Starting phenix.real_space_refine on Wed Sep 17 05:56:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xws_38742/09_2025/8xws_38742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xws_38742/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xws_38742/09_2025/8xws_38742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xws_38742/09_2025/8xws_38742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xws_38742/09_2025/8xws_38742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xws_38742/09_2025/8xws_38742.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 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, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Time building chain proxies: 1.60, per 1000 atoms: 0.28 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: 0.54 Conformation dependent library (CDL) restraints added in 232.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.12 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: 0.90 Time building geometry restraints manager: 0.70 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: 8.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- 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 5780 Z= 0.221 Angle : 0.538 4.407 7871 Z= 0.319 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.001 ARG C 248 TYR 0.006 0.001 TYR R 86 PHE 0.010 0.001 PHE B 62 TRP 0.008 0.001 TRP C 112 HIS 0.003 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 5772) covalent geometry : angle 0.53580 ( 7855) SS BOND : bond 0.00145 ( 8) SS BOND : angle 1.13931 ( 16) hydrogen bonds : bond 0.12503 ( 404) hydrogen bonds : angle 5.08396 ( 1176) *********************** 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 : 0.226 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: 0.0795 time to fit residues: 15.8123 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 : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.0020 overall best weight: 0.4106 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101164 restraints weight = 9555.372| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.09 r_work: 0.3185 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5780 Z= 0.147 Angle : 0.536 4.918 7871 Z= 0.286 Chirality : 0.041 0.169 976 Planarity : 0.004 0.020 949 Dihedral : 3.934 19.471 780 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.71 % Allowed : 8.28 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.33), residues: 722 helix: 2.44 (0.24), residues: 512 sheet: -0.74 (0.70), residues: 58 loop : -0.03 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.006 0.001 TYR R 86 PHE 0.020 0.001 PHE D 62 TRP 0.008 0.001 TRP C 112 HIS 0.002 0.001 HIS D 23 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5772) covalent geometry : angle 0.52932 ( 7855) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.99165 ( 16) hydrogen bonds : bond 0.05102 ( 404) hydrogen bonds : angle 4.27653 ( 1176) *********************** 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 153 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.220 Fit side-chains REVERT: D 41 LYS cc_start: 0.7905 (mttt) cc_final: 0.7628 (mmtm) REVERT: R 143 ASP cc_start: 0.8837 (t0) cc_final: 0.8491 (t0) REVERT: R 207 TRP cc_start: 0.8517 (m100) cc_final: 0.8265 (m100) REVERT: R 213 ILE cc_start: 0.9307 (tt) cc_final: 0.8969 (mt) REVERT: B 41 LYS cc_start: 0.8021 (mttt) cc_final: 0.7727 (mmtm) REVERT: B 68 GLN cc_start: 0.8248 (tp40) cc_final: 0.7865 (tp40) REVERT: C 110 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7914 (t0) REVERT: C 143 ASP cc_start: 0.8837 (t0) cc_final: 0.8618 (t0) REVERT: C 207 TRP cc_start: 0.8520 (m100) cc_final: 0.8265 (m100) REVERT: C 213 ILE cc_start: 0.9308 (tt) cc_final: 0.8971 (mt) REVERT: C 297 ASP cc_start: 0.8611 (m-30) cc_final: 0.8408 (m-30) outliers start: 29 outliers final: 16 residues processed: 140 average time/residue: 0.0827 time to fit residues: 14.9442 Evaluate side-chains 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 107 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 51 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 110 ASN C 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095798 restraints weight = 9663.558| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.11 r_work: 0.3105 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5780 Z= 0.175 Angle : 0.571 7.203 7871 Z= 0.303 Chirality : 0.044 0.264 976 Planarity : 0.004 0.023 949 Dihedral : 3.989 22.637 780 