Starting phenix.real_space_refine on Thu Feb 15 04:47:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tai_25775/02_2024/7tai_25775_updated.pdb" } resolution = 3.2 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= 0.006 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 3 7.16 5 P 18 5.49 5 S 30 5.16 5 C 7350 2.51 5 N 1812 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 296": "OE1" <-> "OE2" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 425": "NH1" <-> "NH2" Residue "C PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11109 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3454 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Chain: "A" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3454 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Chain: "C" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3454 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Chain: "B" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'CLR': 2, 'FAD': 1, 'HEM': 1, 'LBN': 1, 'NAP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'CLR': 2, 'FAD': 1, 'HEM': 1, 'LBN': 1, 'NAP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 249 Unusual residues: {'CLR': 2, 'FAD': 1, 'HEM': 1, 'LBN': 1, 'NAP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 6.82, per 1000 atoms: 0.61 Number of scatterers: 11109 At special positions: 0 Unit cell: (95.141, 93.003, 101.555, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 3 26.01 S 30 16.00 P 18 15.00 O 1896 8.00 N 1812 7.00 C 7350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 2.1 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 6 sheets defined 57.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 63 through 66 No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.818A pdb=" N LEU B 83 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 85' Processing helix chain 'B' and resid 95 through 101 removed outlier: 4.709A pdb=" N THR B 99 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 198 through 206 Proline residue: B 205 - end of helix Processing helix chain 'B' and resid 212 through 234 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 259 through 284 removed outlier: 3.624A pdb=" N ALA B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY B 274 " --> pdb=" O VAL B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 302 through 322 Processing helix chain 'B' and resid 351 through 378 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 388 through 418 removed outlier: 3.897A pdb=" N TYR B 413 " --> pdb=" O HIS B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 450 removed outlier: 3.686A pdb=" N ALA B 435 " --> pdb=" O ASN B 431 " (cutoff:3.500A) Proline residue: B 439 - end of helix Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.652A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.818A pdb=" N LEU A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 85' Processing helix chain 'A' and resid 95 through 101 removed outlier: 4.709A pdb=" N THR A 99 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 198 through 206 Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 212 through 234 Processing helix chain 'A' and resid 236 through 239 No H-bonds generated for 'chain 'A' and resid 236 through 239' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 259 through 284 removed outlier: 3.625A pdb=" N ALA A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 351 through 378 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.897A pdb=" N TYR A 413 " --> pdb=" O HIS A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.686A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.651A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 51 Processing helix chain 'C' and resid 63 through 66 No H-bonds generated for 'chain 'C' and resid 63 through 66' Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.817A pdb=" N LEU C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 85' Processing helix chain 'C' and resid 95 through 101 removed outlier: 4.709A pdb=" N THR C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 172 through 184 Processing helix chain 'C' and resid 198 through 206 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 212 through 234 Processing helix chain 'C' and resid 236 through 239 No H-bonds generated for 'chain 'C' and resid 236 through 239' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 