Starting phenix.real_space_refine on Mon Dec 30 15:01:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xym_33522/12_2024/7xym_33522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xym_33522/12_2024/7xym_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_33522/12_2024/7xym_33522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xym_33522/12_2024/7xym_33522.map" model { file = "/net/cci-nas-00/data/ceres_data/7xym_33522/12_2024/7xym_33522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xym_33522/12_2024/7xym_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.79, per 1000 atoms: 0.77 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=5, symmetry=0 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 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: 3.01 Conformation dependent library (CDL) restraints added in 1.7 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: 1.07 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: 3.02 Time building geometry restraints manager: 3.45 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: 5976 15.47 - 30.94: 686 30.94 - 46.41: 225 46.41 - 61.88: 29 61.88 - 77.35: 14 Dihedral angle restraints: 6930 sinusoidal: 2679 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 6927 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: 256 2.58 - 3.35: 14692 3.35 - 4.13: 27237 4.13 - 4.90: 48115 Nonbonded interactions: 90306 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 90301 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.240 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- 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 11727 Z= 0.639 Angle : 1.576 18.056 15942 Z= 0.936 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 *********************** 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 : 1.311 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: 0.2292 time to fit residues: 32.6454 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 : 1.333 ------------------------------------------------------------------------------- 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: 0.9980 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 0.0070 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 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: 0.4798 ------------------------------------------------------------------------------- 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 90 ASN 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 90 ASN C 149 ASN C 413 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11727 Z= 0.278 Angle : 1.104 12.905 15942 Z= 0.577 Chirality : 0.056 0.318 1731 Planarity : 0.007 0.083 2049 Dihedral : 9.236 46.198 1594 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 2.61 % Allowed : 25.38 % Favored : 72.02 % Rotamer: Outliers : 0.89 % Allowed : 10.76 % Favored : 88.35 % 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: -5.39 (0.18), residues: 1458 helix: -1.61 (0.29), residues: 291 sheet: -3.17 (0.36), residues: 189 loop : -4.66 (0.15), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 405 HIS 0.005 0.001 HIS C 407 PHE 0.014 0.002 PHE A 208 TYR 0.038 0.002 TYR C 212 ARG 0.009 0.001 ARG C 199 *********************** 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 91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.346 Fit side-chains REVERT: A 121 TRP cc_start: 0.5553 (p-90) cc_final: 0.5251 (p-90) REVERT: A 189 ASN cc_start: 0.5167 (m110) cc_final: 0.4911 (m110) REVERT: A 198 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7879 (p) REVERT: A 266 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7213 (p0) REVERT: A 384 CYS cc_start: 0.5497 (m) cc_final: 0.5066 (t) REVERT: A 481 LEU cc_start: 0.6234 (mt) cc_final: 0.5186 (mt) REVERT: B 121 TRP cc_start: 0.5496 (p-90) cc_final: 0.5203 (p-90) REVERT: C 121 TRP cc_start: 0.5330 (p-90) cc_final: 0.5081 (p-90) REVERT: C 266 ASN cc_start: 0.7531 (OUTLIER) cc_final: 0.7307 (p0) outliers start: 11 outliers final: 1 residues processed: 88 average time/residue: 0.1939 time to fit residues: 27.2516 Evaluate side-chains 68 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 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 413 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 293 ASN B 413 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN C 413 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11727 