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.25 % Allowed : 11.53 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.32), residues: 722 helix: 2.24 (0.24), residues: 514 sheet: -0.41 (0.73), residues: 58 loop : 0.04 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 185 TYR 0.007 0.001 TYR C 75 PHE 0.019 0.001 PHE D 62 TRP 0.011 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5772) covalent geometry : angle 0.56590 ( 7855) SS BOND : bond 0.00373 ( 8) SS BOND : angle 1.78578 ( 16) hydrogen bonds : bond 0.05183 ( 404) hydrogen bonds : angle 4.31640 ( 1176) *********************** 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 129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.229 Fit side-chains REVERT: D 41 LYS cc_start: 0.8073 (mttt) cc_final: 0.7824 (mmtm) REVERT: R 110 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7445 (t0) REVERT: R 143 ASP cc_start: 0.8904 (t0) cc_final: 0.8608 (t0) REVERT: R 207 TRP cc_start: 0.8614 (m100) cc_final: 0.8338 (m100) REVERT: R 213 ILE cc_start: 0.9318 (tt) cc_final: 0.8962 (mt) REVERT: B 68 GLN cc_start: 0.8408 (tp40) cc_final: 0.8134 (tp40) REVERT: C 143 ASP cc_start: 0.8929 (t0) cc_final: 0.8643 (t0) REVERT: C 207 TRP cc_start: 0.8610 (m100) cc_final: 0.8323 (m100) REVERT: C 213 ILE cc_start: 0.9322 (tt) cc_final: 0.8959 (mt) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 0.0809 time to fit residues: 12.6074 Evaluate side-chains 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 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 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 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.113041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096045 restraints weight = 9755.017| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.11 r_work: 0.3103 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5780 Z= 0.144 Angle : 0.508 4.952 7871 Z= 0.275 Chirality : 0.041 0.136 976 Planarity : 0.004 0.022 949 Dihedral : 3.926 21.878 780 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.92 % Allowed : 12.50 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.32), residues: 722 helix: 2.25 (0.23), residues: 514 sheet: -0.38 (0.71), residues: 58 loop : 0.01 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.005 0.001 TYR R 75 PHE 0.017 0.001 PHE D 62 TRP 0.010 0.001 TRP C 112 HIS 0.002 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5772) covalent geometry : angle 0.50232 ( 7855) SS BOND : bond 0.00460 ( 8) SS BOND : angle 1.70431 ( 16) hydrogen bonds : bond 0.04846 ( 404) hydrogen bonds : angle 4.25755 ( 1176) *********************** 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 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8054 (mttt) cc_final: 0.7842 (mmtm) REVERT: D 53 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7954 (mm-30) REVERT: R 143 ASP cc_start: 0.8916 (t70) cc_final: 0.8615 (t0) REVERT: R 207 TRP cc_start: 0.8593 (m100) cc_final: 0.8378 (m100) REVERT: R 213 ILE cc_start: 0.9298 (tt) cc_final: 0.8945 (mt) REVERT: B 43 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 68 GLN cc_start: 0.8507 (tp40) cc_final: 0.8236 (tp-100) REVERT: C 143 ASP cc_start: 0.8934 (t70) cc_final: 0.8641 (t0) REVERT: C 207 TRP cc_start: 0.8582 (m100) cc_final: 0.8355 (m100) REVERT: C 213 ILE cc_start: 0.9257 (tt) cc_final: 0.8937 (mt) REVERT: C 283 GLN cc_start: 0.7970 (mp10) cc_final: 0.7714 (mp10) REVERT: C 321 PHE cc_start: 0.7736 (m-80) cc_final: 0.7476 (t80) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 0.0853 time to fit residues: 12.8270 Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.110883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.093666 restraints weight = 10004.838| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.14 r_work: 0.3057 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5780 Z= 0.177 Angle : 0.558 8.768 7871 Z= 0.294 Chirality : 0.043 0.249 976 Planarity : 0.004 0.023 949 Dihedral : 4.019 18.948 780 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.73 % Allowed : 13.