( 8294) hydrogen bonds : bond 0.04258 ( 253) hydrogen bonds : angle 4.61188 ( 732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.236 Fit side-chains REVERT: A 206 GLU cc_start: 0.7027 (tp30) cc_final: 0.6819 (tp30) REVERT: A 220 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7795 (m110) REVERT: A 238 ASP cc_start: 0.8788 (p0) cc_final: 0.8506 (p0) REVERT: B 171 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8251 (mttt) REVERT: C 170 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.6797 (ttp-110) REVERT: C 178 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6245 (m-80) REVERT: C 195 ARG cc_start: 0.7318 (mpt180) cc_final: 0.7021 (mmt180) outliers start: 12 outliers final: 3 residues processed: 102 average time/residue: 0.7702 time to fit residues: 81.1949 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 220 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 192 GLN B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.150844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.118948 restraints weight = 6416.779| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.91 r_work: 0.3038 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6118 Z= 0.164 Angle : 0.542 4.253 8294 Z= 0.291 Chirality : 0.047 0.151 917 Planarity : 0.005 0.049 1087 Dihedral : 4.494 52.935 848 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.21 % Allowed : 10.91 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.30), residues: 749 helix: 2.28 (0.33), residues: 252 sheet: -0.49 (0.38), residues: 176 loop : -0.95 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.019 0.001 TYR C 41 PHE 0.015 0.002 PHE C 130 TRP 0.008 0.001 TRP C 96 HIS 0.011 0.002 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6118) covalent geometry : angle 0.54205 ( 8294) hydrogen bonds : bond 0.06606 ( 253) hydrogen bonds : angle 4.87284 ( 732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.184 Fit side-chains REVERT: A 206 GLU cc_start: 0.7200 (tp30) cc_final: 0.6949 (tp30) REVERT: A 220 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7901 (m110) REVERT: B 171 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8270 (mttt) REVERT: C 107 MET cc_start: 0.8664 (ptm) cc_final: 0.8412 (ptp) REVERT: C 178 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: C 195 ARG cc_start: 0.7385 (mpt180) cc_final: 0.7061 (mmt180) outliers start: 20 outliers final: 8 residues processed: 100 average time/residue: 0.7274 time to fit residues: 75.1949 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 192 GLN B 163 GLN B 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.151910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.119477 restraints weight = 6491.962| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.09 r_work: 0.3061 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6118 Z= 0.123 Angle : 0.481 3.691 8294 Z= 0.260 Chirality : 0.044 0.143 917 Planarity : 0.004 0.044 1087 Dihedral : 4.354 52.570 848 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.57 % Allowed : 12.36 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.30), residues: 749 helix: 2.29 (0.32), residues: 253 sheet: -0.45 (0.39), residues: 174 loop : -0.97 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.018 0.001 TYR C 41 PHE 0.013 0.002 PHE C 92 TRP 0.010 0.001 TRP B 96 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6118) covalent geometry : angle 0.48107 ( 8294) hydrogen bonds : bond 0.05212 ( 253) hydrogen bonds : angle 4.68155 ( 732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.173 Fit side-chains REVERT: A 206 GLU cc_start: 0.7079 (tp30) cc_final: 0.6751 (tp30) REVERT: B 171 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8265 (mttt) REVERT: B 210 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: C 178 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6406 (m-80) REVERT: C 193 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7332 (mp) REVERT: C 195 ARG cc_start: 0.7351 (mpt180) cc_final: 0.7030 (mmt180) outliers start: 16 outliers final: 8 residues processed: 101 average time/residue: 0.7329 time to fit residues: 76.6192 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 15 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 220 ASN C 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122139 restraints weight = 6607.914| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.37 r_work: 0.3086 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6118 Z= 0.101 Angle : 0.442 3.434 8294 Z= 0.240 Chirality : 0.043 0.140 917 Planarity : 0.004 0.041 1087 Dihedral : 4.166 50.963 848 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.41 % Allowed : 13.16 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.30), residues: 