Starting phenix.real_space_refine on Sat Dec 9 18:40:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a6e_3062/12_2023/5a6e_3062_trim.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 3823 2.51 5 N 1024 2.21 5 O 1101 1.98 5 H 5102 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 438": "NH1" <-> "NH2" Residue "C ARG 438": not complete - not flipped Residue "C ARG 438": not complete - not flipped Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 443": not complete - not flipped Residue "C ARG 443": not complete - not flipped Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 534": "NH1" <-> "NH2" Residue "C ARG 534": not complete - not flipped Residue "C ARG 534": not complete - not flipped Residue "C ARG 578": "NH1" <-> "NH2" Residue "C ARG 578": not complete - not flipped Residue "C ARG 578": not complete - not flipped Residue "C ARG 579": "NH1" <-> "NH2" Residue "C ARG 579": not complete - not flipped Residue "C ARG 579": not complete - not flipped Residue "C ARG 592": "NH1" <-> "NH2" Residue "C ARG 592": not complete - not flipped Residue "C ARG 592": not complete - not flipped Residue "C ARG 883": "NH1" <-> "NH2" Residue "C ARG 883": not complete - not flipped Residue "C ARG 883": not complete - not flipped Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11093 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 695 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'TRANS': 138} Chain breaks: 4 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 139 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1516 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 8667 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 8653 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 540, 8653 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 8731 Chain: "D" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 215 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'UNK:plan-1': 43} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 9.03, per 1000 atoms: 0.81 Number of scatterers: 11093 At special positions: 0 Unit cell: (83.2, 108.16, 132.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 1101 8.00 N 1024 7.00 C 3823 6.00 H 5102 1.00 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=0, symmetry=0 Time building additional restraints: 8.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 6 sheets defined 71.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.547A pdb=" N UNK A 74 " --> pdb=" O UNK A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 116 removed outlier: 3.694A pdb=" N UNK A 93 " --> pdb=" O UNK A 89 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N UNK A 116 " --> pdb=" O UNK A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 137 removed outlier: 3.918A pdb=" N UNK A 125 " --> pdb=" O UNK A 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N UNK A 137 " --> pdb=" O UNK A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 167 removed outlier: 3.672A pdb=" N UNK A 152 " --> pdb=" O UNK A 148 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 179 through 199 removed outlier: 4.072A pdb=" N UNK A 183 " --> pdb=" O UNK A 179 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N UNK A 185 " --> pdb=" O UNK A 181 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK A 196 " --> pdb=" O UNK A 192 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N UNK A 199 " --> pdb=" O UNK A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 234 removed outlier: 3.572A pdb=" N UNK A 216 " --> pdb=" O UNK A 212 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N UNK A 217 " --> pdb=" O UNK A 213 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N UNK A 218 " --> pdb=" O UNK A 214 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 276 removed outlier: 4.000A pdb=" N HIS B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 271 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 274 " --> pdb=" O HIS B 270 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 292 Processing helix chain 'B' and resid 303 through 337 removed outlier: 3.554A pdb=" N GLN B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.566A pdb=" N LEU C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 3.674A pdb=" N VAL C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 394 through 399' Processing helix chain 'C' and resid 417 through 424 removed outlier: 3.879A pdb=" N LEU C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 4.059A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP C 447 " --> pdb=" O ARG C 443 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.894A pdb=" N