Starting phenix.real_space_refine on Wed Feb 14 04:17:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vp9_21307/02_2024/6vp9_21307_neut_updated.pdb" } resolution = 3.46 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 ------------------------------------------------------------------------------- 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= 0.005 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 P 3 5.49 5 S 44 5.16 5 C 5507 2.51 5 N 1438 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B GLU 441": "OE1" <-> "OE2" Residue "B GLU 451": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B GLU 579": "OE1" <-> "OE2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B ARG 690": "NH1" <-> "NH2" Residue "B GLU 739": "OE1" <-> "OE2" Residue "B GLU 802": "OE1" <-> "OE2" Residue "B GLU 933": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8610 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1272 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 7245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7245 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 881} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 4.95, per 1000 atoms: 0.57 Number of scatterers: 8610 At special positions: 0 Unit cell: (107.07, 99.6, 100.43, 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 44 16.00 P 3 15.00 O 1618 8.00 N 1438 7.00 C 5507 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 2 sheets defined 58.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.603A pdb=" N TYR A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.671A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 31 through 36 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 62 through 71 removed outlier: 4.329A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.537A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 removed outlier: 4.074A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.575A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.803A pdb=" N PHE B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.139A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.069A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.865A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.966A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 279 removed outlier: 3.733A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.945A pdb=" N PHE B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.804A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 384 through 390 removed outlier: 3.685A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.745A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 450 removed outlier: 4.294A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.244A pdb=" N LEU B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 488 through 501 Processing helix chain 'B' and resid 506 through 519 Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 543 through 550 removed outlier: 4.323A pdb=" N ARG B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 550 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 584 removed outlier: 3.852A pdb=" N ALA B 584 " --> pdb=" O TYR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 604 Processing helix chain 'B' and resid 607 through 624 Processing helix chain 'B' and resid 631 through 638 removed outlier: 3.569A pdb=" N SER B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 700 removed outlier: 3.685A pdb=" N GLY B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 700 " --> pdb=" O LEU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 727 No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'B' and resid 729 through 746 removed outlier: 3.690A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 766 removed outlier: 4.203A pdb=" N PHE B 765 " --> pdb=" O GLY B 762 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASN B 766 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 789 removed outlier: 4.239A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.764A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 829 No H-bonds generated for 'chain 'B' and resid 827 through 829' Processing helix chain 'B' and resid 836 through 868 removed outlier: 3.707A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 884 through 903 removed outlier: 3.847A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 900 " --> pdb=" O GLY B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 911 No H-bonds generated for 'chain 'B' and resid 908 through 911' Processing helix chain 'B' and resid 934 through 968 removed outlier: 