Starting phenix.real_space_refine on Sat Mar 16 05:55:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_2024/7xym_33522_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_2024/7xym_33522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_2024/7xym_33522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_2024/7xym_33522_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xym_33522/03_2024/7xym_33522_neut.pdb" } 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 Residue "A GLU 218": "OE1" <-> "OE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "C GLU 430": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11436 Number of models: 1 Model: "" Number of chains: 3 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 Chain: "B" 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 Chain: "C" 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 Time building chain proxies: 6.11, per 1000 atoms: 0.53 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 B 76 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 284 " distance=2.06 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 284 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.16 Conformation dependent library (CDL) restraints added in 2.1 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: 0.95 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: 2.79 Time building geometry restraints manager: 4.60 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: 95.59 - 104.10: 174 104.10 - 112.62: 5950 112.62 - 121.14: 6146 121.14 - 129.66: 3540 129.66 - 138.17: 132 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 2.440 nonbonded pdb=" OG SER A 74 " pdb=" O ASN A 158 " model vdw 1.417 2.440 ... (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 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: 6.160 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: 22.950 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.960 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.790 ------------------------------------------------------------------------------- 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= 0.600 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 fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 1.455 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: 0.2017 time to fit residues: 28.7878 Evaluate side-chains 68 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 0.0770 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11727 Z= 0.278 Angle : 1.069 11.809 15942 Z= 0.558 Chirality : 0.055 0.288 1731 Planarity : 0.007 0.083 2049 Dihedral : 9.117 47.352 1594 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 24.88 Ramachandran Plot: Outliers : 2.61 % Allowed : 23.73 % Favored : 73.66 % Rotamer: Outliers : 1.13 % Allowed : 10.92 % Favored : 87.94 % 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: -5.50 (0.18), residues: 1458 helix: -1.75 (0.28), residues: 297 sheet: -3.25 (0.36), residues: 183 loop : -4.72 (0.15), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 432 HIS 0.004 0.001 HIS C 65 PHE 0.015 0.002 PHE A 208 TYR 0.032 0.002 TYR C 212 ARG 0.003 0.000 ARG C 359 *********************** 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 88 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.299 Fit side-chains REVERT: A 121 TRP cc_start: 0.5593 (p-90) cc_final: 0.5272 (p-90) REVERT: A 189 ASN cc_start: 0.5710 (m110) cc_final: 0.5496 (m110) REVERT: A 481 LEU cc_start: 0.6345 (mt) cc_final: 0.5337 (mt) REVERT: B 121 TRP cc_start: 0.5675 (p-90) cc_final: 0.5336 (p-90) REVERT: B 266 ASN cc_start: 0.7485 (OUTLIER) cc_final: 0.7044 (p0) REVERT: C 121 TRP cc_start: 0.5405 (p-90) cc_final: 0.5058 (p-90) outliers start: 14 outliers final: 1 residues processed: 83 average time/residue: 0.1961 time to fit residues: 25.6127 Evaluate side-chains 62 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain C residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 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 A 266 ASN A 293 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN 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 266 ASN C 413 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11727 Z= 0.295 Angle : 1.014 11.747 15942 Z= 0.530 Chirality : 0.054 0.313 1731 Planarity : 0.007 0.066 2049 Dihedral : 8.804 44.374 1590 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 25.51 Ramachandran Plot: Outliers : 2.33 % Allowed : 26.47 % Favored : 71.19 % Rotamer: Outliers : 2.67 % Allowed : 12.94 % Favored : 84.39 % 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: -5.17 (0.19), residues: 1458 helix: -1.16 (0.31), residues: 297 sheet: -3.18 (0.36), residues: 183 loop : -4.59 (0.15), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 405 HIS 0.003 0.001 HIS C 337 PHE 0.015 0.002 PHE A 208 TYR 0.027 0.002 TYR A 212 ARG 0.004 0.001 ARG B 69 *********************** 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 93 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 60 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.5651 (p-90) cc_final: 0.5234 (p-90) REVERT: B 121 TRP cc_start: 0.5658 (p-90) cc_final: 0.5155 (p-90) REVERT: B 266 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7251 (p0) REVERT: C 121 TRP cc_start: 0.5543 (p-90) cc_final: 0.5049 (p-90) outliers start: 33 outliers final: 9 residues processed: 92 average time/residue: 0.1818 time to fit residues: 27.0772 Evaluate side-chains 64 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain C residue 34 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 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: 0.5980 chunk 67 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN ** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 293 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: 0.7282 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11727 