Starting phenix.real_space_refine on Wed Jun 11 00:05:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_3062_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_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/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_3062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_3062.map" model { file = "/net/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_3062_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a6e_3062/06_2025/5a6e_3062_trim.cif" } 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 ARG 438": not complete - not flipped Residue "C ARG 438": not complete - not flipped Residue "C ARG 443": not complete - not flipped Residue "C ARG 443": not complete - not flipped Residue "C ARG 534": not complete - not flipped Residue "C ARG 534": not complete - not flipped Residue "C ARG 578": not complete - not flipped Residue "C ARG 578": not complete - not flipped Residue "C ARG 579": not complete - not flipped Residue "C ARG 579": not complete - not flipped Residue "C ARG 592": not complete - not flipped Residue "C ARG 592": not complete - not flipped Residue "C ARG 883": not complete - not flipped Residue "C ARG 883": not complete - not flipped Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.14, per 1000 atoms: 0.82 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 919.0 milliseconds 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: 0.89 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: 3.82 Time building geometry restraints manager: 3.47 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 - 23.86: 19835 23.86 - 47.72: 0 47.72 - 71.58: 7 71.58 - 95.44: 7 95.44 - 119.30: 14 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: 5222 35.98 - 71.97: 159 71.97 - 107.95: 1 107.95 - 143.93: 0 143.93 - 179.91: 7 Dihedral angle restraints: 5389 sinusoidal: 2620 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 5386 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 Time spend for trying shortcut: 0.00 ========== 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: 1.500 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: 0.250 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- 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= 0.640 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 Details of bonding type rmsd hydrogen bonds : bond 0.21444 ( 286) hydrogen bonds : angle 9.21519 ( 822) covalent geometry : bond 0.01049 ( 6094) covalent geometry : angle 3.73482 ( 8281) *********************** 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 to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.022 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: B 291 PHE cc_start: 0.7535 (m-80) cc_final: 0.6971 (m-10) REVERT: C 499 ASN cc_start: 0.9666 (OUTLIER) cc_final: 0.9311 (m-40) REVERT: C 531 MET cc_start: 0.9759 (ttm) cc_final: 0.9518 (tpp) REVERT: C 932 MET cc_start: 0.9166 (ttp) cc_final: 0.8761 (ttp) outliers start: 18 outliers final: 5 residues processed: 101 average time/residue: 0.3267 time to fit residues: 44.9350 Evaluate side-chains 64 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 6.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.046764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.036029 restraints weight = 272666.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037637 restraints weight = 112704.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.038826 restraints weight = 62567.276| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.2904 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= 0.168 Angle : 0.729 8.069 8281 Z= 0.386 Chirality : 0.039 0.152 983 Planarity : 0.006 0.054 1066 Dihedral : 16.877 177.715 867 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -3.76 (0.27), residues: 624 helix: -2.71 (0.26), residues: 230 sheet: -1.26 (0.51), residues: 90 loop : -2.68 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 304 HIS 0.005 0.001 HIS C 567 PHE 0.020 0.002 PHE C 368 TYR 0.012 0.002 TYR C 797 ARG 0.014 0.001 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.06381 ( 286) hydrogen bonds : angle 6.10946 ( 822) covalent geometry : bond 0.00341 ( 6094) covalent geometry : angle 0.72900 ( 8281) *********************** 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 67 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.832 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 revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9330 (mtp) cc_final: 0.9095 (tmm) REVERT: C 932 MET cc_start: 0.8730 (ttp) cc_final: 0.8340 (ttp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3779 time to fit residues: 33.3272 Evaluate side-chains 56 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 30.0000 chunk 70 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 0.0370 chunk 45 optimal weight: 0.0670 chunk 7 optimal weight: 50.0000 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.045308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035197 restraints weight = 304546.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.036853 restraints weight = 117638.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.038024 restraints weight = 63949.650| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6094 Z= 0.123 Angle : 0.557 5.281 8281 Z= 0.287 Chirality : 0.037 0.145 983 Planarity : 0.005 0.054 1066 Dihedral : 16.730 179.362 867 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: -2.54 (0.30), residues: 624 helix: -1.47 (0.29), residues: 237 sheet: -1.01 (0.49), residues: 106 loop : -2.06 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 404 HIS 0.010 0.001 HIS C 514 PHE 0.023 0.002 PHE C 368 TYR 0.016 0.002 TYR C 373 ARG 0.010 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 286) hydrogen bonds : angle 5.03699 ( 822) covalent geometry : bond 0.00266 ( 6094) covalent geometry : angle 0.55709 ( 8281) *********************** 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 58 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.898 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 REVERT: B 333 MET cc_start: 0.9328 (mtp) cc_final: 0.9084 (tmm) REVERT: C 892 THR cc_start: 0.9428 (m) cc_final: 0.9222 (p) REVERT: C 932 MET cc_start: 0.8987 (ttp) cc_final: 0.8464 (ttp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3775 time to fit residues: 29.2863 Evaluate side-chains 51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 514 HIS C 542 HIS C 896 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.044983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.034670 restraints weight = 370014.