3.745A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.542A pdb=" N ILE A 44 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 107 through 113 368 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2775 1.34 - 1.46: 1589 1.46 - 1.58: 4344 1.58 - 1.70: 5 1.70 - 1.82: 73 Bond restraints: 8786 Sorted by residual: bond pdb=" C3B CMC A 201 " pdb=" C4B CMC A 201 " ideal model delta sigma weight residual 1.347 1.525 -0.178 2.00e-02 2.50e+03 7.93e+01 bond pdb=" C9P CMC A 201 " pdb=" N8P CMC A 201 " ideal model delta sigma weight residual 1.485 1.326 0.159 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C5P CMC A 201 " pdb=" N4P CMC A 201 " ideal model delta sigma weight residual 1.493 1.336 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C4B CMC A 201 " pdb=" O4B CMC A 201 " ideal model delta sigma weight residual 1.596 1.452 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 1.468 1.330 0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.03: 164 106.03 - 113.03: 4767 113.03 - 120.03: 3319 120.03 - 127.03: 3550 127.03 - 134.03: 89 Bond angle restraints: 11889 Sorted by residual: angle pdb=" C1B CMC A 201 " pdb=" N9A CMC A 201 " pdb=" C4A CMC A 201 " ideal model delta sigma weight residual 90.87 125.78 -34.91 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N1A CMC A 201 " pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 94.05 118.82 -24.77 3.00e+00 1.11e-01 6.82e+01 angle pdb=" C5A CMC A 201 " pdb=" C6A CMC A 201 " pdb=" N6A CMC A 201 " ideal model delta sigma weight residual 145.98 123.82 22.16 3.00e+00 1.11e-01 5.46e+01 angle pdb=" N PRO B 17 " pdb=" CA PRO B 17 " pdb=" CB PRO B 17 " ideal model delta sigma weight residual 103.25 110.05 -6.80 1.05e+00 9.07e-01 4.19e+01 angle pdb=" C1B CMC A 201 " pdb=" N9A CMC A 201 " pdb=" C8A CMC A 201 " ideal model delta sigma weight residual 141.80 127.63 14.17 3.00e+00 1.11e-01 2.23e+01 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4698 17.97 - 35.94: 472 35.94 - 53.91: 99 53.91 - 71.88: 16 71.88 - 89.86: 11 Dihedral angle restraints: 5296 sinusoidal: 2125 harmonic: 3171 Sorted by residual: dihedral pdb=" CA LYS B 535 " pdb=" C LYS B 535 " pdb=" N HIS B 536 " pdb=" CA HIS B 536 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 652 " pdb=" C LEU B 652 " pdb=" N ARG B 653 " pdb=" CA ARG B 653 " ideal model delta harmonic sigma weight residual -180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA THR A 26 " pdb=" C THR A 26 " pdb=" N TYR A 27 " pdb=" CA TYR A 27 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1194 0.065 - 0.131: 135 0.131 - 0.196: 3 0.196 - 0.261: 1 0.261 - 0.326: 1 Chirality restraints: 1334 Sorted by residual: chirality pdb=" C3B CMC A 201 " pdb=" C2B CMC A 201 " pdb=" C4B CMC A 201 " pdb=" O3B CMC A 201 " both_signs ideal model delta sigma weight residual False -2.35 -2.68 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PRO B 17 " pdb=" N PRO B 17 " pdb=" C PRO B 17 " pdb=" CB PRO B 17 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB THR B 225 " pdb=" CA THR B 225 " pdb=" OG1 THR B 225 " pdb=" CG2 THR B 225 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1331 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC A 201 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C9P CMC A 201 " -0.089 2.00e-02 2.50e+03 pdb=" CAP CMC A 201 " 0.113 2.00e-02 2.50e+03 pdb=" N8P CMC A 201 " -0.535 2.00e-02 2.50e+03 pdb=" O9P CMC A 201 " 0.161 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CMC A 201 " -0.338 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C5P CMC A 201 " 0.087 2.00e-02 2.50e+03 pdb=" C6P CMC A 201 " -0.163 2.00e-02 2.50e+03 pdb=" N4P CMC A 201 " 0.509 2.00e-02 2.50e+03 pdb=" O5P CMC A 201 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 755 " 0.039 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO B 756 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 756 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 756 " 0.033 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 77 2.61 - 3.18: 7793 3.18 - 3.75: 12615 3.75 - 4.33: 18688 4.33 - 4.90: 30428 Nonbonded interactions: 69601 Sorted by model distance: nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 2.032 2.520 nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.139 2.440 nonbonded pdb=" OE1 GLU B 735 " pdb=" OH TYR B 778 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR B 149 " pdb=" O MET B 180 " model vdw 2.219 2.440 nonbonded pdb=" O ASN B 27 " pdb=" N ILE B 31 " model vdw 2.220 2.520 ... (remaining 69596 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.300 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.007 0.178 