Z= 0.283 Angle : 1.022 12.085 15942 Z= 0.534 Chirality : 0.054 0.323 1731 Planarity : 0.006 0.068 2049 Dihedral : 8.825 42.468 1594 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 2.47 % Allowed : 24.62 % Favored : 72.91 % Rotamer: Outliers : 2.02 % Allowed : 13.92 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.22 % 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: -5.12 (0.19), residues: 1458 helix: -1.10 (0.32), residues: 291 sheet: -3.20 (0.35), residues: 183 loop : -4.54 (0.15), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 405 HIS 0.006 0.001 HIS B 65 PHE 0.016 0.002 PHE A 208 TYR 0.030 0.002 TYR B 212 ARG 0.006 0.001 ARG A 199 *********************** 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 91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.5687 (p-90) cc_final: 0.5307 (p-90) REVERT: A 189 ASN cc_start: 0.5393 (m110) cc_final: 0.5149 (m110) REVERT: A 198 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 405 TRP cc_start: 0.5301 (OUTLIER) cc_final: 0.4934 (m100) REVERT: B 121 TRP cc_start: 0.5341 (p-90) cc_final: 0.5114 (p-90) REVERT: B 380 MET cc_start: 0.7675 (tpp) cc_final: 0.7428 (tpp) REVERT: B 405 TRP cc_start: 0.5170 (OUTLIER) cc_final: 0.4488 (m100) REVERT: C 121 TRP cc_start: 0.5266 (p-90) cc_final: 0.5058 (p-90) REVERT: C 405 TRP cc_start: 0.5244 (OUTLIER) cc_final: 0.5017 (m100) outliers start: 25 outliers final: 6 residues processed: 91 average time/residue: 0.2048 time to fit residues: 30.0078 Evaluate side-chains 65 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 129 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN C 293 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11727 Z= 0.272 Angle : 0.973 10.930 15942 Z= 0.505 Chirality : 0.051 0.268 1731 Planarity : 0.006 0.062 2049 Dihedral : 8.520 41.273 1590 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 2.26 % Allowed : 24.42 % Favored : 73.32 % Rotamer: Outliers : 3.56 % Allowed : 15.78 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.15 % 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: -4.99 (0.19), residues: 1458 helix: -0.91 (0.32), residues: 291 sheet: -3.17 (0.35), residues: 183 loop : -4.46 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 405 HIS 0.003 0.001 HIS C 407 PHE 0.029 0.002 PHE C 428 TYR 0.032 0.002 TYR B 212 ARG 0.005 0.001 ARG C 199 *********************** 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: 44 poor density : 58 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.5603 (m110) cc_final: 0.5347 (m110) REVERT: A 198 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7726 (p) REVERT: B 380 MET cc_start: 0.7722 (tpp) cc_final: 0.7505 (tpp) outliers start: 44 outliers final: 15 residues processed: 98 average time/residue: 0.2093 time to fit residues: 32.6068 Evaluate side-chains 70 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 266 ASN Chi-restraints excluded: chain A residue 415 PHE 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 201 THR 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 115 optimal weight: 0.0670 chunk 79 optimal weight: 0.5980 chunk 2 optimal weight: 0.0040 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 0.0050 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- 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 30 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11727 Z= 0.234 Angle : 0.959 14.065 15942 Z= 0.496 Chirality : 0.052 0.336 1731 Planarity : 0.005 0.059 2049 Dihedral : 8.269 38.835 1590 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 2.26 % Allowed : 24.21 % Favored : 73.53 % Rotamer: Outliers : 3.32 % Allowed : 16.26 % Favored : 80.42 % 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: -4.81 (0.20), residues: 1458 helix: -0.48 (0.33), residues: 291 sheet: -2.87 (0.35), residues: 210 loop : -4.51 (0.16), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 405 HIS 0.003 0.001 HIS B 138 PHE 0.019 0.001 PHE A 208 TYR 0.035 0.001 TYR B 212 ARG 0.005 0.000 ARG B 199 *********************** 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 110 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.5248 (m110) cc_final: 0.4906 (m110) REVERT: B 380 MET cc_start: 0.7589 (tpp) cc_final: 0.7307 (tpp) REVERT: C 137 CYS cc_start: 0.4738 (OUTLIER) cc_final: 0.2674 (m) REVERT: C 478 GLU cc_start: 0.6636 (tm-30) cc_final: 0.6327 (tm-30) outliers start: 