749 helix: 2.48 (0.32), residues: 253 sheet: -0.37 (0.39), residues: 174 loop : -0.95 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.018 0.001 TYR C 41 PHE 0.012 0.002 PHE C 92 TRP 0.008 0.001 TRP B 96 HIS 0.005 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 6118) covalent geometry : angle 0.44172 ( 8294) hydrogen bonds : bond 0.04271 ( 253) hydrogen bonds : angle 4.48405 ( 732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.271 Fit side-chains REVERT: A 135 ARG cc_start: 0.6877 (mtp-110) cc_final: 0.6405 (ttp80) REVERT: A 206 GLU cc_start: 0.7005 (tp30) cc_final: 0.6686 (tp30) REVERT: A 238 ASP cc_start: 0.8853 (p0) cc_final: 0.8557 (p0) REVERT: B 171 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8242 (mttt) REVERT: B 195 ARG cc_start: 0.8157 (mtt180) cc_final: 0.7773 (mtt-85) REVERT: B 210 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: C 193 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7325 (mp) REVERT: C 195 ARG cc_start: 0.7329 (tpt170) cc_final: 0.7009 (mmt180) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.7423 time to fit residues: 79.1828 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128763 restraints weight = 6890.124| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6118 Z= 0.185 Angle : 0.562 4.638 8294 Z= 0.302 Chirality : 0.047 0.158 917 Planarity : 0.005 0.047 1087 Dihedral : 4.566 51.278 848 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.69 % Allowed : 12.36 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.29), residues: 749 helix: 2.09 (0.32), residues: 252 sheet: -0.49 (0.38), residues: 174 loop : -1.01 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.020 0.002 TYR C 41 PHE 0.017 0.002 PHE C 130 TRP 0.009 0.001 TRP C 96 HIS 0.009 0.002 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6118) covalent geometry : angle 0.56233 ( 8294) hydrogen bonds : bond 0.06952 ( 253) hydrogen bonds : angle 4.86867 ( 732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.241 Fit side-chains REVERT: A 192 GLN cc_start: 0.7637 (mt0) cc_final: 0.7424 (mt0) REVERT: A 206 GLU cc_start: 0.7118 (tp30) cc_final: 0.6810 (tp30) REVERT: B 74 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5868 (ptt) REVERT: B 171 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8320 (mttt) REVERT: B 210 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7329 (mp10) REVERT: C 195 ARG cc_start: 0.7400 (tpt170) cc_final: 0.7088 (mmt180) outliers start: 23 outliers final: 11 residues processed: 102 average time/residue: 0.7589 time to fit residues: 80.1878 Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128076 restraints weight = 6862.034| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.10 r_work: 0.3213 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6118 Z= 0.179 Angle : 0.562 4.648 8294 Z= 0.302 Chirality : 0.047 0.155 917 Planarity : 0.005 0.044 1087 Dihedral : 4.635 51.962 848 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.37 % Allowed : 13.00 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.29), residues: 749 helix: 1.97 (0.32), residues: 252 sheet: -0.55 (0.38), residues: 174 loop : -1.04 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 170 TYR 0.020 0.002 TYR C 41 PHE 0.016 0.002 PHE C 130 TRP 0.010 0.002 TRP C 96 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 6118) covalent geometry : angle 0.56167 ( 8294) hydrogen bonds : bond 0.06827 ( 253) hydrogen bonds : angle 4.91928 ( 732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.258 Fit side-chains REVERT: A 206 GLU cc_start: 0.7204 (tp30) cc_final: 0.6842 (tp30) REVERT: B 74 MET cc_start: 0.6379 (ptm) cc_final: 0.6078 (ptt) REVERT: B 171 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8384 (mttt) REVERT: B 210 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: C 195 ARG cc_start: 0.7571 (mpt180) cc_final: 0.7242 (mmt180) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.7753 time to fit residues: 81.1366 Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131153 restraints weight = 6961.160| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.17 r_work: 0.3266 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6118 Z= 0.151 Angle : 0.528 4.883 8294 Z= 0.285 Chirality : 0.046 0.150 917 Planarity : 0.005 0.043 1087 Dihedral : 4.531 51.739 848 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.89 % Allowed : 13.96 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.29), residues: 749 helix: 2.04 (0.32), residues: 253 sheet: -0.53 (0.38), residues: 174 loop : -1.07 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.020 0.002 TYR C 41 PHE 0.014 0.002 PHE C 130 TRP 0.010 0.001 TRP C 96 