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.31), residues: 722 helix: 2.11 (0.23), residues: 514 sheet: -0.41 (0.71), residues: 58 loop : -0.21 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.006 0.001 TYR R 197 PHE 0.019 0.002 PHE D 62 TRP 0.012 0.002 TRP R 112 HIS 0.003 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5772) covalent geometry : angle 0.55299 ( 7855) SS BOND : bond 0.00281 ( 8) SS BOND : angle 1.75723 ( 16) hydrogen bonds : bond 0.05144 ( 404) hydrogen bonds : angle 4.37806 ( 1176) *********************** 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 130 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.214 Fit side-chains REVERT: D 41 LYS cc_start: 0.8136 (mttt) cc_final: 0.7914 (mmtm) REVERT: D 43 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: D 53 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7976 (mm-30) REVERT: R 143 ASP cc_start: 0.8931 (t70) cc_final: 0.8609 (t0) REVERT: R 213 ILE cc_start: 0.9265 (tt) cc_final: 0.8957 (mt) REVERT: R 283 GLN cc_start: 0.7936 (mp10) cc_final: 0.7658 (mp10) REVERT: B 43 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: B 68 GLN cc_start: 0.8529 (tp40) cc_final: 0.8211 (tp-100) REVERT: C 143 ASP cc_start: 0.8937 (t70) cc_final: 0.8636 (t0) REVERT: C 207 TRP cc_start: 0.8662 (m100) cc_final: 0.8458 (m100) REVERT: C 213 ILE cc_start: 0.9255 (tt) cc_final: 0.8943 (mt) REVERT: C 283 GLN cc_start: 0.7985 (mp10) cc_final: 0.7711 (mp10) REVERT: C 321 PHE cc_start: 0.7702 (m-80) cc_final: 0.7483 (t80) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 0.0814 time to fit residues: 12.4760 Evaluate side-chains 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 210 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 329 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 210 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.0570 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094623 restraints weight = 9764.606| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.10 r_work: 0.3078 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5780 Z= 0.145 Angle : 0.509 5.359 7871 Z= 0.271 Chirality : 0.040 0.164 976 Planarity : 0.004 0.024 949 Dihedral : 3.915 17.964 780 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.06 % Allowed : 13.96 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.31), residues: 722 helix: 2.19 (0.23), residues: 514 sheet: -0.36 (0.72), residues: 58 loop : -0.29 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.005 0.001 TYR R 197 PHE 0.017 0.001 PHE D 62 TRP 0.010 0.002 TRP R 112 HIS 0.002 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 5772) covalent geometry : angle 0.50740 ( 7855) SS BOND : bond 0.00213 ( 8) SS BOND : angle 1.13962 ( 16) hydrogen bonds : bond 0.04782 ( 404) hydrogen bonds : angle 4.22960 ( 1176) *********************** 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 127 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.221 Fit side-chains REVERT: D 41 LYS cc_start: 0.8132 (mttt) cc_final: 0.7922 (mmtm) REVERT: D 43 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: D 53 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7993 (mm-30) REVERT: R 143 ASP cc_start: 0.8916 (t70) cc_final: 0.8580 (t0) REVERT: R 213 ILE cc_start: 0.9240 (tt) cc_final: 0.8929 (mt) REVERT: R 248 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7250 (ttm-80) REVERT: R 283 GLN cc_start: 0.7946 (mp10) cc_final: 0.7683 (mp10) REVERT: B 43 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: B 68 GLN cc_start: 0.8507 (tp40) cc_final: 0.8213 (tp-100) REVERT: C 143 ASP cc_start: 0.8938 (t70) cc_final: 0.8623 (t0) REVERT: C 213 ILE cc_start: 0.9231 (tt) cc_final: 0.8916 (mt) REVERT: C 248 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7234 (ttm-80) REVERT: C 283 GLN cc_start: 0.7939 (mp10) cc_final: 0.7688 (mp10) outliers start: 25 outliers final: 15 residues processed: 116 average time/residue: 0.0864 time to fit residues: 12.6362 Evaluate side-chains 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain R residue 191 ASN 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 R residue 329 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 180 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.0050 chunk 65 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.111842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094793 restraints weight = 9917.675| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.12 r_work: 0.3081 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5780 Z= 0.139 Angle : 0.504 4.974 7871 Z= 0.273 Chirality : 0.040 0.134 976 Planarity : 0.003 0.024 949 Dihedral : 3.853 17.185 780 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.22 % Allowed : 13.80 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.31), residues: 722 helix: 2.23 (0.23), residues: 514 sheet: -0.33 (0.72), residues: 58 loop : -0.28 