41 outliers final: 19 residues processed: 103 average time/residue: 0.2147 time to fit residues: 33.7817 Evaluate side-chains 81 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 415 PHE 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 B residue 481 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11727 Z= 0.271 Angle : 0.948 10.929 15942 Z= 0.491 Chirality : 0.052 0.344 1731 Planarity : 0.006 0.048 2049 Dihedral : 8.248 37.835 1590 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 2.13 % Allowed : 24.14 % Favored : 73.73 % Rotamer: Outliers : 3.80 % Allowed : 17.31 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.07 % 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: -4.85 (0.19), residues: 1458 helix: -0.42 (0.32), residues: 294 sheet: -3.24 (0.34), residues: 183 loop : -4.48 (0.15), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 405 HIS 0.003 0.001 HIS B 337 PHE 0.022 0.001 PHE B 208 TYR 0.037 0.002 TYR B 212 ARG 0.007 0.001 ARG A 404 *********************** 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 106 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 MET cc_start: 0.7796 (tpp) cc_final: 0.7357 (ttm) REVERT: A 399 ILE cc_start: 0.2043 (OUTLIER) cc_final: 0.1346 (pp) REVERT: B 68 TYR cc_start: 0.3036 (OUTLIER) cc_final: 0.2451 (t80) REVERT: B 380 MET cc_start: 0.7796 (tpp) cc_final: 0.7445 (ttm) REVERT: C 399 ILE cc_start: 0.1980 (OUTLIER) cc_final: 0.1510 (pt) REVERT: C 404 ARG cc_start: 0.5752 (mmt-90) cc_final: 0.5541 (mmt-90) outliers start: 47 outliers final: 18 residues processed: 104 average time/residue: 0.1899 time to fit residues: 31.4768 Evaluate side-chains 75 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 170 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 399 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 201 THR Chi-restraints excluded: chain B residue 212 TYR 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 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11727 Z= 0.274 Angle : 0.944 10.897 15942 Z= 0.489 Chirality : 0.052 0.347 1731 Planarity : 0.006 0.054 2049 Dihedral : 8.263 38.064 1590 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 2.06 % Allowed : 24.55 % Favored : 73.39 % Rotamer: Outliers : 2.99 % Allowed : 19.26 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 2.07 % 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: -4.62 (0.20), residues: 1458 helix: -0.29 (0.32), residues: 300 sheet: -2.25 (0.41), residues: 162 loop : -4.49 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 405 HIS 0.002 0.001 HIS B 407 PHE 0.023 0.001 PHE B 208 TYR 0.038 0.002 TYR C 212 ARG 0.005 0.000 ARG B 199 *********************** 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 99 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 ASN cc_start: 0.5454 (m110) cc_final: 0.5132 (m110) REVERT: B 68 TYR cc_start: 0.3079 (OUTLIER) cc_final: 0.2522 (t80) REVERT: B 405 TRP cc_start: 0.5697 (OUTLIER) cc_final: 0.5390 (m100) REVERT: C 266 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7219 (p0) outliers start: 37 outliers final: 19 residues processed: 95 average time/residue: 0.1972 time to fit residues: 30.1368 Evaluate side-chains 78 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 398 SER 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 201 THR 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 48 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 433 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0270 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11727 Z= 0.239 Angle : 0.927 10.588 15942 Z= 0.480 Chirality : 0.051 0.309 1731 Planarity : 0.005 0.046 2049 Dihedral : 8.162 40.384 1590 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 1.92 % Allowed : 24.35 % Favored : 73.73 % Rotamer: Outliers : 2.18 % Allowed : 20.47 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 1.93 % 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: -4.68 (0.20), residues: 1458 helix: 0.25 (0.33), residues: 285 sheet: -2.98 (0.34), residues: 204 loop : -4.57 (0.15), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 405 HIS 0.003 0.001 HIS B 65 PHE 0.021 0.001 PHE B 208 TYR 0.038 0.002 TYR C 212 ARG 0.003 0.000 ARG A 199 *********************** 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 85 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7353 (p0) REVERT: B 68 TYR cc_start: 