Starting phenix.real_space_refine on Thu Jun 12 00:46:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522.map" model { file = "/net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xym_33522/06_2025/7xym_33522_neut.cif" } resolution = 3.3 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2433 atoms to isotropic. 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 66 5.16 5 C 7218 2.51 5 N 1965 2.21 5 O 2187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3812 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 466} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 28 Restraints were copied for chains: C, B Time building chain proxies: 10.07, per 1000 atoms: 0.88 Number of scatterers: 11436 At special positions: 0 Unit cell: (128.199, 132.444, 159.612, 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 66 16.00 O 2187 8.00 N 1965 7.00 C 7218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS B 384 " distance=1.97 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 284 " distance=2.06 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS C 24 " distance=1.97 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS C 384 " distance=1.97 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 284 " distance=2.06 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 284 " distance=2.06 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 17.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 313 through 350 removed outlier: 3.833A pdb=" N HIS A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 313 through 350 removed outlier: 3.833A pdb=" N HIS B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 313 through 350 removed outlier: 3.833A pdb=" N HIS C 319 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 457 through 469 Processing helix chain 'C' and resid 487 through 508 Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.210A pdb=" N TYR A 154 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.537A pdb=" N CYS A 111 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.572A pdb=" N ALA A 185 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 232 removed outlier: 4.255A pdb=" N TYR A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA8, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.166A pdb=" N GLN B 421 " --> pdb=" O THR C 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.166A pdb=" N GLN A 421 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 78 removed outlier: 4.210A pdb=" N TYR B 154 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.537A pdb=" N CYS B 111 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.573A pdb=" N ALA B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 228 through 232 removed outlier: 4.255A pdb=" N TYR B 261 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.211A pdb=" N TYR C 154 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.537A pdb=" N CYS C 111 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 180 through 182 removed outlier: 3.572A pdb=" N ALA C 185 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 228 through 232 removed outlier: 4.255A pdb=" N TYR C 261 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 236 through 237 259 hydrogen bonds defined for protein. 714 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: 3.08 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1878 1.29 - 1.43: 3210 1.43 - 1.57: 6546 1.57 - 1.71: 6 1.71 - 1.85: 87 Bond restraints: 11727 Sorted by residual: bond pdb=" C ILE A 501 " pdb=" O ILE A 501 " ideal model delta sigma weight residual 1.236 1.459 -0.223 1.19e-02 7.06e+03 3.51e+02 bond pdb=" C ILE B 501 " pdb=" O ILE B 501 " ideal model delta sigma weight residual 1.236 1.459 -0.223 1.19e-02 7.06e+03 3.50e+02 bond pdb=" C ILE C 501 " pdb=" O ILE C 501 " ideal model delta sigma weight residual 1.236 1.459 -0.223 1.19e-02 7.06e+03 3.50e+02 bond pdb=" CA SER A 502 " pdb=" C SER A 502 " ideal model delta sigma weight residual 1.523 1.725 -0.202 1.34e-02 5.57e+03 2.28e+02 bond pdb=" CA SER C 502 " pdb=" C SER C 502 " ideal model delta sigma weight residual 1.523 1.725 -0.202 1.34e-02 5.57e+03 2.27e+02 ... (remaining 11722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.61: 15377 3.61 - 7.22: 433 7.22 - 10.83: 78 10.83 - 14.44: 42 14.44 - 18.06: 12 Bond angle restraints: 15942 Sorted by residual: angle pdb=" CA ILE C 501 " pdb=" C ILE C 501 " pdb=" O ILE C 501 " ideal