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6118) covalent geometry : angle 0.52831 ( 8294) hydrogen bonds : bond 0.06095 ( 253) hydrogen bonds : angle 4.83549 ( 732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.253 Fit side-chains REVERT: A 206 GLU cc_start: 0.7089 (tp30) cc_final: 0.6765 (tp30) REVERT: B 74 MET cc_start: 0.6235 (ptm) cc_final: 0.5889 (ptt) REVERT: B 171 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8333 (mttt) REVERT: B 210 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: C 195 ARG cc_start: 0.7473 (mpt180) cc_final: 0.7254 (mmt180) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.7076 time to fit residues: 70.4081 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.160361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131632 restraints weight = 6997.532| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.23 r_work: 0.3266 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6118 Z= 0.119 Angle : 0.480 5.561 8294 Z= 0.260 Chirality : 0.044 0.142 917 Planarity : 0.004 0.040 1087 Dihedral : 4.342 51.277 848 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 15.09 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.30), residues: 749 helix: 2.26 (0.32), residues: 253 sheet: -0.49 (0.39), residues: 175 loop : -1.03 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.020 0.001 TYR C 41 PHE 0.012 0.002 PHE C 92 TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6118) covalent geometry : angle 0.47978 ( 8294) hydrogen bonds : bond 0.04921 ( 253) hydrogen bonds : angle 4.65720 ( 732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.160 Fit side-chains REVERT: A 135 ARG cc_start: 0.6998 (mtp-110) cc_final: 0.6577 (ttp80) REVERT: A 206 GLU cc_start: 0.7102 (tp30) cc_final: 0.6761 (tp30) REVERT: B 74 MET cc_start: 0.6255 (ptm) cc_final: 0.6012 (ptt) REVERT: B 171 LYS cc_start: 0.8612 (mtpp) cc_final: 0.8358 (mttt) REVERT: B 206 GLU cc_start: 0.7746 (tp30) cc_final: 0.7497 (tp30) REVERT: B 210 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: C 195 ARG cc_start: 0.7525 (mpt180) cc_final: 0.7292 (mmt180) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.6809 time to fit residues: 68.4999 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119719 restraints weight = 6513.281| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.09 r_work: 0.3054 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6118 Z= 0.124 Angle : 0.488 5.680 8294 Z= 0.264 Chirality : 0.044 0.144 917 Planarity : 0.004 0.041 1087 Dihedral : 4.345 51.319 848 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.77 % Allowed : 15.89 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.30), residues: 749 helix: 2.28 (0.32), residues: 253 sheet: -0.48 (0.39), residues: 174 loop : -1.00 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 170 TYR 0.021 0.001 TYR C 41 PHE 0.012 0.002 PHE C 92 TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6118) covalent geometry : angle 0.48792 ( 8294) hydrogen bonds : bond 0.05235 ( 253) hydrogen bonds : angle 4.64600 ( 732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.252 Fit side-chains REVERT: A 135 ARG cc_start: 0.6902 (mtp-110) cc_final: 0.6460 (ttp80) REVERT: A 206 GLU cc_start: 0.7022 (tp30) cc_final: 0.6686 (tp30) REVERT: B 74 MET cc_start: 0.6099 (ptm) cc_final: 0.5888 (ptt) REVERT: B 171 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8235 (mttt) REVERT: B 206 GLU cc_start: 0.7596 (tp30) cc_final: 0.7379 (tp30) REVERT: B 210 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: C 195 ARG cc_start: 0.7433 (mpt180) cc_final: 0.7183 (mmt180) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.6642 time to fit residues: 65.5114 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.152652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.120961 restraints weight = 6505.705| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.16 r_work: 0.3062 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6118 Z= 0.119 Angle : 0.479 5.812 8294 Z= 0.259 Chirality : 0.044 0.143 917 Planarity : 0.004 0.041 1087 Dihedral : 4.308 51.524 848 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 15.73 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.30), residues: 749 helix: 2.32 (0.32), residues: 253 sheet: -0.45 (0.39), residues: 175 loop : -1.01 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 170 TYR 0.022 0.001 TYR C 41 PHE 0.012 0.002 PHE C 92 TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6118) covalent geometry : angle 0.47859 ( 8294) hydrogen bonds : bond 0.04949 ( 253) hydrogen bonds : angle 4.60362 ( 732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2876.98 seconds wall clock time: 49 minutes 30.93 seconds (2970.93 seconds total)