0.2917 (OUTLIER) cc_final: 0.2364 (t80) REVERT: C 266 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.7145 (p0) outliers start: 27 outliers final: 15 residues processed: 81 average time/residue: 0.2002 time to fit residues: 25.9338 Evaluate side-chains 70 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 212 TYR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 433 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.0170 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 435 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11727 Z= 0.270 Angle : 0.950 10.884 15942 Z= 0.490 Chirality : 0.051 0.310 1731 Planarity : 0.005 0.046 2049 Dihedral : 8.199 37.313 1590 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 2.06 % Allowed : 24.62 % Favored : 73.32 % Rotamer: Outliers : 2.35 % Allowed : 20.71 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.07 % 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: -4.48 (0.20), residues: 1458 helix: 0.41 (0.33), residues: 285 sheet: -2.28 (0.41), residues: 162 loop : -4.52 (0.15), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 405 HIS 0.002 0.001 HIS C 337 PHE 0.020 0.001 PHE B 208 TYR 0.039 0.002 TYR C 212 ARG 0.012 0.000 ARG A 404 *********************** 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 84 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 55 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TYR cc_start: 0.2984 (OUTLIER) cc_final: 0.2428 (t80) outliers start: 29 outliers final: 14 residues processed: 82 average time/residue: 0.2064 time to fit residues: 26.5456 Evaluate side-chains 70 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 435 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11727 Z= 0.311 Angle : 0.986 13.918 15942 Z= 0.505 Chirality : 0.054 0.422 1731 Planarity : 0.006 0.063 2049 Dihedral : 8.311 40.968 1590 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 1.85 % Allowed : 25.38 % Favored : 72.77 % Rotamer: Outliers : 1.86 % Allowed : 20.79 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.15 % 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: -4.68 (0.20), residues: 1458 helix: 0.26 (0.33), residues: 285 sheet: -3.00 (0.35), residues: 198 loop : -4.56 (0.15), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 405 HIS 0.003 0.001 HIS B 337 PHE 0.019 0.002 PHE B 208 TYR 0.040 0.002 TYR B 212 ARG 0.016 0.001 ARG B 404 ********************** 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 79 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TRP cc_start: 0.5943 (OUTLIER) cc_final: 0.5636 (m100) REVERT: B 68 TYR cc_start: 0.2965 (OUTLIER) cc_final: 0.2413 (t80) REVERT: B 414 CYS cc_start: 0.5996 (t) cc_final: 0.5323 (p) outliers start: 23 outliers final: 13 residues processed: 78 average time/residue: 0.2011 time to fit residues: 24.5948 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 : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 212 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.0070 chunk 34 optimal weight: 0.0050 chunk 105 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5012 ------------------------------------------------------------------------------- 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 435 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 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 = 0.4576 r_free = 0.4576 target = 0.188588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.125151 restraints weight = 21237.334| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.53 r_work: 0.3638 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11727 Z= 0.252 Angle : 0.959 14.503 15942 Z= 0.490 Chirality : 0.053 0.366 1731 Planarity : 0.006 0.077 2049 Dihedral : 8.180 41.311 1590 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 1.85 % Allowed : 23.94 % Favored : 74.21 % Rotamer: Outliers : 1.46 % Allowed : 21.28 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.07 % 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: -4.60 (0.20), residues: 1458 helix: 0.40 (0.33), residues: 285 sheet: -3.16 (0.34), residues: 201 loop : -4.48 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 405 HIS 0.003 0.001 HIS A 395 PHE 0.018 0.001 PHE C 208 TYR 0.039 0.001 TYR B 212 ARG 0.019 0.001 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2706.54 seconds wall clock time: 51 minutes 10.52 seconds (3070.52 seconds total)