model delta sigma weight residual 120.78 138.17 -17.39 1.25e+00 6.40e-01 1.94e+02 angle pdb=" CA ILE A 501 " pdb=" C ILE A 501 " pdb=" O ILE A 501 " ideal model delta sigma weight residual 120.78 138.15 -17.37 1.25e+00 6.40e-01 1.93e+02 angle pdb=" CA ILE B 501 " pdb=" C ILE B 501 " pdb=" O ILE B 501 " ideal model delta sigma weight residual 120.78 138.12 -17.34 1.25e+00 6.40e-01 1.92e+02 angle pdb=" N THR C 299 " pdb=" CA THR C 299 " pdb=" C THR C 299 " ideal model delta sigma weight residual 113.97 102.74 11.23 1.28e+00 6.10e-01 7.69e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 113.97 102.76 11.21 1.28e+00 6.10e-01 7.67e+01 ... (remaining 15937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 5986 15.47 - 30.94: 698 30.94 - 46.41: 234 46.41 - 61.88: 33 61.88 - 77.35: 18 Dihedral angle restraints: 6969 sinusoidal: 2718 harmonic: 4251 Sorted by residual: dihedral pdb=" CA CYS C 279 " pdb=" C CYS C 279 " pdb=" N LEU C 280 " pdb=" CA LEU C 280 " ideal model delta harmonic sigma weight residual 180.00 133.49 46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA CYS B 279 " pdb=" C CYS B 279 " pdb=" N LEU B 280 " pdb=" CA LEU B 280 " ideal model delta harmonic sigma weight residual 180.00 133.50 46.50 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA CYS A 279 " pdb=" C CYS A 279 " pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta harmonic sigma weight residual 180.00 133.50 46.50 0 5.00e+00 4.00e-02 8.65e+01 ... (remaining 6966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1647 0.139 - 0.277: 63 0.277 - 0.416: 18 0.416 - 0.555: 0 0.555 - 0.693: 3 Chirality restraints: 1731 Sorted by residual: chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 1.74 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ILE C 501 " pdb=" N ILE C 501 " pdb=" C ILE C 501 " pdb=" CB ILE C 501 " both_signs ideal model delta sigma weight residual False 2.43 1.74 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA ILE B 501 " pdb=" N ILE B 501 " pdb=" C ILE B 501 " pdb=" CB ILE B 501 " both_signs ideal model delta sigma weight residual False 2.43 1.74 0.69 2.00e-01 2.50e+01 1.20e+01 ... (remaining 1728 not shown) Planarity restraints: 2049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 486 " 0.037 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C GLY A 486 " -0.118 2.00e-02 2.50e+03 pdb=" O GLY A 486 " 0.041 2.00e-02 2.50e+03 pdb=" N TRP A 487 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 486 " -0.037 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C GLY C 486 " 0.118 2.00e-02 2.50e+03 pdb=" O GLY C 486 " -0.041 2.00e-02 2.50e+03 pdb=" N TRP C 487 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 486 " 0.037 2.00e-02 2.50e+03 6.81e-02 4.64e+01 pdb=" C GLY B 486 " -0.118 2.00e-02 2.50e+03 pdb=" O GLY B 486 " 0.041 2.00e-02 2.50e+03 pdb=" N TRP B 487 " 0.040 2.00e-02 2.50e+03 ... (remaining 2046 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 6 1.80 - 2.58: 243 2.58 - 3.35: 14666 3.35 - 4.13: 27237 4.13 - 4.90: 48115 Nonbonded interactions: 90267 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" C ASN B 158 " model vdw 1.028 3.270 nonbonded pdb=" OG SER C 74 " pdb=" C ASN C 158 " model vdw 1.029 3.270 nonbonded pdb=" OG SER A 74 " pdb=" C ASN A 158 " model vdw 1.029 3.270 nonbonded pdb=" OG SER B 74 " pdb=" O ASN B 158 " model vdw 1.416 3.040 nonbonded pdb=" OG SER A 74 " pdb=" O ASN A 158 " model vdw 1.417 3.040 ... (remaining 90262 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 7.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.009 0.223 11745 Z= 0.674 Angle : 1.583 18.056 15978 Z= 0.939 Chirality : 0.074 0.693 1731 Planarity : 0.009 0.113 2049 Dihedral : 14.866 77.349 4197 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 29.59 Ramachandran Plot: Outliers : 2.88 % Allowed : 25.51 % Favored : 71.60 % Rotamer: Outliers : 0.49 % Allowed : 0.81 % Favored : 98.71 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.36 % 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: -6.19 (0.16), residues: 1458 helix: -3.63 (0.20), residues: 315 sheet: -3.11 (0.37), residues: 171 loop : -4.84 (0.15), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 161 HIS 0.005 0.001 HIS C 397 PHE 0.014 0.002 PHE A 208 TYR 0.039 0.002 TYR B 212 ARG 0.007 0.001 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.19346 ( 259) hydrogen bonds : angle 10.97821 ( 714) SS BOND : bond 