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036333 restraints weight = 139488.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.037544 restraints weight = 75287.785| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6094 Z= 0.161 Angle : 0.542 5.628 8281 Z= 0.280 Chirality : 0.035 0.137 983 Planarity : 0.004 0.052 1066 Dihedral : 16.695 179.906 867 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -1.96 (0.31), residues: 624 helix: -0.82 (0.30), residues: 246 sheet: -0.89 (0.49), residues: 106 loop : -1.84 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.003 0.001 HIS C 593 PHE 0.019 0.002 PHE C 943 TYR 0.012 0.001 TYR C 788 ARG 0.005 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 286) hydrogen bonds : angle 4.80867 ( 822) covalent geometry : bond 0.00316 ( 6094) covalent geometry : angle 0.54209 ( 8281) *********************** 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 to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.807 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: B 333 MET cc_start: 0.9346 (mtp) cc_final: 0.9115 (tmm) REVERT: C 932 MET cc_start: 0.9030 (ttp) cc_final: 0.8538 (ttp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3928 time to fit residues: 28.2384 Evaluate side-chains 45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.0870 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.045003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035198 restraints weight = 390094.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.036872 restraints weight = 136421.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.038064 restraints weight = 71545.657| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 6094 Z= 0.107 Angle : 0.493 6.377 8281 Z= 0.250 Chirality : 0.036 0.143 983 Planarity : 0.004 0.048 1066 Dihedral : 16.658 179.975 867 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -1.44 (0.32), residues: 624 helix: -0.37 (0.31), residues: 248 sheet: -0.71 (0.50), residues: 106 loop : -1.52 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 304 HIS 0.003 0.001 HIS C 514 PHE 0.020 0.001 PHE C 368 TYR 0.009 0.001 TYR C 788 ARG 0.004 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 286) hydrogen bonds : angle 4.47885 ( 822) covalent geometry : bond 0.00236 ( 6094) covalent geometry : angle 0.49292 ( 8281) *********************** 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 52 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.875 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: B 333 MET cc_start: 0.9345 (mtp) cc_final: 0.9074 (tmm) REVERT: C 932 MET cc_start: 0.9163 (ttp) cc_final: 0.8639 (ttp) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.4002 time to fit residues: 28.4339 Evaluate side-chains 47 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 50.0000 chunk 24 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 904 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.054126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.047801 restraints weight = 481101.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.049204 restraints weight = 165519.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050044 restraints weight = 78756.300| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6094 Z= 0.230 Angle : 0.586 5.006 8281 Z= 0.306 Chirality : 0.035 0.133 983 Planarity : 0.004 0.051 1066 Dihedral : 16.650 179.799 867 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: -1.49 (0.33), residues: 624 helix: -0.46 (0.31), residues: 248 sheet: -0.85 (0.49), residues: 114 loop : -1.44 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 404 HIS 0.006 0.002 HIS C 593 PHE 0.016 0.002 PHE C 885 TYR 0.015 0.002 TYR C 788 ARG 0.005 0.001 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 286) hydrogen bonds : angle 4.69910 ( 822) covalent geometry : bond 0.00436 ( 6094) covalent geometry : angle 0.58576 ( 8281) *********************** 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 51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.095 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 REVERT: B 333 MET cc_start: 0.9364 (mtp) cc_final: 0.8937 (tmm) REVERT: C 932 MET cc_start: 0.8645 (ttp) cc_final: 0.8328 (ttp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.4285 time to fit residues: 30.7928 Evaluate side-chains 42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 75 optimal weight: 6.9990 chunk 55 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 8 optimal weight: 50.0000 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.055199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.048968 restraints weight = 417596.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.050319 restraints weight = 148650.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.051133 restraints weight = 71543.764| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6094 Z= 0.136 Angle : 0.484 5.003 8281 Z= 0.248 Chirality : 0.035 0.138 983 Planarity : 0.004 0.049 1066 Dihedral : 16.585 179.966 867 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -1.04 (0.34), residues: 624 helix: -0.10 (0.32), residues: 250 sheet: -0.70 (0.50), residues: 114 loop : -1.14 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 304 HIS 0.003 0.001 HIS C 565 PHE 0.009 0.001 PHE C 931 TYR 0.013 0.001 TYR C 788 ARG 0.004 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 286) hydrogen bonds : angle 4.38255 ( 822) covalent geometry : bond 0.00266 ( 6094) covalent geometry : angle 0.48430 ( 8281) *********************** 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 51 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.877 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: B 272 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8652 (mm-30) REVERT: B 314 ILE cc_start: 0.9788 (pt) cc_final: 0.9581 (pt) REVERT: C 932 MET cc_start: 0.8496 (ttp) cc_final: 0.8236 (ttp) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.4177 time to fit residues: 28.7871 Evaluate side-chains 42 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 50.0000 chunk 11 optimal weight: 60.0000 chunk 77 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.053424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.047303 restraints weight = 455009.