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.009 0.001 TYR R 75 PHE 0.016 0.001 PHE D 62 TRP 0.009 0.002 TRP R 112 HIS 0.002 0.000 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5772) covalent geometry : angle 0.50137 ( 7855) SS BOND : bond 0.00290 ( 8) SS BOND : angle 1.16167 ( 16) hydrogen bonds : bond 0.04687 ( 404) hydrogen bonds : angle 4.21835 ( 1176) *********************** 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 121 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.166 Fit side-chains REVERT: D 41 LYS cc_start: 0.8176 (mttt) cc_final: 0.7969 (mmtm) REVERT: D 43 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: D 53 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8038 (mm-30) REVERT: R 143 ASP cc_start: 0.8900 (t70) cc_final: 0.8600 (t0) REVERT: R 213 ILE cc_start: 0.9228 (tt) cc_final: 0.8898 (mt) REVERT: R 248 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7259 (ttm-80) REVERT: B 43 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: B 53 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7988 (mm-30) REVERT: B 68 GLN cc_start: 0.8524 (tp40) cc_final: 0.8226 (tp-100) REVERT: C 143 ASP cc_start: 0.8941 (t70) cc_final: 0.8622 (t0) REVERT: C 213 ILE cc_start: 0.9222 (tt) cc_final: 0.8888 (mt) REVERT: C 248 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7254 (ttm-80) REVERT: C 283 GLN cc_start: 0.7971 (mp10) cc_final: 0.7730 (mp10) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.0940 time to fit residues: 12.7714 Evaluate side-chains 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 68 GLN 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 R residue 323 HIS 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 248 ARG Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092978 restraints weight = 9766.216| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.09 r_work: 0.3051 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 0.042 5780 Z= 0.186 Angle : 0.538 5.515 7871 Z= 0.291 Chirality : 0.041 0.137 976 Planarity : 0.004 0.025 949 Dihedral : 3.993 17.729 780 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.90 % Allowed : 14.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.31), residues: 722 helix: 2.26 (0.23), residues: 504 sheet: -0.39 (0.72), residues: 58 loop : -0.03 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 248 TYR 0.010 0.001 TYR R 75 PHE 0.020 0.001 PHE D 62 TRP 0.011 0.002 TRP C 112 HIS 0.002 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 5772) covalent geometry : angle 0.53556 ( 7855) SS BOND : bond 0.00392 ( 8) SS BOND : angle 1.34064 ( 16) hydrogen bonds : bond 0.05049 ( 404) hydrogen bonds : angle 4.27544 ( 1176) *********************** 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 123 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8284 (mttt) cc_final: 0.8029 (mmtm) REVERT: D 43 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: D 53 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8049 (mm-30) REVERT: R 143 ASP cc_start: 0.8900 (t70) cc_final: 0.8596 (t0) REVERT: R 213 ILE cc_start: 0.9236 (tt) cc_final: 0.8905 (mt) REVERT: B 68 GLN cc_start: 0.8549 (tp40) cc_final: 0.8236 (tp-100) REVERT: C 143 ASP cc_start: 0.8925 (t70) cc_final: 0.8602 (t0) REVERT: C 213 ILE cc_start: 0.9226 (tt) cc_final: 0.8894 (mt) REVERT: C 283 GLN cc_start: 0.7893 (mp10) cc_final: 0.7658 (mp10) outliers start: 24 outliers final: 13 residues processed: 113 average time/residue: 0.0951 time to fit residues: 13.4686 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 : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 323 HIS 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 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.110473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093611 restraints weight = 9906.755| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.10 r_work: 0.3061 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5780 Z= 0.157 Angle : 0.585 11.155 7871 Z= 0.306 Chirality : 0.042 0.316 976 Planarity : 0.004 0.021 949 Dihedral : 4.184 29.963 780 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.60 % Allowed : 14.61 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.31), residues: 722 helix: 2.30 (0.23), residues: 504 sheet: -0.42 (0.72), residues: 58 loop : -0.04 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 12 TYR 0.006 0.001 TYR R 75 PHE 0.017 0.001 PHE D 62 TRP 0.010 0.002 TRP R 207 HIS 0.001 0.000 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5772) covalent