0.02832 ( 18) SS BOND : angle 3.56474 ( 36) covalent geometry : bond 0.00922 (11727) covalent geometry : angle 1.57614 (15942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 189 ASN cc_start: 0.5260 (m110) cc_final: 0.4956 (m110) REVERT: A 481 LEU cc_start: 0.6174 (mt) cc_final: 0.5901 (mt) REVERT: B 121 TRP cc_start: 0.5582 (p-90) cc_final: 0.5286 (p-90) REVERT: C 121 TRP cc_start: 0.5558 (p-90) cc_final: 0.5225 (p-90) REVERT: C 189 ASN cc_start: 0.5566 (m110) cc_final: 0.5299 (m110) outliers start: 6 outliers final: 2 residues processed: 93 average time/residue: 0.2801 time to fit residues: 40.9483 Evaluate side-chains 68 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain C residue 266 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 0.0070 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 GLN A 149 ASN A 413 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 413 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN C 413 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.188006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.123907 restraints weight = 21303.571| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.69 r_work: 0.3633 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11745 Z= 0.227 Angle : 1.111 13.002 15978 Z= 0.582 Chirality : 0.057 0.314 1731 Planarity : 0.007 0.086 2049 Dihedral : 9.299 46.610 1594 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 2.61 % Allowed : 24.55 % Favored : 72.84 % Rotamer: Outliers : 1.05 % Allowed : 11.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % 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: -5.48 (0.18), residues: 1458 helix: -1.65 (0.28), residues: 291 sheet: -3.30 (0.35), residues: 183 loop : -4.71 (0.15), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 405 HIS 0.005 0.001 HIS C 407 PHE 0.014 0.002 PHE B 225 TYR 0.037 0.002 TYR C 212 ARG 0.009 0.001 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.12955 ( 259) hydrogen bonds : angle 8.29429 ( 714) SS BOND : bond 0.00790 ( 18) SS BOND : angle 1.80092 ( 36) covalent geometry : bond 0.00435 (11727) covalent geometry : angle 1.10873 (15942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 1.248 Fit side-chains REVERT: A 189 ASN cc_start: 0.6412 (m110) cc_final: 0.5664 (m110) REVERT: A 198 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 266 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7802 (p0) REVERT: A 481 LEU cc_start: 0.6893 (mt) cc_final: 0.5728 (mt) REVERT: C 196 GLU cc_start: 0.4068 (tt0) cc_final: 0.3833 (pp20) REVERT: C 266 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7826 (p0) outliers start: 13 outliers final: 1 residues processed: 84 average time/residue: 0.1932 time to fit residues: 26.2684 Evaluate side-chains 65 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 266 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 73 optimal weight: 0.0980 chunk 15 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 413 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.188653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.124590 restraints weight = 21703.020| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.76 r_work: 0.3632 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11745 Z= 0.206 Angle : 1.021 11.121 15978 Z= 0.534 Chirality : 0.054 0.296 1731 Planarity : 0.006 0.069 2049 Dihedral : 8.973 43.793 1594 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 2.40 % Allowed : 24.83 % Favored : 72.77 % Rotamer: Outliers : 2.43 % Allowed : 13.59 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.36 % 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: -5.18 (0.19), residues: 1458 helix: -0.98 (0.32), residues: 285 sheet: -3.15 (0.36), residues: 183 loop : -4.64 (0.15), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 405 HIS 0.004 0.001 HIS B 65 PHE 0.016 0.001 PHE A 208 TYR 0.030 0.001 TYR B 212 ARG 0.007 0.001 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.11620 ( 259) hydrogen bonds : angle 8.09011 ( 714) SS BOND : bond 0.01127 ( 18) SS BOND : angle 1.72335 ( 36) covalent geometry : bond 0.00398 (11727) covalent geometry : angle 1.01914 (15942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.6211 (m110) cc_final: 0.5400 (m110) REVERT: A 198 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7714 (p) REVERT: A 405 TRP cc_start: 0.4103 (OUTLIER) cc_final: 0.3553 (m100) REVERT: B 405 TRP cc_start: 