Starting phenix.real_space_refine on Sun Apr 27 12:29:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xws_38742/04_2025/8xws_38742.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xws_38742/04_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_38742/04_2025/8xws_38742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xws_38742/04_2025/8xws_38742.map" model { file = "/net/cci-nas-00/data/ceres_data/8xws_38742/04_2025/8xws_38742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xws_38742/04_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-5669/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: 5.16, per 1000 atoms: 0.91 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: 1.54 Conformation dependent library (CDL) restraints added in 613.0 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: 0.56 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: 1.54 Time building geometry restraints manager: 1.82 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: 5.000 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.670 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12503 ( 404) hydrogen bonds : angle 5.08396 ( 1176) SS BOND : bond 0.00145 ( 8) SS BOND : angle 1.13931 ( 16) covalent geometry : bond 0.00523 ( 5772) covalent geometry : angle 0.53580 ( 7855) *********************** 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 : 0.714 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: 0.1683 time to fit residues: 33.3369 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 : 0.597 ------------------------------------------------------------------------------- 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 = 0.100190 restraints weight = 9478.582| |-----------------------------------------------------------------------------| 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: 4.61 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 5780 Z= 0.148 Angle : 0.536 4.964 7871 Z= 0.287 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 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 404) hydrogen bonds : angle 4.28437 ( 1176) SS BOND : bond 0.00288 ( 8) SS BOND : angle 1.97861 ( 16) covalent geometry : bond 0.00335 ( 5772) covalent geometry : angle 0.52883 ( 7855) *********************** 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 : 0.642 Fit side-chains REVERT: D 41 LYS cc_start: 0.7970 (mttt) cc_final: 0.7662 (mmtm) REVERT: R 207 TRP cc_start: 0.8529 (m100) cc_final: 0.8279 (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: 0.7720 (mmtm) REVERT: B 53 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7923 (mm-30) REVERT: B 68 GLN cc_start: 0.8258 (tp40) cc_final: 0.7830 (tp40) REVERT: C 143 ASP cc_start: 0.8856 (t0) cc_final: 0.8623 (t0) REVERT: C 207 TRP cc_start: 0.8526 (m100) cc_final: 0.8278 (m100) REVERT: C 213 ILE cc_start: 0.9309 (tt) cc_final: 0.8970 (mt) REVERT: C 297 ASP cc_start: 0.8613 (m-30) cc_final: 0.8320 (m-30) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.2155 time to fit residues: 38.1151 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.0970 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098305 restraints weight = 9649.522| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.10 r_work: 0.3142 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5780 Z= 0.140 Angle : 0.532 7.618 7871 Z= 0.283 Chirality : 0.043 0.244 976 Planarity : 0.004 0.027 949 Dihedral : 3.822 18.487 780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.25 % Allowed : 10.55 % Favored : 86.20 % 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: 2.46 (0.32), residues: 722 helix: 2.31 (0.24), residues: 514 sheet: -0.29 (0.74), residues: 58 loop : 0.09 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.002 0.000 HIS R 247 PHE 0.018 0.001 PHE B 62 TYR 0.005 0.001 TYR C 55 ARG 0.002 0.000 ARG R 289 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 404) hydrogen bonds : angle 4.21977 ( 1176) SS BOND : bond 0.00398 ( 8) SS BOND : angle 1.59463 ( 16) covalent geometry : bond 0.00318 ( 5772) covalent geometry : angle 0.52765 ( 7855) *********************** 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 131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.603 Fit side-chains REVERT: D 41 LYS cc_start: 0.8044 (mttt) cc_final: 0.7766 (mmtm) REVERT: R 110 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7320 (t0) REVERT: R 143 ASP cc_start: 0.8925 (t0) cc_final: 0.8654 (t0) REVERT: R 207 TRP cc_start: 0.8544 (m100) cc_final: 0.8270 (m100) REVERT: R 213 ILE cc_start: 0.9311 (tt) cc_final: 0.8951 (mt) REVERT: B 41 LYS cc_start: 0.7943 (mttt) cc_final: 0.7735 (mmtm) REVERT: B 53 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7876 (mt-10) REVERT: B 68 GLN cc_start: 0.8361 (tp40) cc_final: 0.8090 (tp-100) REVERT: C 110 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7282 (t0) REVERT: C 143 ASP cc_start: 0.8939 (t0) cc_final: 0.8691 (t0) REVERT: C 160 TYR cc_start: 0.6305 (m-80) cc_final: 0.6084 (m-10) REVERT: C 213 ILE cc_start: 0.9311 (tt) cc_final: 0.8948 (mt) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1782 time to fit residues: 27.9362 Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 191 ASN 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: 0.8980 chunk 47 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 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: 0.6980 chunk 15 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.112473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095444 restraints weight = 9928.680| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.13 r_work: 0.3086 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5780 Z= 0.173 Angle : 0.532 5.011 7871 Z= 0.286 Chirality : 0.041 0.136 976 Planarity : 0.004 0.024 949 Dihedral : 3.918 20.331 780 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.41 % Allowed : 12.18 % Favored : 84.42 % 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: 2.37 (0.32), residues: 722 helix: 2.26 (0.24), residues: 514 sheet: -0.35 (0.72), residues: 58 loop : 0.00 (0.44), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 112 HIS 0.002 0.001 HIS C 247 PHE 0.018 0.001 PHE B 62 TYR 0.006 0.001 TYR C 75 ARG 0.002 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.05018 ( 404) hydrogen bonds : angle 4.25507 ( 1176) SS BOND : bond 0.00253 ( 8) SS BOND : angle 1.72272 ( 16) covalent geometry : bond 0.00409 ( 5772) covalent geometry : angle 0.52696 ( 7855) *********************** 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 129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.681 Fit side-chains REVERT: D 41 LYS cc_start: 0.8127 (mttt) cc_final: 0.7900 (mmtm) REVERT: R 143 ASP cc_start: 0.8943 (t0) cc_final: 0.8674 (t0) REVERT: R 207 TRP cc_start: 0.8624 (m100) cc_final: 0.8342 (m100) REVERT: R 213 ILE cc_start: 0.9325 (tt) cc_final: 0.8956 (mt) REVERT: B 41 LYS cc_start: 0.8090 (mttt) cc_final: 0.7889 (mmtm) REVERT: B 68 GLN cc_start: 0.8448 (tp40) cc_final: 0.8218 (tp40) REVERT: C 143 ASP cc_start: 0.8956 (t0) cc_final: 0.8694 (t0) REVERT: C 213 ILE cc_start: 0.9260 (tt) cc_final: 0.8944 (mt) outliers start: 21 outliers final: 16 residues processed: 122 average time/residue: 0.1889 time to fit residues: 30.0521 Evaluate side-chains 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 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=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: 0.3980 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN R 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094473 restraints weight = 9677.525| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.10 r_work: 0.3071 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5780 Z= 0.162 Angle : 0.537 8.947 7871 Z= 0.283 Chirality : 0.043 0.275 976 Planarity : 0.004 0.024 949 Dihedral : 3.883 18.469 780 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.90 % Allowed : 13.47 % Favored : 82.63 % 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: 2.23 (0.31), residues: 722 helix: 2.13 (0.23), residues: 514 sheet: -0.34 (0.71), residues: 58 loop : 0.05 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 112 HIS 0.002 0.001 HIS D 23 PHE 0.019 0.001 PHE D 62 TYR 0.007 0.001 TYR C 314 ARG 0.002 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.04971 ( 404) hydrogen bonds : angle 4.32799 ( 1176) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.27838 ( 16) covalent geometry : bond 0.00386 ( 5772) covalent geometry : angle 0.53413 ( 7855) *********************** 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 125 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.619 Fit side-chains REVERT: D 41 LYS cc_start: 0.8184 (mttt) cc_final: 0.7907 (mmtm) REVERT: D 43 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: R 143 ASP cc_start: 0.8947 (t70) cc_final: 0.8672 (t0) REVERT: R 207 TRP cc_start: 0.8610 (m100) cc_final: 0.8400 (m100) REVERT: R 213 ILE cc_start: 0.9255 (tt) cc_final: 0.8952 (mt) REVERT: R 283 GLN cc_start: 0.7975 (mp10) cc_final: 