geometry : angle 0.56708 ( 7855) SS BOND : bond 0.00469 ( 8) SS BOND : angle 3.21955 ( 16) hydrogen bonds : bond 0.04836 ( 404) hydrogen bonds : angle 4.22297 ( 1176) *********************** 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 114 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.224 Fit side-chains REVERT: D 41 LYS cc_start: 0.8203 (mttt) cc_final: 0.7991 (mmtm) REVERT: D 53 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8078 (mm-30) REVERT: R 143 ASP cc_start: 0.8897 (t70) cc_final: 0.8601 (t0) REVERT: R 213 ILE cc_start: 0.9224 (tt) cc_final: 0.8885 (mt) REVERT: B 68 GLN cc_start: 0.8513 (tp40) cc_final: 0.8206 (tp-100) REVERT: C 143 ASP cc_start: 0.8935 (t70) cc_final: 0.8613 (t0) REVERT: C 213 ILE cc_start: 0.9222 (tt) cc_final: 0.8878 (mt) REVERT: C 283 GLN cc_start: 0.7876 (mp10) cc_final: 0.7658 (mp10) outliers start: 16 outliers final: 15 residues processed: 107 average time/residue: 0.0886 time to fit residues: 12.0989 Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU 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 180 VAL Chi-restraints excluded: chain R residue 210 LEU Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 323 HIS 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 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.110245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093363 restraints weight = 9990.479| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.10 r_work: 0.3054 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5780 Z= 0.163 Angle : 0.595 11.838 7871 Z= 0.310 Chirality : 0.043 0.320 976 Planarity : 0.004 0.024 949 Dihedral : 4.209 30.797 780 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.08 % Allowed : 14.61 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.31), residues: 722 helix: 2.25 (0.23), residues: 504 sheet: -0.43 (0.73), residues: 58 loop : -0.05 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 289 TYR 0.011 0.001 TYR C 75 PHE 0.017 0.001 PHE D 62 TRP 0.011 0.002 TRP R 207 HIS 0.002 0.000 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5772) covalent geometry : angle 0.58318 ( 7855) SS BOND : bond 0.00400 ( 8) SS BOND : angle 2.67462 ( 16) hydrogen bonds : bond 0.04888 ( 404) hydrogen bonds : angle 4.28092 ( 1176) ********************** 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 119 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.218 Fit side-chains REVERT: R 143 ASP cc_start: 0.8891 (t70) cc_final: 0.8595 (t0) REVERT: R 213 ILE cc_start: 0.9222 (tt) cc_final: 0.8878 (mt) REVERT: B 68 GLN cc_start: 0.8507 (tp40) cc_final: 0.8205 (tp-100) REVERT: C 143 ASP cc_start: 0.8910 (t70) cc_final: 0.8615 (t0) REVERT: C 191 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8268 (p0) REVERT: C 213 ILE cc_start: 0.9220 (tt) cc_final: 0.8870 (mt) outliers start: 19 outliers final: 16 residues processed: 111 average time/residue: 0.0856 time to fit residues: 12.2008 Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 68 GLN Chi-restraints excluded: chain R residue 70 MET 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 R residue 323 HIS 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 191 ASN Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 323 HIS Chi-restraints excluded: chain C residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.110717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093834 restraints weight = 9844.712| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.08 r_work: 0.3064 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5780 Z= 0.151 Angle : 0.581 10.785 7871 Z= 0.306 Chirality : 0.042 0.297 976 Planarity : 0.004 0.026 949 Dihedral : 4.176 30.423 780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.60 % Allowed : 16.07 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.31), residues: 722 helix: 2.23 (0.23), residues: 504 sheet: -0.38 (0.74), residues: 58 loop : -0.05 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 289 TYR 0.006 0.001 TYR C 75 PHE 0.017 0.001 PHE D 62 TRP 0.012 0.002 TRP R 207 HIS 0.001 0.000 HIS B 23 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5772) covalent geometry : angle 0.57076 ( 7855) SS BOND : bond 0.00363 ( 8) SS BOND : angle 2.50836 ( 16) hydrogen bonds : bond 0.04826 ( 404) hydrogen bonds : angle 4.28507 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1701.62 seconds wall clock time: 29 minutes 55.07 seconds (1795.07 seconds total)