0.4058 (OUTLIER) cc_final: 0.3117 (m100) REVERT: C 405 TRP cc_start: 0.3984 (OUTLIER) cc_final: 0.3499 (m100) REVERT: C 465 MET cc_start: 0.7978 (mtm) cc_final: 0.7430 (mtm) outliers start: 30 outliers final: 6 residues processed: 97 average time/residue: 0.1905 time to fit residues: 29.2658 Evaluate side-chains 68 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 405 TRP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 405 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 19 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 293 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN B 30 GLN B 65 HIS B 293 ASN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 266 ASN C 293 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.124368 restraints weight = 21210.467| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 4.40 r_work: 0.3551 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11745 Z= 0.233 Angle : 1.016 10.750 15978 Z= 0.529 Chirality : 0.054 0.270 1731 Planarity : 0.006 0.063 2049 Dihedral : 8.738 42.068 1590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 2.26 % Allowed : 24.97 % Favored : 72.77 % Rotamer: Outliers : 3.40 % Allowed : 16.75 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % 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: -5.03 (0.19), residues: 1458 helix: -1.01 (0.31), residues: 291 sheet: -2.58 (0.43), residues: 141 loop : -4.57 (0.15), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 405 HIS 0.003 0.001 HIS B 337 PHE 0.027 0.002 PHE C 428 TYR 0.033 0.002 TYR B 212 ARG 0.006 0.001 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.11574 ( 259) hydrogen bonds : angle 8.02964 ( 714) SS BOND : bond 0.00717 ( 18) SS BOND : angle 1.44427 ( 36) covalent geometry : bond 0.00490 (11727) covalent geometry : angle 1.01533 (15942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.6783 (m110) cc_final: 0.6083 (m110) REVERT: A 198 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7778 (p) REVERT: B 478 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6587 (tm-30) REVERT: C 465 MET cc_start: 0.8253 (mtm) cc_final: 0.7840 (mtm) outliers start: 42 outliers final: 14 residues processed: 97 average time/residue: 0.1892 time to fit residues: 31.1712 Evaluate side-chains 71 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 415 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.177623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117913 restraints weight = 21033.017| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 4.05 r_work: 0.3458 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.168 11745 Z= 0.375 Angle : 1.210 18.870 15978 Z= 0.618 Chirality : 0.064 0.535 1731 Planarity : 0.007 0.062 2049 Dihedral : 9.240 41.264 1590 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.11 Ramachandran Plot: Outliers : 2.33 % Allowed : 27.43 % Favored : 70.23 % Rotamer: Outliers : 4.69 % Allowed : 17.39 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.50 % 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: -5.41 (0.18), residues: 1458 helix: -1.45 (0.29), residues: 315 sheet: -3.39 (0.34), residues: 177 loop : -4.75 (0.15), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 405 HIS 0.005 0.002 HIS B 407 PHE 0.015 0.003 PHE A 208 TYR 0.037 0.003 TYR C 212 ARG 0.006 0.001 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.12934 ( 259) hydrogen bonds : angle 8.18561 ( 714) SS BOND : bond 0.01060 ( 18) SS BOND : angle 2.68812 ( 36) covalent geometry : bond 0.00887 (11727) covalent geometry : angle 1.20470 (15942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 64 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1763 (OUTLIER) cc_final: 0.1338 (p) REVERT: A 189 ASN cc_start: 0.7550 (m110) cc_final: 0.6888 (m110) REVERT: A 198 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7575 (p) REVERT: A 399 ILE cc_start: 0.3136 (OUTLIER) cc_final: 0.1987 (pp) REVERT: A 405 TRP cc_start: 0.5640 (OUTLIER) cc_final: 0.4970 (m100) REVERT: B 157 CYS cc_start: 0.1867 (OUTLIER) cc_final: 0.1601 (p) REVERT: B 399 ILE cc_start: 0.3270 (OUTLIER) cc_final: 0.2685 (pp) REVERT: C 157 CYS cc_start: 0.1726 (OUTLIER) cc_final: 0.1349 (p) REVERT: C 399 ILE cc_start: 0.3236 (OUTLIER) cc_final: 0.2618 (pp) outliers start: 58 outliers final: 20 residues processed: 116 average time/residue: 0.3476 time to fit residues: 62.8810 Evaluate side-chains 87 