Starting phenix.real_space_refine on Tue Feb 11 12:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.map" model { file = "/net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xws_38742/02_2025/8xws_38742.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3733 2.51 5 N 942 2.21 5 O 939 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-5592/modules/chem_data/mon_lib" Total number of atoms: 5656 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2337 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 483 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2353 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 290} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 4.24, per 1000 atoms: 0.75 Number of scatterers: 5656 At special positions: 0 Unit cell: (142.614, 89.794, 81.3428, 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 42 16.00 O 939 8.00 N 942 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 55 " distance=2.03 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 286 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 660.9 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 73.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'D' and resid 23 through 25 No H-bonds generated for 'chain 'D' and resid 23 through 25' Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 65 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 36 removed outlier: 3.813A pdb=" N LEU R 34 " --> pdb=" O PRO R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.185A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN R 157 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.571A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.608A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA R 249 " --> pdb=" O GLN R 245 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'B' and resid 23 through 25 No H-bonds generated for 'chain 'B' and resid 23 through 25' Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.417A pdb=" N LYS B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 36 removed outlier: 3.814A pdb=" N LEU C 34 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 76 removed outlier: 4.185A pdb=" N SER C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 111 Proline residue: C 102 - end of helix Processing helix chain 'C' and resid 115 through 149 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.550A pdb=" N GLN C 157 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 160 " --> pdb=" O GLN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.507A pdb=" N LEU C 181 " --> pdb=" O ALA C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 212 Processing helix chain 'C' and resid 212 through 218 removed outlier: 3.570A pdb=" N GLN C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 240 removed outlier: 3.608A pdb=" N LYS C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 279 removed outlier: 3.547A pdb=" N ALA C 249 " --> pdb=" O GLN C 245 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'C' and resid 285 through 304 Processing helix chain 'C' and resid 305 through 315 Proline residue: C 311 - end of helix Processing helix chain 'C' and resid 318 through 329 Processing sheet with id=AA1, first strand: chain 'D' and resid 53 through 56 removed outlier: 4.517A pdb=" N VAL D 44 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL B 44 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 184 through 187 404 hydrogen bonds defined for protein. 