259 through 284 removed outlier: 3.625A pdb=" N ALA C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 302 through 322 Processing helix chain 'C' and resid 351 through 378 Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 388 through 418 removed outlier: 3.897A pdb=" N TYR C 413 " --> pdb=" O HIS C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 450 removed outlier: 3.686A pdb=" N ALA C 435 " --> pdb=" O ASN C 431 " (cutoff:3.500A) Proline residue: C 439 - end of helix Processing helix chain 'C' and resid 452 through 462 removed outlier: 3.651A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 141 through 144 removed outlier: 4.925A pdb=" N ILE B 88 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS B 55 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL B 35 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 57 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 75 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 164 through 167 removed outlier: 5.893A pdb=" N ILE B 188 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 167 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE B 190 " --> pdb=" O ILE B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 removed outlier: 4.925A pdb=" N ILE A 88 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS A 55 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL A 35 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 57 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP A 75 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 164 through 167 removed outlier: 5.893A pdb=" N ILE A 188 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE A 167 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 190 " --> pdb=" O ILE A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 141 through 144 removed outlier: 4.925A pdb=" N ILE C 88 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N HIS C 55 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL C 35 " --> pdb=" O HIS C 55 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL C 57 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP C 75 " --> pdb=" O ILE C 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 164 through 167 removed outlier: 5.892A pdb=" N ILE C 188 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE C 167 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE C 190 " --> pdb=" O ILE C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 498 hydrogen bonds defined for protein. 1467 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: 3.13 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3473 1.37 - 1.54: 7830 1.54 - 1.71: 88 1.71 - 1.88: 45 1.88 - 2.05: 12 Bond restraints: 11448 Sorted by residual: bond pdb=" O2B NAP B 503 " pdb=" P2B NAP B 503 " ideal model delta sigma weight residual 1.736 1.594 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O2B NAP A 503 " pdb=" P2B NAP A 503 " ideal model delta sigma weight residual 1.736 1.594 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" O2B NAP C 503 " pdb=" P2B NAP C 503 " ideal model delta sigma weight residual 1.736 1.595 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" O3P FAD C 501 " pdb=" P FAD C 501 " ideal model delta sigma weight residual 1.660 1.590 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.590 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 11443 not shown) Histogram of bond angle deviations from ideal: 88.96 - 105.86: 301 105.86 - 122.77: 14393 122.77 - 139.67: 966 139.67 - 156.57: 0 156.57 - 173.47: 6 Bond angle restraints: 15666 Sorted by residual: angle pdb=" C2B NAP C 503 " pdb=" O2B NAP C 503 " pdb=" P2B NAP C 503 " ideal model delta sigma weight residual 117.19 128.37 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" C2B NAP B 503 " pdb=" O2B NAP B 503 " pdb=" P2B NAP B 503 " ideal model delta sigma weight residual 117.19 128.35 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" C2B NAP A 503 " pdb=" O2B NAP A 503 " pdb=" P2B NAP A 503 " ideal model delta sigma weight residual 117.19 128.34 -11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1 LBN C 504 " pdb=" P1 LBN C 504 " pdb=" O2 LBN C 504 " ideal model delta sigma weight residual 93.45 104.06 -10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O1 LBN B 504 " pdb=" P1 LBN B 504 " pdb=" O2 LBN B 504 " ideal model delta sigma weight residual 93.45 104.06 -10.61 3.00e+00 1.11e-01 1.25e+01 ... (remaining 15661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.05: 6786 31.05 - 62.10: 312 62.10 - 93.15: 30 93.15 - 124.20: 27 124.20 - 155.24: 6 Dihedral angle restraints: 7161 sinusoidal: 3402 harmonic: 3759 Sorted by residual: dihedral pdb=" CA ILE B 252 " pdb=" C ILE B 252 " pdb=" N GLU B 253 " pdb=" CA GLU B 253 " ideal model delta harmonic sigma weight residual 180.00 147.76 32.24 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA ILE A 252 " pdb=" C ILE A 252 " pdb=" N GLU A 253 " pdb=" CA GLU A 253 " ideal model delta harmonic sigma weight residual 180.00 147.77 32.23 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ILE C 252 " pdb=" C ILE C 252 " pdb=" N GLU C 253 " pdb=" CA GLU C 253 " ideal model delta harmonic sigma weight residual 180.00 147.79 32.21 0 5.00e+00 4.00e-02 4.15e+01 ... (remaining 7158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1349 0.053 - 0.106: 299 0.106 - 0.159: 71 0.159 - 0.211: 9 0.211 - 0.264: 9 Chirality restraints: 1737 Sorted by residual: chirality pdb=" C2 LBN C 504 " pdb=" C1 LBN C 504 " pdb=" C3 LBN C 504 " pdb=" O7 LBN C 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2 LBN B 504 " pdb=" C1 LBN B 504 " pdb=" C3 LBN B 504 " pdb=" O7 LBN B 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2 LBN A 504 " pdb=" C1 LBN A 504 " pdb=" C3 LBN A 504 " pdb=" O7 LBN A 504 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1734 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD A 501 " -0.013 2.00e-02 2.50e+03 1.71e-02 1.39e+01 pdb=" C10 FAD A 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 FAD A 501 " 0.003 2.00e-02 2.50e+03 pdb=" C4 FAD A 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4X FAD A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5X FAD A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FAD A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FAD A 501 " 0.006 2.00e-02 2.50e+03 pdb=" C7M FAD A 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 FAD A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C8M FAD A 501 " -0.043 2.00e-02 2.50e+03 pdb=" C9 FAD A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C9A FAD A 501 " 0.010 2.00e-02 2.50e+03 pdb=" N1 FAD A 501 " 0.027 2.00e-02 2.50e+03 pdb=" N10 FAD A 501 " 0.013 2.00e-02 2.50e+03 pdb=" N3 FAD A 501 " -0.015 2.00e-02 2.50e+03 pdb=" N5 FAD A 501 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FAD A 501 " -0.013 2.00e-02 2.50e+03 pdb=" O4 FAD A 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD B 501 " -0.013 2.00e-02 2.50e+03 1.70e-02 1.37e+01 pdb=" C10 FAD B 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 FAD B 501 " 0.004 2.00e-02 2.50e+03 pdb=" C4 FAD B 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4X FAD B 501 " 0.008 2.00e-02 2.50e+03 pdb=" C5X FAD B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FAD B 501 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FAD B 501 " 0.006 2.00e-02 2.50e+03 pdb=" C7M FAD B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C8 FAD B 501 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FAD B 501 " -0.043 2.00e-02 2.50e+03 pdb=" C9 FAD B 501 " -0.000 2.00e-02 2.50e+03 pdb=" C9A FAD B 501 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FAD B 501 " 0.027 2.00e-02 2.50e+03 pdb=" N10 FAD B 501 " 0.013 2.00e-02 2.50e+03 pdb=" N3 FAD B 501 " -0.015 2.00e-02 2.50e+03 pdb=" N5 FAD B 501 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FAD B 501 " -0.013 2.00e-02 2.50e+03 pdb=" O4 FAD B 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 501 " 0.013 2.00e-02 2.50e+03 1.69e-02 1.36e+01 pdb=" C10 FAD C 501 " -0.020 2.00e-02 2.50e+03 pdb=" C2 FAD C 501 " -0.003 2.00e-02 2.50e+03 pdb=" C4 FAD C 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4X FAD C 501 " -0.008 2.00e-02 2.50e+03 pdb=" C5X FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" C6 FAD C 501 " -0.015 2.00e-02 2.50e+03 pdb=" C7 FAD C 501 " -0.007 2.00e-02 2.50e+03 pdb=" C7M FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C8 FAD C 501 " 0.006 2.00e-02 2.50e+03 pdb=" C8M FAD C 501 " 0.043 2.00e-02 2.50e+03 pdb=" C9 FAD C 501 " 0.000 2.00e-02 2.50e+03 pdb=" C9A FAD C 501 " -0.009 2.00e-02 2.50e+03 pdb=" N1 FAD C 501 " -0.027 2.00e-02 2.50e+03 pdb=" N10 FAD C 501 " -0.012 2.00e-02 2.50e+03 pdb=" N3 FAD C 501 " 0.015 2.00e-02 2.50e+03 pdb=" N5 FAD C 501 " -0.008 2.00e-02 2.50e+03 pdb=" O2 FAD C 501 " 0.012 2.00e-02 2.50e+03 