Starting phenix.real_space_refine on Tue Mar 11 14:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4q_42975/03_2025/8v4q_42975.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4q_42975/03_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_42975/03_2025/8v4q_42975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4q_42975/03_2025/8v4q_42975.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4q_42975/03_2025/8v4q_42975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4q_42975/03_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-5624/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: 1.32 Conformation dependent library (CDL) restraints added in 752.2 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: 0.76 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: 1.48 Time building geometry restraints manager: 1.57 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: 2.570 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: 0.040 Set scattering table: 0.060 Process input model: 18.500 Find NCS groups from input model: 0.270 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:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- 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 : 0.648 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: 1.6744 time to fit residues: 215.9748 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 : 0.602 ------------------------------------------------------------------------------- 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: 0.3120 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.665 Fit side-chains REVERT: A 220 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7804 (m110) REVERT: A 238 ASP cc_start: 0.8822 (p0) cc_final: 0.8542 (p0) REVERT: B 171 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8255 (mttt) REVERT: C 178 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6164 (m-80) REVERT: C 195 ARG cc_start: 0.7371 (mpt180) cc_final: 0.7063 (mmt180) outliers start: 12 outliers final: 5 residues processed: 96 average time/residue: 1.5859 time to fit residues: 157.7409 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 : 0.597 ------------------------------------------------------------------------------- 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: 0.6980 chunk 66 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 220 ASN C 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123573 restraints weight = 6518.474| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.17 r_work: 0.3109 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1261 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= 0.137 Angle : 0.439 3.319 8294 Z= 0.237 Chirality : 0.043 0.140 917 Planarity : 0.004 0.046 1087 Dihedral : 4.076 51.322 848 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.09 % Allowed : 10.91 % Favored : 87.00 % 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: 0.68 (0.30), residues: 749 helix: 2.59 (0.32), residues: 254 sheet: -0.28 (0.39), residues: 174 loop : -0.89 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 96 HIS 0.006 0.001 HIS B 105 PHE 0.011 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 103 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.605 Fit side-chains REVERT: A 206 GLU cc_start: 0.6941 (tp30) cc_final: 0.6267 (tp30) REVERT: A 238 ASP cc_start: 0.8836 (p0) cc_final: 0.8554 (p0) REVERT: B 74 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.4927 (ptm) REVERT: B 171 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8227 (mttt) REVERT: B 195 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7804 (mtt-85) REVERT: B 210 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: C 170 ARG cc_start: 0.7317 (ttp-110) cc_final: 0.6793 (ttp-110) REVERT: C 178 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: C 195 ARG cc_start: 0.7319 (mpt180) cc_final: 0.7009 (mmt180) outliers start: 13 outliers final: 4 residues processed: 94 average time/residue: 1.5462 time to fit residues: 150.7086 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 : 0.612 ------------------------------------------------------------------------------- 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 B residue 74 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain C residue 178 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.155952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123939 restraints weight = 6616.480| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.17 r_work: 0.3099 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1421 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= 0.130 Angle : 0.426 3.463 8294 Z= 0.230 Chirality : 0.042 0.138 917 Planarity : 0.004 0.043 1087 Dihedral : 3.996 50.610 848 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.57 % Allowed : 12.04 % Favored : 85.39 % 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: 0.75 (0.30), residues: 749 helix: 2.67 (0.32), residues: 255 sheet: -0.25 (0.39), residues: 175 loop : -0.87 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 96 HIS 0.006 0.001 HIS B 105 PHE 0.011 0.001 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: 16 poor density : 98 time to evaluate : 0.662 Fit side-chains REVERT: A 135 ARG cc_start: 0.6836 (mtp-110) cc_final: 0.6380 (ttp80) REVERT: A 206 GLU cc_start: 0.6892 (tp30) cc_final: 0.6204 (tp30) REVERT: A 238 ASP cc_start: 0.8809 (p0) cc_final: 0.8516 (p0) REVERT: B 171 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8244 (mttt) REVERT: B 195 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7876 (mtt-85) REVERT: B 210 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: C 193 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7335 (mp) REVERT: C 195 ARG cc_start: 0.7285 (mpt180) cc_final: 0.6967 (mmt180) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 1.4932 time to fit residues: 162.5989 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET 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 211 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 0.0000 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.163288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.133646 restraints weight = 6941.216| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.11 r_work: 0.3321 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6118 Z= 0.133 Angle : 0.427 3.292 8294 Z= 0.231 Chirality : 0.042 0.140 917 Planarity : 0.004 0.042 1087 Dihedral : 3.987 49.219 848 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.73 % Allowed : 12.36 % Favored : 84.91 % 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: 0.76 (0.30), residues: 749 helix: 2.64 (0.32), residues: 255 sheet: -0.22 (0.39), residues: 175 loop : -0.85 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 96 HIS 0.006 0.001 HIS A 199 PHE 0.011 0.001 PHE C 92 TYR 0.005 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 107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.724 Fit side-chains REVERT: A 206 GLU cc_start: 0.6940 (tp30) cc_final: 0.6299 (tp30) REVERT: A 238 ASP cc_start: 0.8804 (p0) cc_final: 0.8550 (p0) REVERT: B 171 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8344 (mttt) REVERT: B 195 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7883 (mtt-85) REVERT: B 210 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: C 193 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7512 (mp) REVERT: C 195 ARG cc_start: 0.7311 (mpt180) cc_final: 0.7018 (mmt180) outliers start: 17 outliers final: 7 residues processed: 100 average time/residue: 1.5819 time to fit residues: 163.8745 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 211 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132790 restraints weight = 6873.315| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.08 r_work: 0.3285 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6118 Z= 0.155 Angle : 0.453 4.062 8294 Z= 0.245 Chirality : 0.043 0.142 917 Planarity : 0.004 0.044 1087 Dihedral : 4.080 49.148 848 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.89 % Allowed : 12.52 % Favored : 84.59 % 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: 0.72 (0.30), residues: 749 helix: 2.61 (0.32), residues: 253 sheet: -0.25 (0.39), residues: 174 loop : -0.85 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 96 HIS 0.006 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.005 0.001 TYR B 131 ARG 0.003 0.000 ARG A 170 *********************** 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 107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.670 Fit side-chains REVERT: A 135 ARG cc_start: 0.6914 (mtp-110) cc_final: 0.6457 (ttp80) REVERT: A 206 GLU cc_start: 0.7039 (tp30) cc_final: 0.6365 (tp30) REVERT: A 238 ASP cc_start: 0.8854 (p0) cc_final: 0.8619 (p0) REVERT: B 171 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8346 (mttt) REVERT: B 195 ARG cc_start: 0.8288 (mtt180) cc_final: 0.7921 (mtt-85) REVERT: B 210 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7364 (mp10) REVERT: C 193 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7455 (mp) REVERT: C 195 ARG cc_start: 0.7419 (tpt170) cc_final: 0.7118 (mmt180) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 1.4492 time to fit residues: 147.7022 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 214 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 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: 0.5980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.160723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130908 restraints weight = 6947.013| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.08 r_work: 0.3249 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6118 Z= 0.194 Angle : 0.487 4.390 8294 Z= 0.263 Chirality : 0.044 0.146 917 Planarity : 0.004 0.044 1087 Dihedral : 4.232 48.981 848 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.57 % Allowed : 13.16 % Favored : 84.27 % 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: 0.55 (0.30), residues: 749 helix: 2.46 (0.32), residues: 253 sheet: -0.36 (0.39), residues: 174 loop : -0.93 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 96 HIS 0.008 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 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 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.746 Fit side-chains REVERT: A 206 GLU cc_start: 0.6902 (tp30) cc_final: 0.6263 (tp30) REVERT: B 171 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8364 (mttt) REVERT: B 195 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7958 (mtt-85) REVERT: C 195 ARG cc_start: 0.7484 (tpt170) cc_final: 0.7175 (mmt180) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 1.5657 time to fit residues: 159.3184 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 : 0.701 ------------------------------------------------------------------------------- 