0.7677 (mp10) REVERT: B 41 LYS cc_start: 0.8135 (mttt) cc_final: 0.7883 (mmtm) REVERT: B 43 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 68 GLN cc_start: 0.8494 (tp40) cc_final: 0.8236 (tp-100) REVERT: C 143 ASP cc_start: 0.8938 (t70) cc_final: 0.8676 (t0) REVERT: C 213 ILE cc_start: 0.9241 (tt) cc_final: 0.8935 (mt) REVERT: C 329 LEU cc_start: 0.8117 (mt) cc_final: 0.7901 (pp) outliers start: 24 outliers final: 14 residues processed: 115 average time/residue: 0.1857 time to fit residues: 27.7432 Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain R residue 180 VAL 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 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 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: 0.6980 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3443 r_free = 0.3443 target = 0.110913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.093947 restraints weight = 9647.153| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.10 r_work: 0.3061 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5780 Z= 0.166 Angle : 0.523 5.038 7871 Z= 0.279 Chirality : 0.041 0.136 976 Planarity : 0.004 0.024 949 Dihedral : 3.901 17.835 780 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 2.39 (0.31), residues: 722 helix: 2.28 (0.23), residues: 504 sheet: -0.39 (0.72), residues: 58 loop : 0.18 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 112 HIS 0.002 0.000 HIS C 247 PHE 0.018 0.001 PHE D 62 TYR 0.006 0.001 TYR C 75 ARG 0.002 0.000 ARG R 185 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 404) hydrogen bonds : angle 4.24678 ( 1176) SS BOND : bond 0.00387 ( 8) SS BOND : angle 1.28774 ( 16) covalent geometry : bond 0.00393 ( 5772) covalent geometry : angle 0.51985 ( 7855) *********************** 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 120 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.535 Fit side-chains REVERT: D 41 LYS cc_start: 0.8217 (mttt) cc_final: 0.7974 (mmtm) REVERT: D 43 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: R 143 ASP cc_start: 0.8933 (t70) cc_final: 0.8655 (t0) REVERT: R 207 TRP cc_start: 0.8627 (m100) cc_final: 0.8398 (m100) REVERT: R 213 ILE cc_start: 0.9245 (tt) cc_final: 0.8932 (mt) REVERT: R 283 GLN cc_start: 0.7908 (mp10) cc_final: 0.7642 (mp10) REVERT: B 43 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: B 68 GLN cc_start: 0.8507 (tp40) cc_final: 0.8217 (tp-100) REVERT: C 143 ASP cc_start: 0.8927 (t70) cc_final: 0.8655 (t0) REVERT: C 213 ILE cc_start: 0.9234 (tt) cc_final: 0.8917 (mt) REVERT: C 329 LEU cc_start: 0.8137 (mt) cc_final: 0.7914 (pp) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.1895 time to fit residues: 27.2316 Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 99 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 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 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: 0.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN R 110 ASN C 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092731 restraints weight = 9820.990| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.10 r_work: 0.3039 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5780 Z= 0.197 Angle : 0.551 5.084 7871 Z= 0.297 Chirality : 0.042 0.138 976 Planarity : 0.004 0.025 949 Dihedral : 4.034 17.525 780 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.55 % Allowed : 13.64 % 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 (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: 2.23 (0.31), residues: 722 helix: 2.17 (0.23), residues: 504 sheet: -0.48 (0.72), residues: 58 loop : 0.10 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 112 HIS 0.003 0.001 HIS R 247 PHE 0.019 0.002 PHE D 62 TYR 0.011 0.001 TYR R 75 ARG 0.002 0.000 ARG R 184 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 404) hydrogen bonds : angle 4.32961 ( 1176) SS BOND : bond 0.00427 ( 8) SS BOND : angle 1.42418 ( 16) covalent geometry : bond 0.00479 ( 5772) covalent geometry : angle 0.54803 ( 7855) *********************** 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 128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8304 (mttt) cc_final: 0.8040 (mmtm) REVERT: D 43 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: R 143 ASP cc_start: 0.8954 (t70) cc_final: 0.8684 (t0) REVERT: R 207 TRP cc_start: 0.8644 (m100) cc_final: 0.8444 (m100) REVERT: R 213 ILE cc_start: 0.9255 (tt) cc_final: 0.8939 (mt) REVERT: R 248 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7283 (ttm-80) REVERT: B 43 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: B 68 GLN cc_start: 0.8531 (tp40) cc_final: 0.8224 (tp-100) REVERT: C 143 ASP cc_start: 0.8950 (t70) cc_final: 0.8672 (t0) REVERT: C 213 ILE cc_start: 0.9248 (tt) cc_final: 0.8924 (mt) REVERT: C 248 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7273 (ttm-80) REVERT: C 329 LEU cc_start: 0.8155 (mt) cc_final: 0.7942 (pp) outliers start: 28 outliers final: 15 residues processed: 117 average time/residue: 0.1906 time to fit residues: 28.3525 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 : 0.621 ------------------------------------------------------------------------------- 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 110 ASN 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 R residue 329 LEU 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 248 ARG 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: 0.9980 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 110 ASN R 247 HIS C 247 HIS ** C 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.093677 restraints weight = 9678.501| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.09 r_work: 0.3062 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5780 Z= 0.155 Angle : 0.560 9.237 7871 Z= 0.300 Chirality : 0.041 0.159 976 Planarity : 0.004 0.026 949 Dihedral : 4.219 29.838 780 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.25 % Allowed : 14.29 % 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: 2.32 (0.31), residues: 722 helix: 2.25 (0.23), residues: 504 sheet: -0.43 (0.73), residues: 58 loop : 0.06 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 207 HIS 0.001 0.000 HIS B 23 PHE 0.018 0.001 PHE D 62 TYR 0.008 0.001 TYR R 75 ARG 0.003 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 404) hydrogen bonds : angle 4.24424 ( 1176) SS BOND : bond 0.00382 ( 8) SS BOND : angle 3.12749 ( 16) covalent geometry : bond 0.00368 ( 5772) covalent geometry : angle 0.54301 ( 7855) *********************** 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 115 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.618 Fit side-chains REVERT: D 41 LYS cc_start: 0.8281 (mttt) cc_final: 0.8035 (mmtm) REVERT: D 53 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8000 (mt-10) REVERT: R 143 ASP cc_start: 0.8949 (t70) cc_final: 0.8676 (t0) REVERT: R 213 ILE cc_start: 0.9233 (tt) cc_final: 0.8910 (mt) REVERT: R 248 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7257 (ttm-80) REVERT: B 68 GLN cc_start: 0.8501 (tp40) cc_final: 0.8192 (tp-100) REVERT: C 143 ASP cc_start: 0.8948 (t70) cc_final: 0.8672 (t0) REVERT: C 213 ILE cc_start: 0.9234 (tt) cc_final: 0.8909 (mt) REVERT: C 248 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7242 (ttm-80) REVERT: C 329 LEU cc_start: 0.8164 (mt) cc_final: 0.7936 (pp) outliers start: 20 outliers final: 16 residues processed: 107 average time/residue: 0.2372 time to fit residues: 32.2141 Evaluate side-chains 111 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 110 ASN 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 329 LEU 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 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: 0.4980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** 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 = 0.3430 r_free = 0.3430 target = 0.110149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093211 restraints weight = 9715.571| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.08 r_work: 0.3053 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5780 Z= 0.163 Angle : 0.545 6.805 7871 Z= 0.294 Chirality : 0.040 0.137 976 Planarity : 0.004 0.028 949 Dihedral : 4.247 29.053 780 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.25 % Allowed : 14.77 % 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 (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: 2.27 (0.23), residues: 504 sheet: -0.46 (0.73), residues: 58 loop : 0.02 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 112 HIS 0.002 0.000 HIS R 247 PHE 0.017 0.001 PHE B 62 TYR 0.008 0.001 TYR R 75 ARG 0.003 0.000 ARG R 289 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 404) hydrogen bonds : angle 4.21987 ( 1176) SS BOND : bond 0.00419 ( 8) SS BOND : angle 2.39849 ( 16) covalent geometry : bond 0.00388 ( 5772) covalent geometry : angle 0.53481 ( 7855) *********************** 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 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.685 Fit side-chains