1176 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: 1.42 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1746 1.35 - 1.47: 1326 1.47 - 1.58: 2642 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 5772 Sorted by residual: bond pdb=" CA ILE R 46 " pdb=" CB ILE R 46 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.25e-02 6.40e+03 2.31e+00 bond pdb=" CA ILE C 46 " pdb=" CB ILE C 46 " ideal model delta sigma weight residual 1.540 1.521 0.019 1.25e-02 6.40e+03 2.25e+00 bond pdb=" CA CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.78e+00 bond pdb=" CA CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.27e-02 6.20e+03 1.78e+00 bond pdb=" C PHE R 316 " pdb=" N ILE R 317 " ideal model delta sigma weight residual 1.338 1.329 0.009 1.05e-02 9.07e+03 7.74e-01 ... (remaining 5767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 7257 0.88 - 1.76: 501 1.76 - 2.64: 59 2.64 - 3.53: 23 3.53 - 4.41: 15 Bond angle restraints: 7855 Sorted by residual: angle pdb=" N ILE R 317 " pdb=" CA ILE R 317 " pdb=" C ILE R 317 " ideal model delta sigma weight residual 112.80 109.35 3.45 1.15e+00 7.56e-01 9.01e+00 angle pdb=" N ILE C 317 " pdb=" CA ILE C 317 " pdb=" C ILE C 317 " ideal model delta sigma weight residual 112.80 109.39 3.41 1.15e+00 7.56e-01 8.81e+00 angle pdb=" CA VAL R 222 " pdb=" C VAL R 222 " pdb=" N PRO R 223 " ideal model delta sigma weight residual 120.83 119.03 1.80 6.10e-01 2.69e+00 8.69e+00 angle pdb=" CA VAL C 222 " pdb=" C VAL C 222 " pdb=" N PRO C 223 " ideal model delta sigma weight residual 120.83 119.05 1.78 6.10e-01 2.69e+00 8.47e+00 angle pdb=" N VAL R 222 " pdb=" CA VAL R 222 " pdb=" C VAL R 222 " ideal model delta sigma weight residual 112.35 109.57 2.78 1.20e+00 6.94e-01 5.38e+00 ... (remaining 7850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 3186 17.10 - 34.19: 235 34.19 - 51.29: 34 51.29 - 68.39: 6 68.39 - 85.49: 6 Dihedral angle restraints: 3467 sinusoidal: 1331 harmonic: 2136 Sorted by residual: dihedral pdb=" CA LEU R 182 " pdb=" C LEU R 182 " pdb=" N PHE R 183 " pdb=" CA PHE R 183 " ideal model delta harmonic sigma weight residual -180.00 -164.73 -15.27 0 5.00e+00 4.00e-02 9.33e+00 dihedral pdb=" CA LEU C 182 " pdb=" C LEU C 182 " pdb=" N PHE C 183 " pdb=" CA PHE C 183 " ideal model delta harmonic sigma weight residual -180.00 -164.74 -15.26 0 5.00e+00 4.00e-02 9.31e+00 dihedral pdb=" CA LYS R 108 " pdb=" CB LYS R 108 " pdb=" CG LYS R 108 " pdb=" CD LYS R 108 " ideal model delta sinusoidal sigma weight residual -60.00 -112.71 52.71 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 3464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 517 0.023 - 0.045: 226 0.045 - 0.068: 134 0.068 - 0.090: 67 0.090 - 0.113: 32 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA VAL D 42 " pdb=" N VAL D 42 " pdb=" C VAL D 42 " pdb=" CB VAL D 42 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO R 215 " pdb=" N PRO R 215 " pdb=" C PRO R 215 " pdb=" CB PRO R 215 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA ILE C 282 " pdb=" N ILE C 282 " pdb=" C ILE C 282 " pdb=" CB ILE C 282 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 ... (remaining 973 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 37 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO R 38 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 38 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 38 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 37 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO C 38 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 119 " 0.005 2.00e-02 2.50e+03 9.66e-03 9.33e-01 pdb=" C CYS R 119 " -0.017 2.00e-02 2.50e+03 pdb=" O CYS R 119 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS R 120 " 0.006 2.00e-02 2.50e+03 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1038 2.77 - 3.30: 5595 3.30 - 3.84: 9116 3.84 - 4.37: 9566 4.37 - 4.90: 18078 Nonbonded interactions: 43393 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.240 3.040 nonbonded pdb=" O GLY C 201 " pdb=" OG1 THR C 204 " model vdw 2.240 3.040 nonbonded