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 265 LEU 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=2.00 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128244 restraints weight = 6844.048| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.13 r_work: 0.3199 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6118 Z= 0.376 Angle : 0.632 5.736 8294 Z= 0.339 Chirality : 0.051 0.180 917 Planarity : 0.005 0.049 1087 Dihedral : 4.736 50.077 848 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.05 % Allowed : 12.52 % 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: 0.07 (0.29), residues: 749 helix: 1.86 (0.32), residues: 252 sheet: -0.55 (0.38), residues: 174 loop : -1.06 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 96 HIS 0.010 0.002 HIS B 105 PHE 0.018 0.003 PHE C 130 TYR 0.011 0.002 TYR B 131 ARG 0.005 0.001 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 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.697 Fit side-chains REVERT: A 206 GLU cc_start: 0.6939 (tp30) cc_final: 0.6324 (tp30) REVERT: B 74 MET cc_start: 0.6322 (ptm) cc_final: 0.6110 (ptt) REVERT: B 171 LYS cc_start: 0.8631 (mtpp) cc_final: 0.8386 (mttt) REVERT: B 210 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: C 195 ARG cc_start: 0.7567 (tpt170) cc_final: 0.7240 (mmt180) outliers start: 19 outliers final: 11 residues processed: 98 average time/residue: 1.5649 time to fit residues: 159.0551 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 265 LEU 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 54 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 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 = 0.3793 r_free = 0.3793 target = 0.160912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131508 restraints weight = 6885.844| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.10 r_work: 0.3268 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6118 Z= 0.158 Angle : 0.468 5.495 8294 Z= 0.255 Chirality : 0.043 0.140 917 Planarity : 0.004 0.041 1087 Dihedral : 4.279 48.858 848 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.61 % Allowed : 14.29 % Favored : 84.11 % 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: 0.33 (0.30), residues: 749 helix: 2.25 (0.32), residues: 253 sheet: -0.44 (0.39), residues: 175 loop : -1.05 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.011 0.001 TYR C 89 ARG 0.004 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 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.616 Fit side-chains REVERT: A 135 ARG cc_start: 0.7020 (mtp-110) cc_final: 0.6578 (ttp80) REVERT: A 206 GLU cc_start: 0.6893 (tp30) cc_final: 0.6263 (tp30) REVERT: B 74 MET cc_start: 0.6241 (ptm) cc_final: 0.6012 (ptt) REVERT: B 171 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8359 (mttt) REVERT: B 210 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: C 195 ARG cc_start: 0.7564 (tpt170) cc_final: 0.7200 (mmt180) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 1.4686 time to fit residues: 141.9626 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 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 = 0.3781 r_free = 0.3781 target = 0.159757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130409 restraints weight = 6940.555| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.03 r_work: 0.3262 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1740 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= 0.198 Angle : 0.498 5.568 8294 Z= 0.269 Chirality : 0.044 0.147 917 Planarity : 0.004 0.043 1087 Dihedral : 4.312 48.349 848 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.11 % 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: 0.35 (0.30), residues: 749 helix: 2.26 (0.32), residues: 253 sheet: -0.44 (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 0.008 0.001 HIS A 199 PHE 0.013 0.002 PHE C 92 TYR 0.011 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 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.604 Fit side-chains REVERT: A 135 ARG cc_start: 0.7011 (mtp-110) cc_final: 0.6600 (ttp80) REVERT: A 206 GLU cc_start: 0.6887 (tp30) cc_final: 0.6275 (tp30) REVERT: B 74 MET cc_start: 0.6247 (ptm) cc_final: 0.6039 (ptt) REVERT: B 171 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8382 (mttt) REVERT: B 210 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: C 195 ARG cc_start: 0.7545 (tpt170) cc_final: 0.7196 (mmt180) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 1.4777 time to fit residues: 139.7268 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.162038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.132582 restraints weight = 7024.665| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.06 r_work: 0.3309 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6118 Z= 0.144 Angle : 0.448 5.746 8294 Z= 0.244 Chirality : 0.043 0.139 917 Planarity : 0.004 0.039 1087 Dihedral : 4.109 47.206 848 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.44 % Allowed : 14.61 % 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: 0.51 (0.30), residues: 749 helix: 2.46 (0.33), residues: 254 sheet: -0.37 (0.39), residues: 175 loop : -1.01 (0.30), residues: 320 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 0.011 0.002 PHE C 92 TYR 0.011 0.001 TYR C 89 ARG 0.005 0.000 ARG B 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5755.77 seconds wall clock time: 98 minutes 12.21 seconds (5892.21 seconds total)