Starting phenix.real_space_refine on Tue Jan 14 06:48:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4q_42975/01_2025/8v4q_42975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4q_42975/01_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_42975/01_2025/8v4q_42975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4q_42975/01_2025/8v4q_42975.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4q_42975/01_2025/8v4q_42975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4q_42975/01_2025/8v4q_42975.cif" } resolution = 2.71 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.18, per 1000 atoms: 0.86 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: 1.36 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 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: 0.67 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: 1.53 Time building geometry restraints manager: 1.58 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: 4.970 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.590 Find NCS groups from input model: 0.310 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.520 ------------------------------------------------------------------------------- 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= 0.174 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 (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: 0.26 (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 TRP 0.009 0.001 TRP B 96 HIS 0.010 0.001 HIS A 199 PHE 0.015 0.001 PHE C 178 TYR 0.006 0.001 TYR C 197 ARG 0.006 0.000 ARG B 223 *********************** 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 : 0.701 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: 1.7863 time to fit residues: 230.4359 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 : 0.645 ------------------------------------------------------------------------------- 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 63 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3716 r_free = 0.3716 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123450 restraints weight = 6492.507| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.25 r_work: 0.3119 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1108 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= 0.131 Angle : 0.445 3.292 8294 Z= 0.240 Chirality : 0.043 0.135 917 Planarity : 0.004 0.050 1087 Dihedral : 4.206 52.230 850 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 0.92 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 (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: 0.56 (0.30), residues: 749 helix: 2.45 (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 TRP 0.007 0.001 TRP B 96 HIS 0.007 0.001 HIS B 105 PHE 0.011 0.001 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.004 0.000 ARG A 170 *********************** 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 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.747 Fit side-chains REVERT: A 220 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7809 (m110) REVERT: A 238 ASP cc_start: 0.8819 (p0) cc_final: 0.8541 (p0) REVERT: B 171 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8258 (mttt) REVERT: C 178 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6169 (m-80) REVERT: C 195 ARG cc_start: 0.7379 (mpt180) cc_final: 0.7071 (mmt180) outliers start: 12 outliers final: 5 residues processed: 96 average time/residue: 1.6568 time to fit residues: 164.8040 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 214 ASP 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 211 LEU 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 49 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.154467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122628 restraints weight = 6497.356| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.10 r_work: 0.3075 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6118 Z= 0.156 Angle : 0.457 3.494 8294 Z= 0.246 Chirality : 0.043 0.142 917 Planarity : 0.004 0.047 1087 Dihedral : 4.156 51.594 848 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.57 % Allowed : 10.75 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.62 (0.30), residues: 749 helix: 2.56 (0.32), residues: 253 sheet: -0.33 (0.39), residues: 174 loop : -0.91 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 96 HIS 0.008 0.001 HIS B 105 PHE 0.012 0.002 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.004 0.000 ARG C 29 *********************** 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 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.646 Fit side-chains REVERT: A 206 GLU cc_start: 0.6953 (tp30) cc_final: 0.6288 (tp30) REVERT: A 220 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7828 (m110) REVERT: A 238 ASP cc_start: 0.8870 (p0) cc_final: 0.8605 (p0) REVERT: B 74 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.4978 (ptm) REVERT: B 171 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8240 (mttt) REVERT: B 195 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7793 (mtt-85) REVERT: B 210 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: C 178 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: C 195 ARG cc_start: 0.7304 (mpt180) cc_final: 0.6998 (mmt180) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 1.6413 time to fit residues: 166.6592 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain A residue 220 ASN 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 235 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.154587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122354 restraints weight = 6587.399| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.12 r_work: 0.3082 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6118 Z= 0.148 Angle : 0.447 3.476 8294 Z= 0.242 Chirality : 0.043 0.141 917 Planarity : 0.004 