pdb=" NE1 TRP R 112 " pdb=" O GLY R 115 " model vdw 2.404 3.120 nonbonded pdb=" NE1 TRP C 112 " pdb=" O GLY C 115 " model vdw 2.405 3.120 nonbonded pdb=" O CYS D 13 " pdb=" NH1 ARG R 289 " model vdw 2.435 3.120 ... (remaining 43388 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 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 31 through 47 or (resid 48 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 through 239 or (resid 240 throu \ gh 241 and (name N or name CA or name C or name O or name CB )) or resid 242 thr \ ough 318 or (resid 319 through 320 and (name N or name CA or name C or name O or \ name CB )) or resid 321 through 330)) selection = chain 'R' } 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: 4.530 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 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 : 0.005 0.031 5772 Z= 0.356 Angle : 0.536 4.407 7855 Z= 0.318 Chirality : 0.039 0.113 976 Planarity : 0.003 0.025 949 Dihedral : 12.604 85.485 2055 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.32), residues: 722 helix: 2.39 (0.24), residues: 508 sheet: -1.46 (0.64), residues: 58 loop : -0.16 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 112 HIS 0.003 0.001 HIS R 242 PHE 0.010 0.001 PHE B 62 TYR 0.006 0.001 TYR R 86 ARG 0.004 0.001 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.684 Fit side-chains REVERT: D 41 LYS cc_start: 0.7634 (mttt) cc_final: 0.7238 (pttp) REVERT: D 54 ILE cc_start: 0.8251 (mt) cc_final: 0.8038 (mm) REVERT: R 160 TYR cc_start: 0.6272 (m-80) cc_final: 0.6060 (m-10) REVERT: R 199 ASP cc_start: 0.8083 (t0) cc_final: 0.7824 (t0) REVERT: R 207 TRP cc_start: 0.7555 (m100) cc_final: 0.6965 (m100) REVERT: R 213 ILE cc_start: 0.8716 (tt) cc_final: 0.8403 (mt) REVERT: R 277 MET cc_start: 0.8327 (ttp) cc_final: 0.8020 (ttp) REVERT: R 301 ILE cc_start: 0.9154 (mt) cc_final: 0.8822 (mp) REVERT: R 305 LEU cc_start: 0.8897 (mt) cc_final: 0.8646 (mp) REVERT: B 41 LYS cc_start: 0.7579 (mttt) cc_final: 0.6862 (mmtm) REVERT: B 54 ILE cc_start: 0.8255 (mt) cc_final: 0.8051 (mm) REVERT: C 160 TYR cc_start: 0.6314 (m-80) cc_final: 0.6099 (m-10) REVERT: C 199 ASP cc_start: 0.8075 (t0) cc_final: 0.7810 (t0) REVERT: C 207 TRP cc_start: 0.7572 (m100) cc_final: 0.6967 (m100) REVERT: C 213 ILE cc_start: 0.8736 (tt) cc_final: 0.8427 (mt) REVERT: C 277 MET cc_start: 0.8322 (ttp) cc_final: 0.7995 (ttp) REVERT: C 301 ILE cc_start: 0.9161 (mt) cc_final: 0.8943 (mp) REVERT: C 305 LEU cc_start: 0.8891 (mt) cc_final: 0.8639 (mp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1771 time to fit residues: 34.9575 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN R 47 ASN R 89 ASN R 110 ASN R 203 ASN R 291 HIS B 68 GLN C 47 ASN C 89 ASN C 110 ASN C 203 ASN C 291 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100191 restraints weight = 9478.590| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.09 r_work: 0.3181 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5772 Z= 0.214 Angle : 0.529 4.964 7855 Z= 0.284 Chirality : 0.042 0.194 976 Planarity : 0.004 0.020 949 Dihedral : 3.954 18.558 780 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.06 % Allowed : 9.25 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.33), residues: 722 helix: 2.43 (0.24), residues: 512 sheet: -0.74 (0.70), residues: 58 loop : 0.02 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.001 HIS D 23 PHE 0.021 0.001 PHE B 62 TYR 0.006 0.001 TYR R 314 ARG 0.002 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.644 Fit side-chains REVERT: D 41 LYS cc_start: 0.7968 (mttt) cc_final: 0.7659 (mmtm) REVERT: R 207 TRP cc_start: 0.8528 (m100) cc_final: 0.8277 (m100) REVERT: R 213 ILE cc_start: 0.9308 (tt) cc_final: 0.8967 (mt) REVERT: B 41 LYS cc_start: 