Z= 0.294 Angle : 0.986 11.349 15942 Z= 0.513 Chirality : 0.053 0.289 1731 Planarity : 0.006 0.055 2049 Dihedral : 8.631 39.149 1590 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 2.47 % Allowed : 24.42 % Favored : 73.11 % Rotamer: Outliers : 3.32 % Allowed : 17.31 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.08 (0.19), residues: 1458 helix: -1.08 (0.31), residues: 303 sheet: -3.13 (0.35), residues: 183 loop : -4.54 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 405 HIS 0.003 0.001 HIS B 337 PHE 0.016 0.002 PHE C 208 TYR 0.031 0.002 TYR C 212 ARG 0.002 0.000 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 106 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 65 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.5769 (p-90) cc_final: 0.5215 (p-90) REVERT: B 266 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7267 (p0) REVERT: C 121 TRP cc_start: 0.5595 (p-90) cc_final: 0.5067 (p-90) outliers start: 41 outliers final: 10 residues processed: 101 average time/residue: 0.2241 time to fit residues: 34.2327 Evaluate side-chains 71 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 266 ASN 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 415 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11727 Z= 0.291 Angle : 0.985 12.992 15942 Z= 0.510 Chirality : 0.054 0.365 1731 Planarity : 0.006 0.049 2049 Dihedral : 8.548 39.715 1590 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 2.33 % Allowed : 25.51 % Favored : 72.15 % Rotamer: Outliers : 4.05 % Allowed : 18.04 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.05 (0.19), residues: 1458 helix: -0.90 (0.32), residues: 303 sheet: -3.18 (0.35), residues: 183 loop : -4.58 (0.15), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 405 HIS 0.002 0.001 HIS B 337 PHE 0.024 0.002 PHE B 428 TYR 0.034 0.002 TYR B 212 ARG 0.003 0.000 ARG A 404 *********************** 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 112 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 62 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TRP cc_start: 0.6133 (OUTLIER) cc_final: 0.5781 (m100) REVERT: C 121 TRP cc_start: 0.5613 (p-90) cc_final: 0.5072 (p-90) outliers start: 50 outliers final: 18 residues processed: 105 average time/residue: 0.1830 time to fit residues: 30.2670 Evaluate side-chains 76 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 212 TYR Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 212 TYR 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 98 THR 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 415 PHE Chi-restraints excluded: chain C residue 453 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 266 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3415 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= 0.259 Angle : 0.963 11.280 15942 Z= 0.499 Chirality : 0.053 0.291 1731 Planarity : 0.006 0.046 2049 Dihedral : 8.518 39.917 1590 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 2.13 % Allowed : 24.49 % Favored : 73.39 % Rotamer: Outliers : 3.32 % Allowed : 19.34 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 2.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.19), residues: 1458 helix: -0.74 (0.32), residues: 303 sheet: -3.18 (0.35), residues: 183 loop : -4.56 (0.15), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 405 HIS 0.002 0.001 HIS B 337 PHE 0.021 0.001 PHE C 428 TYR 0.035 0.001 TYR B 212 ARG 0.003 0.000 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 109 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 68 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TRP cc_start: 0.5994 (OUTLIER) cc_final: 0.5215 (m100) REVERT: B 405 TRP cc_start: 0.6149 (OUTLIER) cc_final: 0.5811 (m100) REVERT: C 180 LEU cc_start: 0.8558 (mt) cc_final: 0.8340 (mp) REVERT: C 405 TRP cc_start: 0.5947 (OUTLIER) cc_final: 0.5414 (m100) outliers start: 41 outliers final: 23 residues processed: 101 average time/residue: 0.2143 time to fit residues: 33.7778 Evaluate side-chains 89 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 212 TYR Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 405 TRP Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 481 LEU 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 405 TRP 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 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 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: 0.7241 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 11727 Z= 0.277 Angle : 0.997 18.800 15942 Z= 0.513 Chirality : 0.054 0.400 1731 Planarity : 0.006 0.047 2049 Dihedral : 8.485 40.100 1590 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 1.85 % Allowed : 26.20 % Favored : 71.95 % Rotamer: Outliers : 2.67 % Allowed : 20.71 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 1.79 % 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: -0.47 (0.33), residues: 297 sheet: -3.22 (0.34), residues: 183 loop : -4.57 (0.15), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 405 HIS 0.002 0.001 HIS C 407 PHE 0.021 0.002 PHE B 428 TYR 0.037 0.001 TYR A 212 ARG 0.004 0.000 ARG A 404 *********************** 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 102 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 69 time to evaluate : 1.435 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: 0.5830 (OUTLIER) cc_final: 0.5585 (m100) outliers start: 33 outliers final: 22 residues processed: 97 average time/residue: 0.1975 time to fit residues: 30.1303 Evaluate side-chains 88 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain A residue 481 LEU 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 170 ILE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 481 LEU 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 453 PHE Chi-restraints excluded: chain C residue 481 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 