0.044 1087 Dihedral : 4.102 49.950 848 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.05 % Allowed : 11.40 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.67 (0.30), residues: 749 helix: 2.61 (0.32), residues: 253 sheet: -0.30 (0.39), residues: 174 loop : -0.90 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 96 HIS 0.007 0.001 HIS B 105 PHE 0.012 0.002 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.003 0.000 ARG C 29 *********************** 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 114 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 1.208 Fit side-chains REVERT: A 135 ARG cc_start: 0.6851 (mtp-110) cc_final: 0.6401 (ttp80) REVERT: A 206 GLU cc_start: 0.6884 (tp30) cc_final: 0.6202 (tp30) REVERT: A 238 ASP cc_start: 0.8856 (p0) cc_final: 0.8576 (p0) REVERT: B 171 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8255 (mttt) REVERT: B 195 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7791 (mtt-85) REVERT: B 210 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7263 (mp10) REVERT: C 193 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7331 (mp) REVERT: C 195 ARG cc_start: 0.7354 (tpt170) cc_final: 0.7045 (mmt180) outliers start: 19 outliers final: 9 residues processed: 104 average time/residue: 1.6603 time to fit residues: 179.4178 Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 244 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131754 restraints weight = 6926.691| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.06 r_work: 0.3198 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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= 0.170 Angle : 0.465 3.692 8294 Z= 0.252 Chirality : 0.044 0.143 917 Planarity : 0.004 0.044 1087 Dihedral : 4.178 49.611 848 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.21 % Allowed : 11.56 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.58 (0.30), residues: 749 helix: 2.49 (0.32), residues: 253 sheet: -0.33 (0.39), residues: 174 loop : -0.91 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.006 0.001 HIS A 199 PHE 0.013 0.002 PHE C 92 TYR 0.006 0.001 TYR B 131 ARG 0.003 0.000 ARG B 170 *********************** 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 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.683 Fit side-chains REVERT: A 206 GLU cc_start: 0.7010 (tp30) cc_final: 0.6339 (tp30) REVERT: B 171 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8346 (mttt) REVERT: B 195 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7918 (mtt-85) REVERT: B 210 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: C 193 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7454 (mp) REVERT: C 195 ARG cc_start: 0.7404 (tpt170) cc_final: 0.7108 (mmt180) outliers start: 20 outliers final: 10 residues processed: 100 average time/residue: 1.5647 time to fit residues: 162.4664 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131076 restraints weight = 6820.221| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.09 r_work: 0.3279 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1591 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= 0.186 Angle : 0.481 4.153 8294 Z= 0.260 Chirality : 0.044 0.144 917 Planarity : 0.004 0.044 1087 Dihedral : 4.231 48.749 848 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 11.88 % 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 (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: 0.51 (0.30), residues: 749 helix: 2.41 (0.32), residues: 253 sheet: -0.38 (0.39), residues: 174 loop : -0.94 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.006 0.001 HIS A 199 PHE 0.013 0.002 PHE C 92 TYR 0.006 0.001 TYR B 131 ARG 0.004 0.000 ARG C 29 *********************** 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 112 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.673 Fit side-chains REVERT: A 135 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6486 (ttp80) REVERT: A 206 GLU cc_start: 0.6957 (tp30) cc_final: 0.6301 (tp30) REVERT: B 171 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8327 (mttt) REVERT: B 195 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7916 (mtt-85) REVERT: C 195 ARG cc_start: 0.7400 (tpt170) cc_final: 0.7076 (mmt180) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 1.6511 time to fit residues: 176.3559 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.162875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134403 restraints weight = 6910.810| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.10 r_work: 0.3255 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1597 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= 0.164 Angle : 0.463 4.520 8294 Z= 0.251 Chirality : 0.043 0.142 917 Planarity : 0.004 0.042 1087 Dihedral : 4.174 48.502 848 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.09 % Allowed : 12.84 % 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 (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: 0.54 (0.30), residues: 749 helix: 2.46 (0.32), residues: 253 sheet: -0.37 (0.39), residues: 174 loop : -0.93 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.008 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.006 0.001 TYR B 131 ARG 0.004 0.000 ARG B 170 *********************** 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 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.713 Fit side-chains REVERT: A 206 GLU cc_start: 0.6913 (tp30) cc_final: 0.6258 (tp30) REVERT: B 74 MET cc_start: 0.6109 (ptm) cc_final: 0.5878 (ptt) REVERT: B 171 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8323 (mttt) REVERT: B 195 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7838 (mtt-85) REVERT: B 210 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: C 195 ARG cc_start: 0.7411 (tpt170) cc_final: 0.7070 (mmt180) outliers start: 13 outliers final: 9 