0.8014 (mttt) cc_final: 0.7718 (mmtm) REVERT: B 53 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7923 (mm-30) REVERT: B 68 GLN cc_start: 0.8246 (tp40) cc_final: 0.7818 (tp40) REVERT: C 143 ASP cc_start: 0.8855 (t0) cc_final: 0.8621 (t0) REVERT: C 207 TRP cc_start: 0.8526 (m100) cc_final: 0.8277 (m100) REVERT: C 213 ILE cc_start: 0.9309 (tt) cc_final: 0.8969 (mt) REVERT: C 297 ASP cc_start: 0.8611 (m-30) cc_final: 0.8317 (m-30) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.1774 time to fit residues: 31.4775 Evaluate side-chains 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 ASN R 110 ASN B 50 ASN C 110 ASN C 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.097736 restraints weight = 9678.283| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.11 r_work: 0.3143 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5772 Z= 0.218 Angle : 0.535 7.123 7855 Z= 0.284 Chirality : 0.043 0.264 976 Planarity : 0.004 0.025 949 Dihedral : 3.845 18.373 780 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.73 % Allowed : 9.90 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.32), residues: 722 helix: 2.33 (0.24), residues: 512 sheet: -0.37 (0.73), residues: 58 loop : -0.00 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 112 HIS 0.002 0.000 HIS C 247 PHE 0.018 0.001 PHE B 62 TYR 0.005 0.001 TYR C 75 ARG 0.002 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.692 Fit side-chains REVERT: D 41 LYS cc_start: 0.8032 (mttt) cc_final: 0.7754 (mmtm) REVERT: R 110 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7357 (t0) REVERT: R 143 ASP cc_start: 0.8921 (t0) cc_final: 0.8681 (t0) REVERT: R 160 TYR cc_start: 0.6363 (m-80) cc_final: 0.6151 (m-10) REVERT: R 207 TRP cc_start: 0.8554 (m100) cc_final: 0.8283 (m100) REVERT: R 213 ILE cc_start: 0.9309 (tt) cc_final: 0.8953 (mt) REVERT: R 321 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (t80) REVERT: B 41 LYS cc_start: 0.8006 (mttt) cc_final: 0.7773 (mmtm) REVERT: B 68 GLN cc_start: 0.8377 (tp40) cc_final: 0.8097 (tp-100) REVERT: C 110 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7356 (t0) REVERT: C 143 ASP cc_start: 0.8953 (t0) cc_final: 0.8725 (t0) REVERT: C 213 ILE cc_start: 0.9314 (tt) cc_final: 0.8955 (mt) outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 0.1787 time to fit residues: 28.8396 Evaluate side-chains 121 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.094099 restraints weight = 9925.474| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.12 r_work: 0.3067 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5772 Z= 0.334 Angle : 0.563 5.071 7855 Z= 0.302 Chirality : 0.043 0.140 976 Planarity : 0.004 0.024 949 Dihedral : 4.057 21.283 780 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.41 % Allowed : 12.34 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.32), residues: 722 helix: 2.14 (0.23), residues: 514 sheet: -0.39 (0.71), residues: 58 loop : -0.05 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 112 HIS 0.003 0.001 HIS R 247 PHE 0.019 0.002 PHE B 62 TYR 0.008 0.001 TYR C 75 ARG 0.003 0.001 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.621 Fit side-chains REVERT: D 41 LYS cc_start: 0.8177 (mttt) cc_final: 0.7935 (mmtm) REVERT: R 143 ASP cc_start: 0.8947 (t0) cc_final: 0.8683 (t0) REVERT: R 207 TRP cc_start: 0.8650 (m100) cc_final: 0.8386 (m100) REVERT: R 213 ILE cc_start: 0.9296 (tt) cc_final: 0.8971 (mt) REVERT: B 41 LYS cc_start: 0.8122 (mttt) cc_final: 0.7922 (mmtm) REVERT: B 68 GLN cc_start: 0.8469 (tp40) cc_final: 0.8230 (tp40) REVERT: C 143 ASP cc_start: 0.8950 (t0) cc_final: 0.8677 (t0) REVERT: C 213 ILE cc_start: 0.9279 (tt) cc_final: 0.8958 (mt) outliers start: 21 outliers final: 14 residues processed: 115 average time/residue: 0.1837 time to fit