Starting phenix.real_space_refine on Wed Feb 14 04:17:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7stx_25438/02_2024/7stx_25438_updated.pdb" } resolution = 3.14 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 P 3 5.49 5 S 44 5.16 5 C 5508 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 GLU 62": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 451": "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 643": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B ASP 670": "OD1" <-> "OD2" Residue "B GLU 673": "OE1" <-> "OE2" 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 746": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B GLU 802": "OE1" <-> "OE2" Residue "B GLU 933": "OE1" <-> "OE2" Residue "B GLU 965": "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: 8611 Number of models: 1 Model: "" Number of chains: 5 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: 7246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 914, 7246 Classifications: {'peptide': 914} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 31, 'TRANS': 882} Chain breaks: 4 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TYR:plan': 1, 'UNK:plan-1': 28, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 86 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.00, per 1000 atoms: 0.58 Number of scatterers: 8611 At special positions: 0 Unit cell: (94.62, 101.26, 114.54, 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 5508 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 2 sheets defined 57.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.913A pdb=" N GLN A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.573A pdb=" N UNK B 22 " --> pdb=" O UNK B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.567A pdb=" N UNK B 32 " --> pdb=" O UNK B 28 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N UNK B 33 " --> pdb=" O UNK B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 62 through 71 removed outlier: 4.558A pdb=" N LEU B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.804A pdb=" N ILE B 87 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.952A pdb=" N THR B 99 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 100 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 102 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.870A pdb=" N GLN B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N GLN B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 removed outlier: 3.884A pdb=" N SER B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 186 removed outlier: 4.202A pdb=" N MET B 184 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.770A pdb=" N ASP B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.959A pdb=" N MET B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.956A pdb=" N LEU B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 removed outlier: 3.911A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.537A pdb=" N VAL B 303 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 305 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 310 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 312 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS B 315 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.839A pdb=" N LEU B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) removed outlier: 3.592A 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: 3.822A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.676A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS B 414 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 448 removed outlier: 4.174A pdb=" N VAL B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 removed outlier: 4.140A pdb=" N LEU B 469 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 482 removed outlier: 3.704A pdb=" N GLU B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) 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 543 through 550 removed outlier: 4.629A pdb=" N ARG B 548 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 550 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 584 removed outlier: 3.977A 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 623 Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 673 through 699 removed outlier: 3.543A pdb=" N GLY B 699 " --> pdb=" O ARG B 695 " (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: 3.648A pdb=" N GLU B 739 " --> pdb=" O GLU B 735 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.750A pdb=" N ASN B 766 " --> pdb=" O GLY B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 789 removed outlier: 4.172A pdb=" N SER B 776 " --> pdb=" O CYS B 772 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 781 " --> pdb=" O PHE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.790A pdb=" N GLU B 799 " --> pdb=" O MET B 795 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 800 " --> pdb=" O GLU B 796 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 810 " --> pdb=" O LYS B 806 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 814 " --> pdb=" O ASP B 810 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 817 " --> pdb=" O LYS B 813 " (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 867 removed outlier: 3.965A pdb=" N LEU B 841 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 844 " --> pdb=" O ASN B 840 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 847 " --> pdb=" O PHE B 843 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 850 " --> pdb=" O GLU B 846 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 860 " --> pdb=" O SER B 856 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 884 