PHE C 477 " --> pdb=" O GLU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 Processing helix chain 'C' and resid 504 through 513 removed outlier: 3.572A pdb=" N LEU C 508 " --> pdb=" O ALA C 504 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.529A pdb=" N CYS C 535 " --> pdb=" O MET C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 567 removed outlier: 3.950A pdb=" N ALA C 562 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 563 " --> pdb=" O PHE C 559 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS C 567 " --> pdb=" O ALA C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 4.143A pdb=" N TYR C 788 " --> pdb=" O GLY C 784 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 789 " --> pdb=" O ASN C 785 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 792 " --> pdb=" O TYR C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.806A pdb=" N LEU C 820 " --> pdb=" O GLU C 816 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 821 " --> pdb=" O HIS C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 838 through 844 Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'C' and resid 871 through 885 removed outlier: 3.689A pdb=" N ILE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN C 877 " --> pdb=" O LYS C 873 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 880 " --> pdb=" O VAL C 876 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 882 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 883 " --> pdb=" O GLN C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 903 removed outlier: 4.402A pdb=" N ARG C 901 " --> pdb=" O SER C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 924 removed outlier: 4.603A pdb=" N SER C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 918 " --> pdb=" O ALA C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 939 Processing helix chain 'C' and resid 945 through 956 removed outlier: 3.784A pdb=" N ASP C 949 " --> pdb=" O ILE C 945 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU C 951 " --> pdb=" O MET C 947 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 953 " --> pdb=" O ASP C 949 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.569A pdb=" N ILE C 964 " --> pdb=" O TYR C 960 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 965 " --> pdb=" O MET C 961 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG C 966 " --> pdb=" O ILE C 962 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 967 " --> pdb=" O THR C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 992 Processing helix chain 'C' and resid 995 through 1003 removed outlier: 3.641A pdb=" N LYS C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1098 removed outlier: 3.764A pdb=" N UNK D1088 " --> pdb=" O UNK D1084 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK D1097 " --> pdb=" O UNK D1093 " (cutoff:3.500A) Processing helix chain 'D' and resid 1100 through 1113 removed outlier: 3.655A pdb=" N UNK D1110 " --> pdb=" O UNK D1106 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N UNK D1111 " --> pdb=" O UNK D1107 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N UNK D1112 " --> pdb=" O UNK D1108 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N UNK D1113 " --> pdb=" O UNK D1109 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'C' and resid 408 through 412 removed outlier: 3.598A pdb=" N CYS C 387 " --> pdb=" O LEU C 411 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 431 " --> pdb=" O HIS C 352 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'C' and resid 467 through 470 removed outlier: 3.589A pdb=" N VAL C 468 " --> pdb=" O HIS C 484 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.664A pdb=" N TYR C 603 " --> pdb=" O TYR C 541 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS C 573 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'C' and resid 829 through 833 removed outlier: 3.711A pdb=" N LEU C 811 " --> pdb=" O MET C 832 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 780 " --> pdb=" O LEU C 810 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 777 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 855 " --> pdb=" O ILE C 891 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU C 893 " --> pdb=" O VAL C 855 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 894 " --> pdb=" O PHE C 943 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'C' and resid 979 through 984 removed outlier: 3.637A pdb=" N VAL C1162 " --> pdb=" O MET C 983 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C1009 " --> pdb=" O ILE C1165 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'C' and