residues: 27.3205 Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.0670 chunk 35 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN C 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095686 restraints weight = 9658.206| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.10 r_work: 0.3092 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5772 Z= 0.208 Angle : 0.516 9.097 7855 Z= 0.273 Chirality : 0.042 0.280 976 Planarity : 0.003 0.023 949 Dihedral : 3.848 19.040 780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.25 % Allowed : 13.80 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.31), residues: 722 helix: 2.19 (0.23), residues: 514 sheet: -0.39 (0.71), residues: 58 loop : 0.09 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.002 0.000 HIS C 247 PHE 0.017 0.001 PHE D 62 TYR 0.006 0.001 TYR C 86 ARG 0.002 0.000 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8161 (mttt) cc_final: 0.7922 (mmtm) REVERT: R 143 ASP cc_start: 0.8956 (t70) cc_final: 0.8671 (t0) REVERT: R 160 TYR cc_start: 0.6484 (m-80) cc_final: 0.6191 (m-10) REVERT: R 213 ILE cc_start: 0.9242 (tt) cc_final: 0.8949 (mt) REVERT: R 283 GLN cc_start: 0.7964 (mp10) cc_final: 0.7661 (mp10) REVERT: R 329 LEU cc_start: 0.8133 (mt) cc_final: 0.7921 (pp) REVERT: B 41 LYS cc_start: 0.8110 (mttt) cc_final: 0.7893 (mmtm) REVERT: B 68 GLN cc_start: 0.8467 (tp40) cc_final: 0.8195 (tp-100) REVERT: C 143 ASP cc_start: 0.8965 (t70) cc_final: 0.8685 (t0) REVERT: C 213 ILE cc_start: 0.9228 (tt) cc_final: 0.8934 (mt) REVERT: C 283 GLN cc_start: 0.7976 (mp10) cc_final: 0.7681 (mp10) REVERT: C 329 LEU cc_start: 0.8119 (mt) cc_final: 0.7903 (pp) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.1955 time to fit residues: 27.3963 Evaluate side-chains 110 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.093531 restraints weight = 9642.080| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.10 r_work: 0.3058 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5772 Z= 0.267 Angle : 0.525 5.025 7855 Z= 0.281 Chirality : 0.041 0.150 976 Planarity : 0.004 0.024 949 Dihedral : 3.929 18.022 780 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.41 % Allowed : 14.29 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.31), residues: 722 helix: 2.13 (0.23), residues: 514 sheet: -0.39 (0.72), residues: 58 loop : -0.03 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 112 HIS 0.003 0.001 HIS C 247 PHE 0.018 0.001 PHE D 62 TYR 0.006 0.001 TYR R 75 ARG 0.002 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.695 Fit side-chains REVERT: D 41 LYS cc_start: 0.8214 (mttt) cc_final: 0.7969 (mmtm) REVERT: D 43 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: R 143 ASP cc_start: 0.8946 (t70) cc_final: 0.8682 (t0) REVERT: R 213 ILE cc_start: 0.9254 (tt) cc_final: 0.8942 (mt) REVERT: R 283 GLN cc_start: 0.7904 (mp10) cc_final: 0.7640 (mp10) REVERT: R 329 LEU cc_start: 0.8164 (mt) cc_final: 0.7925 (pp) REVERT: B 41 LYS cc_start: 0.8160 (mttt) cc_final: 0.7944 (mmtm) REVERT: B 43 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: B 68 GLN cc_start: 0.8481 (tp40) cc_final: 0.8198 (tp-100) REVERT: C 143 ASP cc_start: 0.8939 (t70) cc_final: 0.8667 (t0) REVERT: C 213 ILE cc_start: 0.9242 (tt) cc_final: 0.8934 (mt) REVERT: C 283 GLN cc_start: 0.7949 (mp10) cc_final: 0.7687 (mp10) REVERT: C 329 LEU cc_start: 0.8170 (mt) cc_final: 0.7935 (pp) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 0.1811 time to fit residues: 25.8382 Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 CYS Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093516 restraints weight = 9798.966| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.11 r_work: 0.3058 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5772 Z= 0.268 Angle : 