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 415 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 65 HIS C 266 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.184965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126975 restraints weight = 20420.160| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.35 r_work: 0.3580 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 11745 Z= 0.245 Angle : 1.054 18.815 15978 Z= 0.537 Chirality : 0.055 0.416 1731 Planarity : 0.006 0.063 2049 Dihedral : 8.935 41.619 1590 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 1.85 % Allowed : 25.24 % Favored : 72.91 % Rotamer: Outliers : 3.96 % Allowed : 19.01 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.58 % 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: -5.32 (0.19), residues: 1458 helix: -1.20 (0.30), residues: 315 sheet: -3.55 (0.32), residues: 177 loop : -4.72 (0.15), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 405 HIS 0.007 0.001 HIS B 65 PHE 0.017 0.002 PHE A 208 TYR 0.036 0.002 TYR A 212 ARG 0.006 0.001 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.11526 ( 259) hydrogen bonds : angle 7.98097 ( 714) SS BOND : bond 0.00859 ( 18) SS BOND : angle 1.94095 ( 36) covalent geometry : bond 0.00528 (11727) covalent geometry : angle 1.05161 (15942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 62 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1823 (OUTLIER) cc_final: 0.1282 (p) REVERT: A 189 ASN cc_start: 0.7101 (m110) cc_final: 0.6563 (m110) REVERT: A 198 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 380 MET cc_start: 0.8837 (tpp) cc_final: 0.8288 (ttm) REVERT: A 405 TRP cc_start: 0.6033 (OUTLIER) cc_final: 0.5271 (m100) REVERT: B 68 TYR cc_start: 0.3140 (OUTLIER) cc_final: 0.2713 (t80) REVERT: B 157 CYS cc_start: 0.1912 (OUTLIER) cc_final: 0.1554 (p) REVERT: B 478 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6881 (tm-30) REVERT: C 29 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5728 (mt0) REVERT: C 157 CYS cc_start: 0.1525 (OUTLIER) cc_final: 0.1152 (p) REVERT: C 266 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7762 (p0) REVERT: C 405 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.5792 (m100) REVERT: C 465 MET cc_start: 0.8326 (mtp) cc_final: 0.8117 (mtm) outliers start: 49 outliers final: 23 residues processed: 107 average time/residue: 0.1912 time to fit residues: 32.2840 Evaluate side-chains 91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 453 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.126092 restraints weight = 20631.965| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.43 r_work: 0.3548 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11745 Z= 0.245 Angle : 1.041 16.162 15978 Z= 0.532 Chirality : 0.056 0.349 1731 Planarity : 0.006 0.051 2049 Dihedral : 8.918 42.133 1590 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 1.92 % Allowed : 26.75 % Favored : 71.33 % Rotamer: Outliers : 4.69 % Allowed : 19.58 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.50 % 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: -5.25 (0.19), residues: 1458 helix: -1.06 (0.30), residues: 321 sheet: -3.58 (0.32), residues: 177 loop : -4.71 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 405 HIS 0.007 0.001 HIS B 65 PHE 0.017 0.002 PHE A 208 TYR 0.037 0.002 TYR B 212 ARG 0.005 0.001 ARG C 199 Details of bonding type rmsd hydrogen bonds : bond 0.11381 ( 259) hydrogen bonds : angle 7.86165 ( 714) SS BOND : bond 0.00751 ( 18) SS BOND : angle 1.85584 ( 36) covalent geometry : bond 0.00524 (11727) covalent geometry : angle 1.03868 (15942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 59 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1698 (OUTLIER) cc_final: 0.1242 (p) REVERT: A 189 ASN cc_start: 0.6890 (m110) cc_final: 0.6260 (m110) REVERT: A 198 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7903 (p) REVERT: A 380 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8388 (ttm) REVERT: A 405 TRP cc_start: 0.6030 (OUTLIER) cc_final: 0.5391 (m100) REVERT: B 68 TYR cc_start: 0.3160 (OUTLIER) cc_final: 0.2710 (t80) REVERT: B 157 CYS cc_start: 0.2014 (OUTLIER) cc_final: 0.1667 (p) REVERT: B 399 ILE cc_start: 0.2532 (OUTLIER) cc_final: 0.2275 (pp) REVERT: C 29 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6256 (mt0) REVERT: C 157 CYS cc_start: 0.1586 (OUTLIER) cc_final: 0.1216 (p) REVERT: C 266 