resid 1012 through 1013 removed outlier: 3.749A pdb=" N LEU C1147 " --> pdb=" O ILE C1013 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 822 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: 3.74 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.28: 6087 1.28 - 1.73: 5030 1.73 - 2.18: 65 2.18 - 2.63: 7 2.63 - 3.07: 7 Bond restraints: 11196 Sorted by residual: bond pdb=" NH2 ARG C 883 " pdb="HH21BARG C 883 " ideal model delta sigma weight residual 0.860 3.073 -2.213 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 579 " pdb="HH21BARG C 579 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 438 " pdb="HH21BARG C 438 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 592 " pdb="HH21BARG C 592 " ideal model delta sigma weight residual 0.860 3.070 -2.210 2.00e-02 2.50e+03 1.22e+04 bond pdb=" NH2 ARG C 578 " pdb="HH21BARG C 578 " ideal model delta sigma weight residual 0.860 3.068 -2.208 2.00e-02 2.50e+03 1.22e+04 ... (remaining 11191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 26.84: 14 26.84 - 53.68: 14 53.68 - 80.53: 0 80.53 - 107.37: 612 107.37 - 134.21: 19223 Bond angle restraints: 19863 Sorted by residual: angle pdb=" NH1 ARG C 443 " pdb=" CZ ARG C 443 " pdb=" NH2 ARG C 443 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 534 " pdb=" CZ ARG C 534 " pdb=" NH2 ARG C 534 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 579 " pdb=" CZ ARG C 579 " pdb=" NH2 ARG C 579 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 883 " pdb=" CZ ARG C 883 " pdb=" NH2 ARG C 883 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 angle pdb=" NH1 ARG C 592 " pdb=" CZ ARG C 592 " pdb=" NH2 ARG C 592 " ideal model delta sigma weight residual 119.30 0.00 119.30 1.30e+00 5.92e-01 8.42e+03 ... (remaining 19858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 5158 35.98 - 71.97: 129 71.97 - 107.95: 1 107.95 - 143.93: 0 143.93 - 179.91: 7 Dihedral angle restraints: 5295 sinusoidal: 2526 harmonic: 2769 Sorted by residual: dihedral pdb=" CD ARG C 592 " pdb=" NE ARG C 592 " pdb=" CZ ARG C 592 " pdb=" NH1 ARG C 592 " ideal model delta sinusoidal sigma weight residual 0.00 -179.91 179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG C 883 " pdb=" NE ARG C 883 " pdb=" CZ ARG C 883 " pdb=" NH1 ARG C 883 " ideal model delta sinusoidal sigma weight residual 0.00 179.88 -179.88 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG C 534 " pdb=" NE ARG C 534 " pdb=" CZ ARG C 534 " pdb=" NH1 ARG C 534 " ideal model delta sinusoidal sigma weight residual 0.00 179.86 -179.86 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 5292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 612 0.036 - 0.072: 241 0.072 - 0.108: 94 0.108 - 0.145: 26 0.145 - 0.181: 10 Chirality restraints: 983 Sorted by residual: chirality pdb=" CA ASN C 785 " pdb=" N ASN C 785 " pdb=" C ASN C 785 " pdb=" CB ASN C 785 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA MET C 828 " pdb=" N MET C 828 " pdb=" C MET C 828 " pdb=" CB MET C 828 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE C1013 " pdb=" N ILE C1013 " pdb=" C ILE C1013 " pdb=" CB ILE C1013 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 980 not shown) Planarity restraints: 1669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 499 " -0.162 2.00e-02 2.50e+03 1.83e-01 5.00e+02 pdb=" CG ASN C 499 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 499 " 0.156 2.00e-02 2.50e+03 pdb=" ND2 ASN C 499 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 499 " 0.269 2.00e-02 2.50e+03 pdb="HD22 ASN C 499 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 529 " 0.147 2.00e-02 2.50e+03 1.65e-01 4.10e+02 pdb=" CD GLN C 529 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN C 529 " -0.144 2.00e-02 2.50e+03 pdb=" NE2 GLN C 529 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN C 529 " -0.246 2.00e-02 2.50e+03 pdb="HE22 GLN C 529 " 0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 336 " -0.143 2.00e-02 2.50e+03 1.60e-01 3.83e+02 pdb=" CD GLN B 336 " 0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 336 " 0.138 2.00e-02 2.50e+03 pdb=" NE2 GLN B 336 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 336 " 0.235 2.00e-02 2.50e+03 pdb="HE22 GLN B 336 " -0.241 2.00e-02 2.50e+03 ... (remaining 1666 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 16 1.61 - 2.36: 3638 2.36 - 3.10: 31127 3.10 - 3.85: 38142 3.85 - 4.60: 62965 Warning: very small nonbonded interaction distances. Nonbonded interactions: 135888 Sorted by model distance: nonbonded pdb=" NH1 ARG C 883 " pdb="HH22AARG C 883 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 534 " pdb="HH21AARG C 534 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 443 " pdb="HH22AARG C 443 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 579 " pdb="HH22AARG C 579 " model vdw 0.860 2.080 nonbonded pdb=" NH1 ARG C 438 " pdb="HH22AARG C 438 " model vdw 0.860 2.080 ... (remaining 135883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 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: 0.000 Extract box with map and model: 3.590 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 41.570 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 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 : 0.010 0.090 6094 Z= 0.696 Angle : 3.735 119.300 8281 Z= 2.818 Chirality : 0.048 0.181 983 Planarity : 0.006 0.073 1066 Dihedral : 15.551 179.913 2097 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.06 % Favored : 88.78 % Rotamer: Outliers : 3.19 % Allowed : 7.61 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -5.00 (0.24), residues: 624 helix: -4.12 (0.19), residues: 212 sheet: -1.55 (0.48), residues: 85 loop : -3.29 (0.26), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 528 HIS 0.010 0.002 HIS C 478 PHE 0.018 0.002 PHE C 564 TYR 0.033 0.003 TYR C 788 ARG 0.004 0.000 ARG C 901 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 101 average time/residue: 0.3212 time to fit residues: 43.9499 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1287 time to fit residues: 2.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.5984 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6094 Z= 0.221 Angle : 0.723 7.335 8281 Z= 0.386 Chirality : 0.039 0.149 983 Planarity : 0.006 0.055 1066 Dihedral : 16.837 177.659 867 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -3.89 (0.27), residues: 624 helix: -2.83 (0.25), residues: 230 sheet: -1.27 (0.51), residues: 90 loop : -2.77 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.006 0.001 HIS C 478 PHE 0.020 0.002 PHE C 368 TYR 0.021 0.002 TYR C 532 ARG 0.012 0.001 ARG C 795 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.4064 time to fit residues: 35.2877 Evaluate side-chains 58 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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: 0.6032 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6094 Z= 0.259 Angle : 0.620 5.920 8281 Z= 0.326 Chirality : 0.037 0.222 983 Planarity : 0.005 0.074 1066 Dihedral : 16.883 179.986 867 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % 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: -3.02 (0.29), residues: 624 helix: -1.95 (0.27), residues: 234 sheet: -1.13 (0.50), residues: 104 loop : -2.31 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 404 HIS 0.006 0.001 HIS C 593 PHE 0.021 0.002 PHE C 368 TYR 0.015 0.002 TYR C 532 ARG 0.009 0.001 ARG C 795 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3735 time to fit residues: 28.0177 Evaluate side-chains 48 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.838 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 8 optimal weight: 50.0000 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.0030 chunk 77 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 5.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 542 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6094 Z= 0.179 Angle : 0.534 6.315 8281 Z= 0.275 Chirality : 0.036 0.138 983 Planarity : 0.004 0.054 1066 Dihedral : 16.719 179.947 867 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.31), residues: 624 helix: -1.04 (0.29), residues: 244 sheet: -0.98 (0.51), residues: 104 loop : -1.86 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.003 0.001 HIS C 565 PHE 0.018 0.002 PHE B 291 TYR 0.015 0.001 TYR C 532 ARG 0.003 0.000 ARG C 795 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3957 time to fit residues: 28.5106 Evaluate side-chains 47 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 50.0000 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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: 0.5969 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6094 Z= 0.141 Angle : 0.485 5.697 8281 Z= 0.248 Chirality : 0.035 0.142 983 Planarity : 0.004 0.051 1066 Dihedral : 16.662 179.815 867 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 624 helix: -0.41 (0.31), residues: 242 sheet: -0.81 (0.51), residues: 104 loop : -1.47 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.008 0.001 HIS C 542 PHE 0.016 0.001 PHE C 368 TYR 0.013 0.001 TYR C 532 ARG 0.003 0.000 ARG C 966 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3686 time to fit residues: 27.0999 Evaluate side-chains 49 