0.521 5.042 7855 Z= 0.283 Chirality : 0.041 0.137 976 Planarity : 0.004 0.024 949 Dihedral : 3.939 17.613 780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.73 % Allowed : 13.96 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.31), residues: 722 helix: 2.24 (0.23), residues: 504 sheet: -0.38 (0.72), residues: 58 loop : 0.13 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 PHE 0.018 0.001 PHE D 62 TYR 0.006 0.001 TYR R 197 ARG 0.002 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.671 Fit side-chains REVERT: D 41 LYS cc_start: 0.8286 (mttt) cc_final: 0.8012 (mmtm) REVERT: R 143 ASP cc_start: 0.8954 (t70) cc_final: 0.8676 (t0) REVERT: R 213 ILE cc_start: 0.9244 (tt) cc_final: 0.8933 (mt) REVERT: R 248 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7283 (ttm-80) REVERT: R 329 LEU cc_start: 0.8147 (mt) cc_final: 0.7933 (pp) REVERT: B 41 LYS cc_start: 0.8271 (mttt) cc_final: 0.8006 (mmtm) REVERT: B 43 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: B 68 GLN cc_start: 0.8517 (tp40) cc_final: 0.8220 (tp-100) REVERT: C 143 ASP cc_start: 0.8963 (t70) cc_final: 0.8684 (t0) REVERT: C 213 ILE cc_start: 0.9236 (tt) cc_final: 0.8919 (mt) REVERT: C 329 LEU cc_start: 0.8149 (mt) cc_final: 0.7940 (pp) outliers start: 23 outliers final: 12 residues processed: 106 average time/residue: 0.1925 time to fit residues: 26.2325 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 175 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093991 restraints weight = 9651.349| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.09 r_work: 0.3064 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5772 Z= 0.253 Angle : 0.562 10.743 7855 Z= 0.299 Chirality : 0.042 0.291 976 Planarity : 0.004 0.024 949 Dihedral : 4.180 30.568 780 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.25 % Allowed : 13.47 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.31), residues: 722 helix: 2.28 (0.23), residues: 504 sheet: -0.38 (0.73), residues: 58 loop : -0.02 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 207 HIS 0.002 0.001 HIS C 247 PHE 0.018 0.001 PHE D 62 TYR 0.005 0.001 TYR R 197 ARG 0.003 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.673 Fit side-chains REVERT: D 41 LYS cc_start: 0.8270 (mttt) cc_final: 0.8001 (mmtm) REVERT: D 53 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7981 (mm-30) REVERT: R 143 ASP cc_start: 0.8948 (t70) cc_final: 0.8676 (t0) REVERT: R 213 ILE cc_start: 0.9242 (tt) cc_final: 0.8920 (mt) REVERT: R 248 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7264 (ttm-80) REVERT: R 329 LEU cc_start: 0.8156 (mt) cc_final: 0.7924 (pp) REVERT: B 41 LYS cc_start: 0.8290 (mttt) cc_final: 0.8055 (mmtm) REVERT: B 53 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 68 GLN cc_start: 0.8492 (tp40) cc_final: 0.8196 (tp-100) REVERT: C 143 ASP cc_start: 0.8947 (t70) cc_final: 0.8664 (t0) REVERT: C 213 ILE cc_start: 0.9235 (tt) cc_final: 0.8909 (mt) REVERT: C 248 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7221 (ttm-80) REVERT: C 329 LEU cc_start: 0.8169 (mt) cc_final: 0.7932 (pp) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 0.1964 time to fit residues: 27.0915 Evaluate side-chains 108 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.093560 restraints weight = 9699.943| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.08 r_work: 0.3058 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5772 Z= 0.255 Angle : 0.543 8.793 7855 Z= 0.292 Chirality : 0.041 0.253 976 Planarity : 0.004 0.027 949 Dihedral : 4.161 29.319 780 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.44 % Allowed : 14.61 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.31), residues: 722 helix: 2.29 (0.23), residues: 504 sheet: -0.45 (0.73), residues: 58 loop : 