pdb=" O4 FAD C 501 " 0.030 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 156 2.65 - 3.21: 10373 3.21 - 3.77: 17425 3.77 - 4.34: 24817 4.34 - 4.90: 40071 Nonbonded interactions: 92842 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD1 ASP B 115 " model vdw 2.087 2.440 nonbonded pdb=" OH TYR C 98 " pdb=" OD1 ASP C 115 " model vdw 2.087 2.440 nonbonded pdb=" OH TYR A 98 " pdb=" OD1 ASP A 115 " model vdw 2.087 2.440 nonbonded pdb=" OG SER B 381 " pdb=" OG SER A 381 " model vdw 2.120 2.440 nonbonded pdb=" OG SER A 381 " pdb=" OG SER C 381 " model vdw 2.126 2.440 ... (remaining 92837 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.720 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 34.000 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.006 0.142 11448 Z= 0.416 Angle : 0.857 11.179 15666 Z= 0.427 Chirality : 0.050 0.264 1737 Planarity : 0.006 0.062 1827 Dihedral : 19.148 155.244 4731 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.06 % Allowed : 0.62 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.97 (0.25), residues: 1260 helix: 1.18 (0.19), residues: 747 sheet: 0.24 (0.55), residues: 108 loop : -0.08 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.005 0.001 HIS B 79 PHE 0.021 0.002 PHE A 69 TYR 0.023 0.002 TYR B 271 ARG 0.009 0.001 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.235 Fit side-chains REVERT: B 65 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7112 (t80) REVERT: B 415 TRP cc_start: 0.6647 (t60) cc_final: 0.6210 (t60) REVERT: B 463 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7686 (ttpt) REVERT: A 325 MET cc_start: 0.5738 (mmt) cc_final: 0.3469 (ptp) REVERT: A 415 TRP cc_start: 0.6482 (t60) cc_final: 0.6104 (t60) REVERT: C 80 GLU cc_start: 0.7891 (mp0) cc_final: 0.7661 (mp0) REVERT: C 325 MET cc_start: 0.5514 (mmt) cc_final: 0.4311 (ptm) outliers start: 12 outliers final: 1 residues processed: 110 average time/residue: 0.2600 time to fit residues: 40.3530 Evaluate side-chains 86 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 463 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11448 Z= 0.200 Angle : 0.615 7.596 15666 Z= 0.292 Chirality : 0.043 0.167 1737 Planarity : 0.005 0.059 1827 Dihedral : 15.398 131.168 2302 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.80 % Allowed : 7.07 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1260 helix: 1.55 (0.19), residues: 750 sheet: 0.92 (0.52), residues: 120 loop : -0.32 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 355 HIS 0.003 0.001 HIS B 316 PHE 0.021 0.001 PHE A 65 TYR 0.039 0.002 TYR C 360 ARG 0.006 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.360 Fit side-chains REVERT: B 65 PHE cc_start: 0.7271 (t80) cc_final: 0.7050 (t80) REVERT: B 81 ASP cc_start: 0.8551 (t0) cc_final: 0.8216 (t0) REVERT: A 81 ASP cc_start: 0.8626 (t0) cc_final: 0.8355 (t0) REVERT: C 80 GLU cc_start: 0.7868 (mp0) cc_final: 0.7614 (mp0) REVERT: C 325 MET cc_start: 0.5872 (mmt) cc_final: 0.4364 (ptp) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.2282 time to fit residues: 33.0176 Evaluate side-chains 93 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 354 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11448 Z= 0.192 Angle : 0.547 7.257 15666 Z= 0.263 Chirality : 0.042 0.130 1737 Planarity : 0.005 0.058 1827 Dihedral : 14.060 127.784 2292 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.41 % Allowed : 7.96 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1260 helix: 1.76 (0.20), residues: 732 sheet: 1.08 (0.53), residues: 120 loop : -0.33 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 PHE 0.009 0.001 PHE A 65 TYR 0.029 0.002 TYR C 360 ARG 0.002 0.000 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.212 Fit side-chains REVERT: B 65 PHE cc_start: 0.7381 (t80) cc_final: 0.7085 (t80) REVERT: B 81 ASP cc_start: 0.8637 (t0) cc_final: 0.8218 (t0) REVERT: A 81 ASP cc_start: 0.8737 (t0) cc_final: 0.8360 (t0) REVERT: C 81 ASP cc_start: 0.8739 (t0) cc_final: 0.8231 (t0) REVERT: C 325 MET cc_start: 0.5792 (mmt) cc_final: 0.4351 (ptp) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.2383 time to fit residues: 37.6831 Evaluate side-chains 102 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11448 Z= 0.188 Angle : 0.537 7.461 15666 Z= 0.257 Chirality : 0.042 0.134 1737 Planarity : 0.005 0.057 1827 Dihedral : 13.719 124.256 2292 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.50 % Allowed : 9.99 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1260 helix: 1.79 (0.20), residues: 735 sheet: 1.20 (0.53), residues: 120 loop : -0.17 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 355 HIS 0.003 0.001 HIS C 409 PHE 0.014 0.001 PHE A 65 TYR 0.027 0.002 TYR C 360 ARG 0.006 0.000 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7419 (t80) cc_final: 0.7121 (t80) REVERT: B 81 ASP cc_start: 0.8701 (t0) cc_final: 0.8293 (t0) REVERT: A 81 ASP cc_start: 0.8729 (t0) cc_final: 0.8311 (t0) REVERT: C 81 ASP cc_start: 0.8779 (t0) cc_final: 0.8224 (t0) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.2215 time to fit residues: 35.8042 Evaluate side-chains 103 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 417 ARG Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 30 optimal weight: 9.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11448 Z= 0.162 Angle : 0.518 6.764 15666 Z= 0.249 Chirality : 0.042 0.129 1737 Planarity : 0.004 0.057 1827 Dihedral : 13.333 121.801 2292 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.50 % Allowed : 11.05 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1260 helix: 1.88 (0.20), residues: 738 sheet: 1.45 (0.55), residues: 120 loop : -0.13 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 355 HIS 0.002 0.001 HIS A 409 PHE 0.015 0.001 PHE C 65 TYR 0.024 0.001 TYR C 360 ARG 0.003 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7436 (t80) cc_final: 0.7091 (t80) REVERT: B 81 ASP cc_start: 0.8725 (t0) cc_final: 0.8291 (t0) REVERT: B 275 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 81 ASP cc_start: 0.8773 (t0) cc_final: 0.8336 (t0) REVERT: A 325 MET cc_start: 0.5474 (mmt) cc_final: 0.3888 (ptp) REVERT: C 81 ASP cc_start: 0.8784 (t0) cc_final: 0.8226 (t0) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.2068 time to fit residues: 34.5353 Evaluate side-chains 107 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 0.0470 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11448 Z= 0.178 Angle : 0.518 7.333 15666 Z= 0.247 Chirality : 0.042 0.131 1737 Planarity : 0.004 0.056 1827 Dihedral : 13.146 119.675 2292 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.50 % Allowed : 11.32 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1260 helix: 1.91 (0.20), residues: 735 sheet: 1.50 (0.54), residues: 120 loop : -0.10 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 355 HIS 0.003 0.001 HIS C 409 PHE 0.011 0.001 PHE A 65 TYR 0.024 0.001 TYR C 427 ARG 0.003 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7442 (t80) cc_final: 0.7108 (t80) REVERT: B 81 ASP cc_start: 0.8724 (t0) cc_final: 0.8268 (t0) REVERT: A 81 ASP cc_start: 0.8797 (t0) cc_final: 0.8337 (t0) REVERT: A 325 MET cc_start: 0.5595 (mmt) cc_final: 0.4229 (ptp) REVERT: C 81 ASP cc_start: 0.8900 (t0) cc_final: 0.8370 (t0) outliers start: 17 outliers final: 14 residues processed: 110 average time/residue: 0.2132 time to fit residues: 35.2926 Evaluate side-chains 108 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 0.0170 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11448 Z= 0.159 Angle : 0.505 6.631 15666 Z= 0.241 Chirality : 0.041 0.130 1737 Planarity : 0.004 0.056 1827 Dihedral : 12.912 116.606 2292 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 12.02 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1260 helix: 1.97 (0.20), residues: 738 sheet: 1.57 (0.54), residues: 120 loop : -0.05 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.016 0.001 PHE C 65 TYR 0.024 0.001 TYR C 427 ARG 0.002 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7469 (t80) cc_final: 0.7161 (t80) REVERT: B 81 ASP cc_start: 0.8676 (t0) cc_final: 0.8191 (t0) REVERT: B 275 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 81 ASP cc_start: 0.8808 (t0) cc_final: 0.8315 (t0) REVERT: A 325 MET cc_start: 0.5467 (mmt) cc_final: 0.4247 (ptp) REVERT: C 81 ASP cc_start: 0.8905 (t0) cc_final: 0.8348 (t0) REVERT: C 204 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8802 (tt) REVERT: C 463 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7508 (ttpp) outliers start: 18 outliers final: 14 residues processed: 108 average time/residue: 0.2065 time to fit residues: 33.4080 Evaluate side-chains 111 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 463 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11448 Z= 0.166 Angle : 0.507 6.770 15666 Z= 