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.5988 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6094 Z= 0.197 Angle : 0.511 5.703 8281 Z= 0.262 Chirality : 0.035 0.135 983 Planarity : 0.004 0.049 1066 Dihedral : 16.627 179.899 867 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 (0.32), residues: 624 helix: -0.23 (0.31), residues: 246 sheet: -0.95 (0.48), residues: 114 loop : -1.39 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 404 HIS 0.005 0.001 HIS C 567 PHE 0.011 0.002 PHE C 931 TYR 0.013 0.001 TYR C 788 ARG 0.002 0.000 ARG C 901 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.3560 time to fit residues: 27.1517 Evaluate side-chains 48 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6094 Z= 0.252 Angle : 0.554 4.969 8281 Z= 0.290 Chirality : 0.035 0.153 983 Planarity : 0.004 0.048 1066 Dihedral : 16.631 179.822 867 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.33), residues: 624 helix: -0.21 (0.32), residues: 247 sheet: -0.98 (0.47), residues: 116 loop : -1.29 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 404 HIS 0.005 0.001 HIS C 593 PHE 0.016 0.002 PHE C 368 TYR 0.015 0.002 TYR C 788 ARG 0.004 0.001 ARG C 941 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.3400 time to fit residues: 23.5982 Evaluate side-chains 45 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 50.0000 chunk 60 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6094 Z= 0.174 Angle : 0.494 4.951 8281 Z= 0.253 Chirality : 0.035 0.136 983 Planarity : 0.004 0.045 1066 Dihedral : 16.613 179.813 867 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.33), residues: 624 helix: 0.00 (0.32), residues: 250 sheet: -0.94 (0.47), residues: 118 loop : -1.23 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.004 0.001 HIS B 270 PHE 0.011 0.001 PHE C 931 TYR 0.013 0.001 TYR C 788 ARG 0.003 0.000 ARG C 901 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 51 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3491 time to fit residues: 24.8212 Evaluate side-chains 44 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6094 Z= 0.197 Angle : 0.505 4.930 8281 Z= 0.263 Chirality : 0.035 0.135 983 Planarity : 0.004 0.045 1066 Dihedral : 16.607 179.744 867 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.33), residues: 624 helix: -0.01 (0.31), residues: 253 sheet: -0.92 (0.47), residues: 118 loop : -1.19 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 455 HIS 0.003 0.001 HIS C 565 PHE 0.016 0.002 PHE C 933 TYR 0.013 0.001 TYR C 788 ARG 0.004 0.000 ARG C 934 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3469 time to fit residues: 23.4280 Evaluate side-chains 44 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 73 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6094 Z= 0.154 Angle : 0.468 4.925 8281 Z= 0.238 Chirality : 0.035 0.136 983 Planarity : 0.004 0.040 1066 Dihedral : 16.575 179.861 867 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.34), residues: 624 helix: 0.24 (0.32), residues: 253 sheet: -0.71 (0.49), residues: 116 loop : -0.75 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 455 HIS 0.003 0.001 HIS C 565 PHE 0.008 0.001 PHE C 931 TYR 0.011 0.001 TYR C 788 ARG 0.002 0.000 ARG C 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 244 is missing expected H atoms. Skipping. Residue TYR 769 is missing expected H atoms. Skipping. Evaluate side-chains 49 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3522 time to fit residues: 23.9231 Evaluate side-chains 44 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 60.0000 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 50.0000 chunk 11 optimal weight: 70.0000 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.053974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.048224 restraints weight = 354887.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.049449 restraints weight = 134044.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050183 restraints weight = 65661.184| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6094 Z= 0.172 Angle : 0.476 4.939 8281 Z= 0.245 Chirality : 0.035 0.135 983 Planarity : 0.004 0.040 1066 Dihedral : 16.563 179.849 867 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.56 (0.34), residues: 624 helix: 0.25 (0.32), residues: 257 sheet: -0.64 (0.49), residues: 116 loop : -0.73 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 455 HIS 0.003 0.001 HIS C 565 PHE 0.014 0.001 PHE C 368 TYR 0.011 0.001 TYR C 788 ARG 0.002 0.000 ARG C 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2318.01 seconds wall clock time: 42 minutes 17.81 seconds (2537.81 seconds total)