8786 Z= 0.467 Angle : 0.832 34.914 11889 Z= 0.406 Chirality : 0.043 0.326 1334 Planarity : 0.012 0.302 1508 Dihedral : 15.411 89.856 3240 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -3.63 (0.22), residues: 1061 helix: -1.76 (0.17), residues: 668 sheet: -3.84 (0.67), residues: 40 loop : -3.28 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 686 HIS 0.010 0.001 HIS B 907 PHE 0.033 0.002 PHE A 43 TYR 0.015 0.001 TYR A 42 ARG 0.006 0.000 ARG B 445 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.984 Fit side-chains REVERT: B 115 TYR cc_start: 0.8039 (m-80) cc_final: 0.7780 (m-10) REVERT: B 195 GLU cc_start: 0.7720 (mp0) cc_final: 0.7298 (mp0) REVERT: B 219 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8311 (tptm) REVERT: B 297 TYR cc_start: 0.7233 (m-80) cc_final: 0.6206 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2466 time to fit residues: 41.7242 Evaluate side-chains 103 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 0.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 116 HIS B 159 GLN B 249 ASN B 387 GLN B 413 GLN B 447 GLN B 462 GLN B 490 GLN B 555 GLN B 605 ASN B 608 HIS B 659 ASN B 750 GLN B 766 ASN B 834 HIS B 868 ASN B 891 GLN B 898 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8786 Z= 0.223 Angle : 0.584 9.373 11889 Z= 0.288 Chirality : 0.040 0.153 1334 Planarity : 0.004 0.051 1508 Dihedral : 6.502 101.691 1187 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.54 % Allowed : 12.51 % Favored : 85.95 % 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: -2.45 (0.25), residues: 1061 helix: -0.76 (0.20), residues: 669 sheet: -3.78 (0.72), residues: 39 loop : -2.94 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 686 HIS 0.006 0.001 HIS B 907 PHE 0.025 0.001 PHE A 15 TYR 0.021 0.002 TYR B 239 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.680 Fit side-chains revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: B 115 TYR cc_start: 0.8055 (m-80) cc_final: 0.7820 (m-10) REVERT: B 195 GLU cc_start: 0.7687 (mp0) cc_final: 0.7345 (mp0) REVERT: B 219 LYS cc_start: 0.8529 (tmtt) cc_final: 0.8154 (tptm) REVERT: B 297 TYR cc_start: 0.7413 (m-80) cc_final: 0.6852 (m-10) REVERT: B 555 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7896 (mm110) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 0.2530 time to fit residues: 43.2779 Evaluate side-chains 115 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 555 GLN Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8786 Z= 0.173 Angle : 0.538 8.602 11889 Z= 0.267 Chirality : 0.039 0.149 1334 Planarity : 0.004 0.041 1508 Dihedral : 6.338 108.072 1187 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.54 % Allowed : 14.38 % Favored : 84.08 % 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: -1.71 (0.26), residues: 1061 helix: -0.19 (0.20), residues: 665 sheet: -3.55 (0.76), residues: 39 loop : -2.59 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 907 PHE 0.025 0.001 PHE A 15 TYR 0.023 0.001 TYR B 239 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.045 Fit side-chains REVERT: A 146 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: B 115 TYR cc_start: 0.8067 (m-80) cc_final: 0.7809 (m-10) REVERT: B 137 MET cc_start: 0.8181 (mmm) cc_final: 0.7973 (mmm) REVERT: B 195 GLU cc_start: 0.7624 (mp0) cc_final: 0.7251 (mp0) REVERT: B 219 LYS cc_start: 0.8521 (tmtt) cc_final: 0.8247 (tptm) REVERT: B 297 TYR cc_start: 0.7367 (m-80) cc_final: 0.6727 (m-80) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.2167 time to fit residues: 37.0046 Evaluate side-chains 118 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 882 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 555 GLN B 798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8786 Z= 0.230 Angle : 0.551 8.477 11889 Z= 0.271 Chirality : 0.040 0.130 1334 Planarity : 0.004 0.044 1508 Dihedral : 6.296 107.486 1187 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.31 % Allowed : 16.14 % Favored : 81.56 % 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: -1.33 (0.26), residues: 1061 helix: 0.12 (0.21), residues: 658 sheet: -3.22 (0.81), residues: 38 loop : -2.45 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.006 0.001 HIS B 448 PHE 0.026 0.001 PHE A 15 TYR 0.011 0.001 TYR B 580 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.983 Fit side-chains REVERT: B 195 GLU cc_start: 0.7591 (mp0) cc_final: 0.7267 (mp0) REVERT: B 217 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7881 (ttt-90) REVERT: B 219 LYS cc_start: 0.8522 (tmtt) cc_final: 0.8248 (tptm) REVERT: B 297 TYR cc_start: 0.7372 (m-80) cc_final: 0.6876 (m-80) outliers start: 21 outliers final: 16 residues processed: 120 average time/residue: 0.2119 time to fit residues: 35.5694 Evaluate side-chains 118 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 655 ASN Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 73 HIS B 555 GLN B 561 GLN ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8786 Z= 0.419 Angle : 0.647 10.779 11889 Z= 0.319 Chirality : 0.044 0.157 1334 Planarity : 0.004 0.052 1508 Dihedral : 6.571 107.157 1187 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.73 % Allowed : 15.70 % Favored : 80.57 % 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: -1.58 (0.26), residues: 1061 helix: -0.05 (0.20), residues: 661 sheet: -3.37 (0.78), residues: 39 loop : -2.61 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 686 HIS 0.006 0.001 HIS B 907 PHE 0.036 0.002 PHE A 15 TYR 0.017 0.001 TYR A 42 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.917 Fit side-chains REVERT: A 146 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: B 195 GLU cc_start: 0.7618 (mp0) cc_final: 0.7243 (mp0) REVERT: B 219 LYS cc_start: 0.8580 (tmtt) cc_final: 0.8296 (tptm) REVERT: B 297 TYR cc_start: 0.7448 (m-80) cc_final: 0.7072 (m-80) outliers start: 34 outliers final: 23 residues processed: 130 average time/residue: 0.2230 time to fit residues: 39.9116 Evaluate side-chains 125 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.0570 chunk 98 optimal weight: 9.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 538 GLN B 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8786 Z= 0.161 Angle : 0.534 8.780 11889 Z= 0.264 Chirality : 0.039 0.162 1334 Planarity : 0.004 0.039 1508 Dihedral : 6.537 117.983 1187 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.07 % Allowed : 16.90 % Favored : 80.02 % 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: -1.09 (0.26), residues: 1061 helix: 0.30 (0.21), residues: 664 sheet: -3.04 (0.80), residues: 38 loop : -2.38 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.017 0.001 PHE A 15 TYR 0.021 0.001 TYR B 239 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 0.997 Fit side-chains REVERT: B 109 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6689 (m) REVERT: B 195 GLU cc_start: 0.7622 (mp0) cc_final: 0.7270 (mp0) REVERT: B 217 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.7861 (ttt-90) REVERT: B 219 LYS cc_start: 0.8531 (tmtt) cc_final: 0.8253 (tptm) REVERT: B 297 TYR cc_start: 0.7421 (m-80) cc_final: 0.7110 (m-80) REVERT: B 537 ILE cc_start: 0.8476 (tp) cc_final: 0.7665 (mp) outliers start: 28 outliers final: 21 residues processed: 129 average time/residue: 0.2265 time to fit residues: 40.1721 Evaluate side-chains 126 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 795 MET Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 832 LYS Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 899 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 891 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8786 Z= 0.149 Angle : 0.519 9.518 11889 Z= 0.256 Chirality : 0.038 0.145 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.407 122.883 1187 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.74 % Allowed : 17.78 % Favored : 79.47 % 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: -0.82 (0.27), residues: 1061 helix: 0.51 (0.21), residues: 664 sheet: -2.79 (0.80), residues: 37 loop : -2.29 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.020 0.001 PHE A 15 TYR 0.020 0.001 TYR B 123 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 146 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: B 109 VAL cc_start: 0.7111 (OUTLIER) cc_final: 0.6743 (m) REVERT: B 195 GLU cc_start: 0.7585 (mp0) cc_final: 0.7216 (mp0) REVERT: B 217 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8024 (mmm-85) REVERT: B 219 LYS cc_start: 0.8503 (tmtt) cc_final: 0.8223 (tptm) REVERT: B 297 TYR cc_start: 0.7382 (m-80) cc_final: 0.7153 (m-80) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 0.2255 time to fit residues: 39.7637 Evaluate side-chains 123 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 882 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8786 Z= 0.161 Angle : 0.544 13.643 11889 Z= 0.261 Chirality : 0.039 0.136 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.275 125.371 1187 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.31 % Allowed : 18.99 % Favored : 78.70 % 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: -0.68 (0.27), residues: 1061 helix: 0.63 (0.21), residues: 665 sheet: -2.46 (0.83), residues: 36 loop : -2.28 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.020 