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.048630 restraints weight = 159977.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.049426 restraints weight = 76553.150| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6094 Z= 0.213 Angle : 0.561 4.891 8281 Z= 0.295 Chirality : 0.035 0.133 983 Planarity : 0.004 0.048 1066 Dihedral : 16.612 179.749 867 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % 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: -1.25 (0.33), residues: 624 helix: -0.37 (0.31), residues: 246 sheet: -0.74 (0.50), residues: 114 loop : -1.18 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.005 0.002 HIS C 593 PHE 0.016 0.002 PHE C 368 TYR 0.014 0.001 TYR C 788 ARG 0.003 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 286) hydrogen bonds : angle 4.60534 ( 822) covalent geometry : bond 0.00404 ( 6094) covalent geometry : angle 0.56107 ( 8281) *********************** 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 44 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.937 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: B 272 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8890 (mm-30) REVERT: B 333 MET cc_start: 0.9372 (mtp) cc_final: 0.9020 (tmm) REVERT: C 932 MET cc_start: 0.9257 (ttp) cc_final: 0.8781 (ttp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4045 time to fit residues: 25.7311 Evaluate side-chains 38 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 3 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.054089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.048211 restraints weight = 379212.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.049471 restraints weight = 139922.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.050237 restraints weight = 68175.958| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6094 Z= 0.150 Angle : 0.500 6.406 8281 Z= 0.256 Chirality : 0.035 0.138 983 Planarity : 0.004 0.050 1066 Dihedral : 16.582 179.933 867 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % 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: -0.99 (0.34), residues: 624 helix: -0.11 (0.31), residues: 250 sheet: -0.69 (0.50), residues: 116 loop : -1.03 (0.40), residues: 258 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 0.010 0.001 PHE C 931 TYR 0.013 0.001 TYR C 788 ARG 0.003 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 286) hydrogen bonds : angle 4.42487 ( 822) covalent geometry : bond 0.00290 ( 6094) covalent geometry : angle 0.50024 ( 8281) *********************** 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 45 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.099 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: B 314 ILE cc_start: 0.9760 (pt) cc_final: 0.9548 (pt) REVERT: C 932 MET cc_start: 0.8626 (ttp) cc_final: 0.8336 (ttp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5306 time to fit residues: 34.4272 Evaluate side-chains 40 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 60.0000 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 1 optimal weight: 50.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.054419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.048482 restraints weight = 368469.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.049729 restraints weight = 136487.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.050478 restraints weight = 66827.147| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6094 Z= 0.122 Angle : 0.480 5.421 8281 Z= 0.244 Chirality : 0.035 0.139 983 Planarity : 0.004 0.041 1066 Dihedral : 16.559 179.922 867 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % 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: -0.73 (0.34), residues: 624 helix: 0.13 (0.32), residues: 255 sheet: -0.57 (0.50), residues: 114 loop : -0.94 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.003 0.001 HIS C 565 PHE 0.010 0.001 PHE C 368 TYR 0.013 0.001 TYR C 532 ARG 0.003 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.02396 ( 286) hydrogen bonds : angle 4.27411 ( 822) covalent geometry : bond 0.00247 ( 6094) covalent geometry : angle 0.47961 ( 8281) ********************** 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 47 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.902 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: B 314 ILE cc_start: 0.9764 (pt) cc_final: 0.9508 (pt) REVERT: C 932 MET cc_start: 0.8547 (ttp) cc_final: 0.8229 (ttp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.3487 time to fit residues: 22.5172 Evaluate side-chains 39 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 50.0000 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.055217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.049208 restraints weight = 374078.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050481 restraints weight = 137478.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.051234 restraints weight = 66470.575| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.042 | | 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) = 0.042 | | 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: 0.7533 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6094 Z= 0.092 Angle : 0.461 6.077 8281 Z= 0.230 Chirality : 0.035 0.142 983 Planarity : 0.003 0.037 1066 Dihedral : 16.529 179.762 867 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: -0.41 (0.35), residues: 624 helix: 0.43 (0.32), residues: 255 sheet: -0.47 (0.50), residues: 114 loop : -0.76 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 455 HIS 0.002 0.001 HIS C 565 PHE 0.009 0.001 PHE C 368 TYR 0.013 0.001 TYR C 532 ARG 0.003 0.000 ARG C 795 Details of bonding type rmsd hydrogen bonds : bond 0.02266 ( 286) hydrogen bonds : angle 4.10878 ( 822) covalent geometry : bond 0.00210 ( 6094) covalent geometry : angle 0.46063 ( 8281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5226.03 seconds wall clock time: 94 minutes 29.30 seconds (5669.30 seconds total)