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.8050 (p0) REVERT: C 465 MET cc_start: 0.8348 (mtp) cc_final: 0.8141 (mtm) outliers start: 58 outliers final: 25 residues processed: 110 average time/residue: 0.2060 time to fit residues: 36.2856 Evaluate side-chains 93 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 415 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.187422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131786 restraints weight = 20406.101| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.29 r_work: 0.3613 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11745 Z= 0.206 Angle : 1.019 14.557 15978 Z= 0.521 Chirality : 0.054 0.349 1731 Planarity : 0.006 0.054 2049 Dihedral : 8.870 41.332 1590 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 1.71 % Allowed : 25.72 % Favored : 72.57 % Rotamer: Outliers : 3.48 % Allowed : 20.23 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.50 % 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: -4.96 (0.19), residues: 1458 helix: -0.65 (0.33), residues: 294 sheet: -2.55 (0.40), residues: 162 loop : -4.66 (0.15), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 432 HIS 0.008 0.001 HIS B 65 PHE 0.018 0.002 PHE A 208 TYR 0.037 0.002 TYR B 212 ARG 0.016 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.10704 ( 259) hydrogen bonds : angle 7.86649 ( 714) SS BOND : bond 0.01026 ( 18) SS BOND : angle 2.35284 ( 36) covalent geometry : bond 0.00421 (11727) covalent geometry : angle 1.01362 (15942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 62 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1686 (OUTLIER) cc_final: 0.1114 (p) REVERT: A 189 ASN cc_start: 0.6593 (m110) cc_final: 0.5885 (m110) REVERT: A 198 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.7888 (p) REVERT: A 380 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8283 (ttm) REVERT: A 405 TRP cc_start: 0.5882 (OUTLIER) cc_final: 0.4550 (m100) REVERT: B 68 TYR cc_start: 0.3034 (OUTLIER) cc_final: 0.2537 (t80) REVERT: B 157 CYS cc_start: 0.1725 (OUTLIER) cc_final: 0.1331 (p) REVERT: B 384 CYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7555 (m) REVERT: B 478 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6760 (tm-30) REVERT: C 29 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.6093 (mt0) REVERT: C 157 CYS cc_start: 0.1407 (OUTLIER) cc_final: 0.1039 (p) REVERT: C 266 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7988 (p0) REVERT: C 465 MET cc_start: 0.8268 (mtp) cc_final: 0.8064 (mtm) outliers start: 43 outliers final: 22 residues processed: 102 average time/residue: 0.1896 time to fit residues: 30.3359 Evaluate side-chains 92 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 453 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 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 = 0.4484 r_free = 0.4484 target = 0.180765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121142 restraints weight = 20585.630| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.47 r_work: 0.3530 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11745 Z= 0.295 Angle : 1.098 16.695 15978 Z= 0.560 Chirality : 0.058 0.412 1731 Planarity : 0.007 0.079 2049 Dihedral : 9.044 41.151 1590 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 1.92 % Allowed : 26.82 % Favored : 71.26 % Rotamer: Outliers : 3.32 % Allowed : 20.95 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.50 % 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: -5.40 (0.18), residues: 1458 helix: -1.34 (0.27), residues: 336 sheet: -3.91 (0.33), residues: 162 loop : -4.73 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 405 HIS 0.005 0.001 HIS B 65 PHE 0.016 0.002 PHE A 208 TYR 0.039 0.002 TYR A 212 ARG 0.004 0.001 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.11557 ( 259) hydrogen bonds : angle 7.92492 ( 714) SS BOND : bond 0.01118 ( 18) SS BOND : angle 3.05211 ( 36) covalent geometry : bond 0.00659 (11727) covalent geometry : angle 1.08959 (15942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 62 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1713 (OUTLIER) cc_final: 0.1275 (p) REVERT: A 189 ASN cc_start: 0.6915 (m110) cc_final: 0.6180 (m110) REVERT: A 198 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7858 (p) REVERT: A 380 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8340 (ttm) REVERT: A 399 ILE cc_start: 0.2651 (OUTLIER) cc_final: 0.1834 (pt) REVERT: A 405 TRP cc_start: 0.5573 (OUTLIER) cc_final: 0.5116 (m100) REVERT: B 68 TYR cc_start: 0.3065 (OUTLIER) cc_final: 0.2612 (t80) REVERT: B 157 CYS cc_start: 0.2097 (OUTLIER) cc_final: 0.1752 (p) REVERT: B 384 CYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7692 (m) REVERT: B 404 ARG cc_start: 0.7057 (mpt180) cc_final: 0.6779 (mtt90) REVERT: B 478 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 157 CYS cc_start: 0.1718 (OUTLIER) cc_final: 0.1370 (p) outliers start: 41 outliers final: 24 residues processed: 100 average time/residue: 0.2108 time to fit residues: 32.4391 Evaluate side-chains 92 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 453 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 123 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 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 = 0.4542 r_free = 0.4542 target = 0.186298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127134 restraints weight = 20938.307| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 4.05 r_work: 0.3583 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11745 Z= 0.196 Angle : 1.017 14.542 15978 Z= 0.519 Chirality : 0.054 0.369 1731 Planarity : 0.006 0.080 2049 Dihedral : 8.817 43.181 1590 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 1.71 % Allowed : 26.47 % Favored : 71.81 % Rotamer: Outliers : 2.67 % Allowed : 21.20 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.58 % 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: -4.93 (0.19), residues: 1458 helix: -0.81 (0.31), residues: 306 sheet: -2.46 (0.40), residues: 162 loop : -4.62 (0.15), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 432 HIS 0.008 0.001 HIS B 65 PHE 0.019 0.002 PHE A 208 TYR 0.037 0.001 TYR B 212 ARG 0.017 0.001 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.10241 ( 259) hydrogen bonds : angle 7.87765 ( 714) SS BOND : bond 0.01116 ( 18) SS BOND : angle 2.85307 ( 36) covalent geometry : bond 0.00390 (11727) covalent geometry : angle 1.00921 (15942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.1516 (OUTLIER) cc_final: 0.0920 (p) REVERT: A 189 ASN cc_start: 0.6340 (m110) cc_final: 0.5653 (m110) REVERT: B 68 TYR cc_start: 0.2952 (OUTLIER) cc_final: 0.2523 (t80) REVERT: B 157 CYS cc_start: 0.1501 (OUTLIER) cc_final: 0.1074 (p) REVERT: B 384 CYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7724 (m) REVERT: B 478 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6657 (tm-30) REVERT: C 157 CYS cc_start: 0.1157 (OUTLIER) cc_final: 0.0696 (p) REVERT: C 335 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 404 ARG cc_start: 0.6184 (mtm180) cc_final: 0.5910 (mtm180) REVERT: C 465 MET cc_start: 0.8183 (mtp) cc_final: 0.7940 (mtm) REVERT: C 478 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6644 (tm-30) outliers start: 33 outliers final: 22 residues processed: 101 average time/residue: 0.2003 time to fit residues: 31.6807 Evaluate side-chains 91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 453 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 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 = 0.4528 r_free = 0.4528 target = 0.184988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.126148 restraints weight = 20944.401| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.15 r_work: 0.3569 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11745 Z= 0.205 Angle : 1.017 14.878 15978 Z= 0.519 Chirality : 0.056 0.385 1731 Planarity : 0.006 0.086 2049 Dihedral : 8.726 41.773 1590 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 1.71 % Allowed : 26.47 % Favored : 71.81 % Rotamer: Outliers : 2.35 % Allowed : 21.76 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 2.29 % 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: -4.78 (0.20), residues: 1458 helix: -0.41 (0.32), residues: 291 sheet: -2.36 (0.41), residues: 162 loop : -4.58 (0.15), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 432 HIS 0.007 0.001 HIS B 65 PHE 0.017 0.002 PHE A 208 TYR 0.038 0.002 TYR B 212 ARG 0.021 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.10266 ( 259) hydrogen bonds : angle 7.79171 ( 714) SS BOND : bond 0.00947 ( 18) SS BOND : angle 2.75157 ( 36) covalent geometry : bond 0.00421 (11727) covalent geometry : angle 1.00925 (15942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8121.66 seconds wall clock time: 143 minutes 8.65 seconds (8588.65 seconds total)