0.001 PHE A 15 TYR 0.010 0.001 TYR B 580 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 1.063 Fit side-chains REVERT: A 146 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: B 109 VAL cc_start: 0.7086 (OUTLIER) cc_final: 0.6730 (m) REVERT: B 195 GLU cc_start: 0.7596 (mp0) cc_final: 0.7217 (mp0) REVERT: B 217 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8001 (mmm-85) REVERT: B 219 LYS cc_start: 0.8483 (tmtt) cc_final: 0.8211 (tptm) REVERT: B 297 TYR cc_start: 0.7369 (m-80) cc_final: 0.7139 (m-80) REVERT: B 652 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7986 (mp) outliers start: 21 outliers final: 17 residues processed: 119 average time/residue: 0.2206 time to fit residues: 36.4461 Evaluate side-chains 123 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 882 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8786 Z= 0.201 Angle : 0.559 12.482 11889 Z= 0.268 Chirality : 0.040 0.171 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.239 126.165 1187 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.63 % Allowed : 19.43 % Favored : 77.94 % 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: -0.68 (0.27), residues: 1061 helix: 0.61 (0.21), residues: 665 sheet: -2.53 (0.84), residues: 37 loop : -2.25 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.023 0.001 PHE A 15 TYR 0.012 0.001 TYR B 580 ARG 0.006 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.941 Fit side-chains REVERT: A 146 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: B 109 VAL cc_start: 0.7097 (OUTLIER) cc_final: 0.6746 (m) REVERT: B 195 GLU cc_start: 0.7596 (mp0) cc_final: 0.7217 (mp0) REVERT: B 217 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.7989 (mmm-85) REVERT: B 219 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8218 (tptm) REVERT: B 388 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 579 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7492 (tt0) outliers start: 24 outliers final: 18 residues processed: 118 average time/residue: 0.2248 time to fit residues: 36.8680 Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 882 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.0010 chunk 89 optimal weight: 0.7980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8786 Z= 0.173 Angle : 0.540 10.458 11889 Z= 0.261 Chirality : 0.039 0.176 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.225 127.412 1187 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.63 % Allowed : 19.32 % Favored : 78.05 % 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: -0.58 (0.27), residues: 1061 helix: 0.69 (0.21), residues: 664 sheet: -2.31 (0.85), residues: 36 loop : -2.22 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.021 0.001 PHE A 15 TYR 0.011 0.001 TYR B 297 ARG 0.006 0.000 ARG A 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 146 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: B 109 VAL cc_start: 0.7088 (OUTLIER) cc_final: 0.6736 (m) REVERT: B 195 GLU cc_start: 0.7585 (mp0) cc_final: 0.7221 (mp0) REVERT: B 217 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.7968 (mmm-85) REVERT: B 219 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8213 (tptm) REVERT: B 652 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7989 (mp) outliers start: 24 outliers final: 20 residues processed: 116 average time/residue: 0.2178 time to fit residues: 35.1019 Evaluate side-chains 122 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 290 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 830 ASN Chi-restraints excluded: chain B residue 882 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 40.0000 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114990 restraints weight = 9659.121| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.34 r_work: 0.3053 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8786 Z= 0.173 Angle : 0.543 10.884 11889 Z= 0.262 Chirality : 0.039 0.207 1334 Planarity : 0.003 0.038 1508 Dihedral : 6.214 128.354 1187 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.63 % Allowed : 19.32 % Favored : 78.05 % 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: -0.50 (0.27), residues: 1061 helix: 0.78 (0.21), residues: 658 sheet: -2.37 (0.82), residues: 36 loop : -2.19 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 686 HIS 0.005 0.001 HIS B 448 PHE 0.021 0.001 PHE A 15 TYR 0.016 0.001 TYR B 297 ARG 0.006 0.000 ARG A 67 =============================================================================== Job complete usr+sys time: 1983.55 seconds wall clock time: 36 minutes 53.56 seconds (2213.56 seconds total)