residues processed: 93 average time/residue: 1.5465 time to fit residues: 149.7657 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain C residue 211 LEU 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 10 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.158215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128766 restraints weight = 6814.194| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.03 r_work: 0.3231 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6118 Z= 0.269 Angle : 0.548 4.702 8294 Z= 0.295 Chirality : 0.047 0.156 917 Planarity : 0.005 0.046 1087 Dihedral : 4.464 48.121 848 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 (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: 0.31 (0.30), residues: 749 helix: 2.17 (0.32), residues: 252 sheet: -0.48 (0.38), residues: 174 loop : -0.99 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.007 0.001 HIS A 199 PHE 0.016 0.002 PHE C 130 TYR 0.008 0.001 TYR B 131 ARG 0.005 0.000 ARG B 170 *********************** 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 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.579 Fit side-chains REVERT: A 206 GLU cc_start: 0.6862 (tp30) cc_final: 0.6243 (tp30) REVERT: B 74 MET cc_start: 0.6316 (ptm) cc_final: 0.5985 (ptt) REVERT: B 171 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8372 (mttt) REVERT: B 195 ARG cc_start: 0.8293 (mtt180) cc_final: 0.7972 (mtt-85) REVERT: B 210 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: C 195 ARG cc_start: 0.7533 (tpt170) cc_final: 0.7183 (mmt180) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 1.6100 time to fit residues: 165.7120 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 253 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.157664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127152 restraints weight = 6888.279| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.08 r_work: 0.3008 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1835 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= 0.291 Angle : 0.573 5.466 8294 Z= 0.309 Chirality : 0.048 0.157 917 Planarity : 0.005 0.045 1087 Dihedral : 4.587 48.224 848 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.57 % Allowed : 13.48 % 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 (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: 0.12 (0.29), residues: 749 helix: 1.98 (0.32), residues: 252 sheet: -0.57 (0.38), residues: 174 loop : -1.08 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 96 HIS 0.007 0.002 HIS B 105 PHE 0.017 0.002 PHE C 130 TYR 0.011 0.002 TYR C 89 ARG 0.005 0.000 ARG B 170 *********************** 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 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.640 Fit side-chains REVERT: A 206 GLU cc_start: 0.6697 (tp30) cc_final: 0.6032 (tp30) REVERT: B 74 MET cc_start: 0.6195 (ptm) cc_final: 0.5880 (ptt) REVERT: B 171 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8141 (mttt) REVERT: B 210 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: C 195 ARG cc_start: 0.7440 (tpt170) cc_final: 0.7188 (mmt180) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 1.5766 time to fit residues: 155.3762 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 192 GLN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.160217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130646 restraints weight = 6932.784| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.04 r_work: 0.3168 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1728 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= 0.178 Angle : 0.485 5.515 8294 Z= 0.263 Chirality : 0.044 0.143 917 Planarity : 0.004 0.041 1087 Dihedral : 4.316 47.293 848 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.25 % Allowed : 13.80 % 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 (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: 0.30 (0.30), residues: 749 helix: 2.23 (0.32), residues: 253 sheet: -0.49 (0.39), residues: 174 loop : -1.05 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.008 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.013 0.001 TYR C 89 ARG 0.005 0.000 ARG B 170 ********************** 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 103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.667 Fit side-chains REVERT: A 135 ARG cc_start: 0.7009 (mtp-110) cc_final: 0.6579 (ttp80) REVERT: A 206 GLU cc_start: 0.6855 (tp30) cc_final: 0.6225 (tp30) REVERT: B 74 MET cc_start: 0.6243 (ptm) cc_final: 0.6029 (ptt) REVERT: B 171 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8326 (mttt) REVERT: B 195 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7918 (mtt-85) REVERT: B 210 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: C 195 ARG cc_start: 0.7476 (tpt170) cc_final: 0.7221 (mmt180) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 1.5544 time to fit residues: 158.2911 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.160478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131299 restraints weight = 7008.818| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.19 r_work: 0.3273 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6118 Z= 0.176 Angle : 0.481 5.810 8294 Z= 0.261 Chirality : 0.044 0.144 917 Planarity : 0.004 0.041 1087 Dihedral : 4.243 46.534 848 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.93 % Allowed : 14.13 % 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 (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: 0.36 (0.30), residues: 749 helix: 2.31 (0.33), residues: 253 sheet: -0.47 (0.39), residues: 174 loop : -1.03 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.012 0.001 TYR C 89 ARG 0.004 0.000 ARG B 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5877.08 seconds wall clock time: 104 minutes 4.16 seconds (6244.16 seconds total)