REVERT: D 41 LYS cc_start: 0.8227 (mttt) cc_final: 0.8027 (mmtm) REVERT: D 53 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8008 (mt-10) REVERT: R 143 ASP cc_start: 0.8940 (t70) cc_final: 0.8657 (t0) REVERT: R 213 ILE cc_start: 0.9226 (tt) cc_final: 0.8887 (mt) REVERT: B 53 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7987 (mt-10) REVERT: B 68 GLN cc_start: 0.8488 (tp40) cc_final: 0.8182 (tp-100) REVERT: C 143 ASP cc_start: 0.8954 (t70) cc_final: 0.8677 (t0) REVERT: C 213 ILE cc_start: 0.9233 (tt) cc_final: 0.8903 (mt) REVERT: C 329 LEU cc_start: 0.8166 (mt) cc_final: 0.7931 (pp) outliers start: 20 outliers final: 17 residues processed: 110 average time/residue: 0.1953 time to fit residues: 27.3833 Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ASN 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 329 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 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 ** 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 = 0.3427 r_free = 0.3427 target = 0.109957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092991 restraints weight = 9848.649| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.10 r_work: 0.3052 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4164 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= 0.172 Angle : 0.578 12.338 7871 Z= 0.308 Chirality : 0.042 0.311 976 Planarity : 0.004 0.029 949 Dihedral : 4.224 28.572 780 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.76 % Allowed : 15.75 % Favored : 81.49 % 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: 2.28 (0.31), residues: 722 helix: 2.24 (0.23), residues: 504 sheet: -0.48 (0.73), residues: 58 loop : 0.02 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 207 HIS 0.001 0.000 HIS D 23 PHE 0.017 0.001 PHE D 62 TYR 0.006 0.001 TYR C 197 ARG 0.003 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 404) hydrogen bonds : angle 4.26482 ( 1176) SS BOND : bond 0.00404 ( 8) SS BOND : angle 2.34758 ( 16) covalent geometry : bond 0.00412 ( 5772) covalent geometry : angle 0.56902 ( 7855) ********************** 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 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.672 Fit side-chains REVERT: D 41 LYS cc_start: 0.8249 (mttt) cc_final: 0.8019 (mmtm) REVERT: R 143 ASP cc_start: 0.8948 (t70) cc_final: 0.8667 (t0) REVERT: R 213 ILE cc_start: 0.9225 (tt) cc_final: 0.8882 (mt) REVERT: R 256 VAL cc_start: 0.8987 (t) cc_final: 0.8786 (p) REVERT: B 68 GLN cc_start: 0.8490 (tp40) cc_final: 0.8186 (tp-100) REVERT: C 143 ASP cc_start: 0.8956 (t70) cc_final: 0.8669 (t0) REVERT: C 213 ILE cc_start: 0.9230 (tt) cc_final: 0.8900 (mt) REVERT: C 329 LEU cc_start: 0.8156 (mt) cc_final: 0.7915 (pp) outliers start: 17 outliers final: 17 residues processed: 104 average time/residue: 0.2045 time to fit residues: 27.5194 Evaluate side-chains 112 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ASN 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 329 LEU 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 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=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: 0.6980 chunk 62 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 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 ** 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 = 0.3430 r_free = 0.3430 target = 0.110283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093323 restraints weight = 9796.368| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.09 r_work: 0.3053 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5780 Z= 0.171 Angle : 0.572 10.367 7871 Z= 0.306 Chirality : 0.042 0.290 976 Planarity : 0.004 0.029 949 Dihedral : 4.216 28.122 780 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.92 % Allowed : 15.91 % Favored : 81.17 % 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: 2.27 (0.31), residues: 722 helix: 2.22 (0.23), residues: 504 sheet: -0.50 (0.73), residues: 58 loop : 0.03 (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 C 247 PHE 0.017 0.001 PHE D 62 TYR 0.006 0.001 TYR C 197 ARG 0.003 0.000 ARG C 289 Details of bonding type rmsd hydrogen bonds : bond 0.05027 ( 404) hydrogen bonds : angle 4.27212 ( 1176) SS BOND : bond 0.00410 ( 8) SS BOND : angle 2.22973 ( 16) covalent geometry : bond 0.00413 ( 5772) covalent geometry : angle 0.56392 ( 7855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.70 seconds wall clock time: 72 minutes 26.12 seconds (4346.12 seconds total)