0.03 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 207 HIS 0.004 0.001 HIS C 242 PHE 0.017 0.001 PHE B 62 TYR 0.005 0.001 TYR R 197 ARG 0.003 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.586 Fit side-chains REVERT: D 53 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8012 (mt-10) REVERT: R 143 ASP cc_start: 0.8946 (t70) cc_final: 0.8674 (t0) REVERT: R 213 ILE cc_start: 0.9229 (tt) cc_final: 0.8904 (mt) REVERT: R 248 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7254 (ttm-80) REVERT: R 329 LEU cc_start: 0.8176 (mt) cc_final: 0.7945 (pp) REVERT: B 53 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 68 GLN cc_start: 0.8478 (tp40) cc_final: 0.8185 (tp-100) REVERT: C 143 ASP cc_start: 0.8955 (t70) cc_final: 0.8678 (t0) REVERT: C 213 ILE cc_start: 0.9222 (tt) cc_final: 0.8894 (mt) REVERT: C 329 LEU cc_start: 0.8141 (mt) cc_final: 0.7919 (pp) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2021 time to fit residues: 26.6734 Evaluate side-chains 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 248 ARG Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.094056 restraints weight = 9844.623| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.10 r_work: 0.3062 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5772 Z= 0.241 Angle : 0.565 11.631 7855 Z= 0.300 Chirality : 0.042 0.306 976 Planarity : 0.004 0.027 949 Dihedral : 4.112 28.615 780 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.27 % Allowed : 15.26 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.31), residues: 722 helix: 2.31 (0.23), residues: 504 sheet: -0.49 (0.73), residues: 58 loop : 0.11 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 207 HIS 0.003 0.001 HIS C 242 PHE 0.016 0.001 PHE D 62 TYR 0.005 0.001 TYR C 197 ARG 0.002 0.000 ARG R 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.614 Fit side-chains REVERT: D 53 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8102 (mm-30) REVERT: R 143 ASP cc_start: 0.8963 (t70) cc_final: 0.8694 (t0) REVERT: R 213 ILE cc_start: 0.9227 (tt) cc_final: 0.8897 (mt) REVERT: R 329 LEU cc_start: 0.8169 (mt) cc_final: 0.7941 (pp) REVERT: B 68 GLN cc_start: 0.8479 (tp40) cc_final: 0.8173 (tp-100) REVERT: C 143 ASP cc_start: 0.8963 (t70) cc_final: 0.8687 (t0) REVERT: C 213 ILE cc_start: 0.9224 (tt) cc_final: 0.8896 (mt) REVERT: C 329 LEU cc_start: 0.8171 (mt) cc_final: 0.7945 (pp) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.2199 time to fit residues: 28.0516 Evaluate side-chains 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 107 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 207 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 323 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.0060 chunk 13 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN ** C 319 GLN ** 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 = 0.3429 r_free = 0.3429 target = 0.110273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093432 restraints weight = 9821.904| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.09 r_work: 0.3050 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5772 Z= 0.278 Angle : 0.576 10.324 7855 Z= 0.307 Chirality : 0.042 0.280 976 Planarity : 0.004 0.027 949 Dihedral : 4.167 28.324 780 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.27 % Allowed : 15.42 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.31), residues: 722 helix: 2.24 (0.23), residues: 504 sheet: -0.50 (0.73), residues: 58 loop : 0.11 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 207 HIS 0.002 0.000 HIS R 247 PHE 0.017 0.001 PHE B 62 TYR 0.006 0.001 TYR R 197 ARG 0.003 0.000 ARG R 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3375.34 seconds wall clock time: 60 minutes 51.68 seconds (3651.68 seconds total)