0.241 Chirality : 0.041 0.131 1737 Planarity : 0.004 0.056 1827 Dihedral : 12.675 114.323 2292 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.59 % Allowed : 12.20 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1260 helix: 1.98 (0.20), residues: 738 sheet: 1.51 (0.53), residues: 120 loop : -0.03 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.011 0.001 PHE A 65 TYR 0.027 0.001 TYR C 427 ARG 0.001 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 1.207 Fit side-chains REVERT: B 65 PHE cc_start: 0.7467 (t80) cc_final: 0.7140 (t80) REVERT: B 81 ASP cc_start: 0.8707 (t0) cc_final: 0.8249 (t0) REVERT: B 275 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 81 ASP cc_start: 0.8836 (t0) cc_final: 0.8333 (t0) REVERT: A 325 MET cc_start: 0.5459 (mmt) cc_final: 0.4394 (ptp) REVERT: C 81 ASP cc_start: 0.8912 (t0) cc_final: 0.8368 (t0) REVERT: C 204 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8800 (tt) REVERT: C 325 MET cc_start: 0.5009 (mmt) cc_final: 0.4201 (ppp) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.2161 time to fit residues: 34.9951 Evaluate side-chains 106 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11448 Z= 0.185 Angle : 0.522 7.286 15666 Z= 0.247 Chirality : 0.042 0.132 1737 Planarity : 0.004 0.055 1827 Dihedral : 12.523 112.013 2292 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.41 % Allowed : 12.38 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1260 helix: 1.94 (0.20), residues: 738 sheet: 1.46 (0.53), residues: 120 loop : -0.03 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.020 0.001 PHE C 65 TYR 0.027 0.001 TYR C 427 ARG 0.002 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7469 (t80) cc_final: 0.7170 (t80) REVERT: B 81 ASP cc_start: 0.8687 (t0) cc_final: 0.8237 (t0) REVERT: B 275 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8428 (mm) REVERT: A 81 ASP cc_start: 0.8839 (t0) cc_final: 0.8311 (t0) REVERT: A 325 MET cc_start: 0.5301 (mmt) cc_final: 0.4253 (ptp) REVERT: C 81 ASP cc_start: 0.8923 (t0) cc_final: 0.8393 (t0) REVERT: C 204 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8809 (tt) REVERT: C 325 MET cc_start: 0.5059 (mmt) cc_final: 0.4172 (ppp) outliers start: 16 outliers final: 14 residues processed: 108 average time/residue: 0.2126 time to fit residues: 34.6035 Evaluate side-chains 111 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11448 Z= 0.208 Angle : 0.535 7.758 15666 Z= 0.252 Chirality : 0.042 0.132 1737 Planarity : 0.004 0.056 1827 Dihedral : 12.453 109.826 2292 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.50 % Allowed : 12.20 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1260 helix: 1.86 (0.20), residues: 738 sheet: 1.41 (0.53), residues: 120 loop : -0.04 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 355 HIS 0.003 0.001 HIS C 409 PHE 0.009 0.001 PHE A 65 TYR 0.037 0.002 TYR B 427 ARG 0.002 0.000 ARG C 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: B 65 PHE cc_start: 0.7460 (t80) cc_final: 0.7188 (t80) REVERT: B 81 ASP cc_start: 0.8706 (t0) cc_final: 0.8227 (t0) REVERT: B 275 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 81 ASP cc_start: 0.8831 (t0) cc_final: 0.8272 (t0) REVERT: A 325 MET cc_start: 0.5510 (mmt) cc_final: 0.4388 (ptp) REVERT: C 81 ASP cc_start: 0.8931 (t0) cc_final: 0.8374 (t0) REVERT: C 204 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8769 (tt) REVERT: C 415 TRP cc_start: 0.6398 (t60) cc_final: 0.5996 (t60) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.2019 time to fit residues: 34.5960 Evaluate side-chains 115 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099189 restraints weight = 14516.262| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.45 r_work: 0.2962 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11448 Z= 0.345 Angle : 0.635 10.265 15666 Z= 0.295 Chirality : 0.044 0.143 1737 Planarity : 0.005 0.055 1827 Dihedral : 13.004 112.102 2292 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.59 % Allowed : 12.11 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1260 helix: 1.53 (0.20), residues: 738 sheet: 1.34 (0.54), residues: 120 loop : -0.17 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 355 HIS 0.006 0.001 HIS C 79 PHE 0.015 0.001 PHE C 65 TYR 0.035 0.002 TYR B 427 ARG 0.004 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.53 seconds wall clock time: 39 minutes 45.68 seconds (2385.68 seconds total)