11727 Z= 0.275 Angle : 0.994 17.881 15942 Z= 0.511 Chirality : 0.054 0.418 1731 Planarity : 0.006 0.048 2049 Dihedral : 8.421 39.846 1590 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 1.99 % Allowed : 25.10 % Favored : 72.91 % Rotamer: Outliers : 2.99 % Allowed : 20.63 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.86 % 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: -4.83 (0.20), residues: 1458 helix: -0.49 (0.32), residues: 300 sheet: -2.86 (0.35), residues: 204 loop : -4.55 (0.15), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 405 HIS 0.002 0.001 HIS A 337 PHE 0.018 0.002 PHE C 208 TYR 0.039 0.002 TYR B 212 ARG 0.009 0.000 ARG A 404 *********************** 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 104 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 67 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 266 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7495 (p0) REVERT: C 404 ARG cc_start: 0.5308 (mpt180) cc_final: 0.5073 (mtm180) outliers start: 37 outliers final: 20 residues processed: 98 average time/residue: 0.1943 time to fit residues: 30.1837 Evaluate side-chains 86 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 481 LEU 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 201 THR Chi-restraints excluded: chain B residue 212 TYR 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 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 266 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 481 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 129 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.0970 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11727 Z= 0.242 Angle : 0.977 17.208 15942 Z= 0.503 Chirality : 0.053 0.308 1731 Planarity : 0.005 0.045 2049 Dihedral : 8.302 40.307 1590 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 1.92 % Allowed : 25.79 % Favored : 72.29 % Rotamer: Outliers : 2.18 % Allowed : 21.36 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 1.79 % 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: -4.66 (0.20), residues: 1458 helix: 0.22 (0.34), residues: 279 sheet: -2.74 (0.36), residues: 204 loop : -4.57 (0.15), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 405 HIS 0.002 0.001 HIS B 247 PHE 0.019 0.001 PHE C 208 TYR 0.038 0.001 TYR A 212 ARG 0.008 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 101 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 1.320 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 405 TRP cc_start: 0.5976 (OUTLIER) cc_final: 0.5708 (m100) REVERT: C 68 TYR cc_start: 0.2554 (OUTLIER) cc_final: 0.1937 (t80) REVERT: C 266 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7375 (p0) outliers start: 27 outliers final: 15 residues processed: 97 average time/residue: 0.1988 time to fit residues: 30.2157 Evaluate side-chains 81 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 212 TYR Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 405 TRP Chi-restraints excluded: chain B residue 34 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 68 TYR 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 266 ASN Chi-restraints excluded: chain C residue 415 PHE Chi-restraints excluded: chain C residue 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 11727 Z= 0.272 Angle : 0.990 15.748 15942 Z= 0.508 Chirality : 0.055 0.388 1731 Planarity : 0.006 0.082 2049 Dihedral : 8.332 42.139 1590 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 1.78 % Allowed : 25.31 % Favored : 72.91 % Rotamer: Outliers : 1.62 % Allowed : 22.49 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 1.79 % 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: -4.63 (0.20), residues: 1458 helix: 0.28 (0.33), residues: 276 sheet: -2.66 (0.36), residues: 204 loop : -4.56 (0.15), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 405 HIS 0.002 0.001 HIS B 247 PHE 0.018 0.002 PHE C 208 TYR 0.039 0.002 TYR A 212 ARG 0.019 0.001 ARG A 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 81 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 TRP cc_start: 0.6042 (OUTLIER) cc_final: 0.5394 (m100) REVERT: B 68 TYR cc_start: 0.3122 (OUTLIER) cc_final: 0.1340 (t80) REVERT: C 266 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7471 (p0) outliers start: 20 outliers final: 12 residues processed: 79 average time/residue: 0.2120 time to fit residues: 25.7644 Evaluate side-chains 73 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 212 TYR 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 C residue 34 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 266 ASN Chi-restraints excluded: chain C residue 481 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 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 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 = 0.4517 r_free = 0.4517 target = 0.183242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119069 restraints weight = 20850.973| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.16 r_work: 0.3537 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 11727 Z= 0.338 Angle : 1.035 18.699 15942 Z= 0.529 Chirality : 0.057 0.446 1731 Planarity : 0.007 0.114 2049 Dihedral : 8.408 38.668 1590 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 1.71 % Allowed : 27.64 % Favored : 70.64 % Rotamer: Outliers : 1.94 % Allowed : 22.17 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 1.86 % 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: -4.84 (0.19), residues: 1458 helix: -0.26 (0.30), residues: 300 sheet: -3.08 (0.36), residues: 183 loop : -4.60 (0.15), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 451 HIS 0.003 0.001 HIS A 65 PHE 0.017 0.002 PHE C 208 TYR 0.041 0.002 TYR A 212 ARG 0.025 0.001 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.35 seconds wall clock time: 52 minutes 42.90 seconds (3162.90 seconds total)