through 904 removed outlier: 3.921A pdb=" N SER B 889 " --> pdb=" O PRO B 885 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 895 " --> pdb=" O GLN B 891 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 896 " --> pdb=" O ASP B 892 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.540A pdb=" N SER B 938 " --> pdb=" O GLU B 934 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS B 939 " --> pdb=" O ARG B 935 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 940 " --> pdb=" O LYS B 936 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS B 951 " --> pdb=" O SER B 947 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR B 967 " --> pdb=" O ARG B 963 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS B 968 " --> pdb=" O LEU B 964 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'A' and resid 111 through 113 333 hydrogen bonds defined for protein. 957 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: 2.24 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.80: 8771 1.80 - 2.42: 13 2.42 - 3.03: 0 3.03 - 3.65: 0 3.65 - 4.27: 2 Bond restraints: 8786 Sorted by residual: bond pdb=" AP1 COA A 201 " pdb="AO5* COA A 201 " ideal model delta sigma weight residual 1.610 4.271 -2.661 2.00e-02 2.50e+03 1.77e+04 bond pdb=" AO6 COA A 201 " pdb=" AP2 COA A 201 " ideal model delta sigma weight residual 1.610 4.182 -2.572 2.00e-02 2.50e+03 1.65e+04 bond pdb="AC1* COA A 201 " pdb="AO4* COA A 201 " ideal model delta sigma weight residual 1.410 1.641 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" PC9 COA A 201 " pdb=" PO9 COA A 201 " ideal model delta sigma weight residual 1.410 1.202 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb="AC1* COA A 201 " pdb="AC2* COA A 201 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 8781 not shown) Histogram of bond angle deviations from ideal: 14.37 - 38.35: 2 38.35 - 62.33: 0 62.33 - 86.31: 3 86.31 - 110.29: 2161 110.29 - 134.26: 9723 Bond angle restraints: 11889 Sorted by residual: angle pdb=" AO3 COA A 201 " pdb=" AP1 COA A 201 " pdb="AO5* COA A 201 " ideal model delta sigma weight residual 102.60 14.37 88.23 3.00e+00 1.11e-01 8.65e+02 angle pdb=" AO3 COA A 201 " pdb=" AP2 COA A 201 " pdb=" AO6 COA A 201 " ideal model delta sigma weight residual 102.60 18.36 84.24 3.00e+00 1.11e-01 7.88e+02 angle pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" C GLN B 462 " ideal model delta sigma weight residual 110.41 79.86 30.55 1.23e+00 6.61e-01 6.17e+02 angle pdb=" N PRO B 701 " pdb=" CA PRO B 701 " pdb=" C PRO B 701 " ideal model delta sigma weight residual 111.77 80.65 31.12 1.67e+00 3.59e-01 3.47e+02 angle pdb=" N LEU B 640 " pdb=" CA LEU B 640 " pdb=" C LEU B 640 " ideal model delta sigma weight residual 109.07 81.03 28.04 1.61e+00 3.86e-01 3.03e+02 ... (remaining 11884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 4933 25.94 - 51.87: 319 51.87 - 77.81: 36 77.81 - 103.74: 11 103.74 - 129.68: 2 Dihedral angle restraints: 5301 sinusoidal: 2128 harmonic: 3173 Sorted by residual: dihedral pdb=" C LYS B 145 " pdb=" N LYS B 145 " pdb=" CA LYS B 145 " pdb=" CB LYS B 145 " ideal model delta harmonic sigma weight residual -122.60 -93.42 -29.18 0 2.50e+00 1.60e-01 1.36e+02 dihedral pdb=" C GLN B 462 " pdb=" N GLN B 462 " pdb=" CA GLN B 462 " pdb=" CB GLN B 462 " ideal model delta harmonic sigma weight residual -122.60 -95.16 -27.44 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C LYS B 667 " pdb=" N LYS B 667 " pdb=" CA LYS B 667 " pdb=" CB LYS B 667 " ideal model delta harmonic sigma weight residual -122.60 -98.27 -24.33 0 2.50e+00 1.60e-01 9.47e+01 ... (remaining 5298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1283 0.145 - 0.291: 36 0.291 - 0.436: 10 0.436 - 0.581: 3 0.581 - 0.727: 2 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA LYS B 145 " pdb=" N LYS B 145 " pdb=" C LYS B 145 " pdb=" CB LYS B 145 " both_signs ideal model delta sigma weight residual False 2.51 3.24 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA GLN B 462 " pdb=" N GLN B 462 " pdb=" C GLN B 462 " pdb=" CB GLN B 462 " both_signs ideal model delta sigma weight residual False 2.51 3.21 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA LEU B 640 " pdb=" N LEU B 640 " pdb=" C LEU B 640 " pdb=" CB LEU B 640 " both_signs ideal model delta sigma weight residual False 2.51 3.04 -0.53 2.00e-01 2.50e+01 6.95e+00 ... (remaining 1331 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 43 " -0.032 2.00e-02 2.50e+03 3.72e-02 2.42e+01 pdb=" CG PHE A 43 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A 43 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 43 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 43 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE A 43 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 43 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 666 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C PRO B 666 " 0.082 2.00e-02 2.50e+03 pdb=" O PRO B 666 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 667 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.060 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO B 758 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.048 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 2076 2.78 - 3.48: 10781 3.48 - 4.19: 20066 4.19 - 4.90: 36013 Nonbonded interactions: 68943 Sorted by model distance: nonbonded pdb=" CG2 ILE B 277 " pdb=" OG SER B 298 " model vdw 1.362 3.460 nonbonded pdb=" AO6 COA A 201 " pdb=" AP1 COA A 201 " model vdw 1.635 2.720 nonbonded pdb=" AP2 COA A 201 " pdb="AO5* COA A 201 " model vdw 1.641 2.720 nonbonded pdb=" OD1 ASN A 16 " pdb=" NE2 GLN B 538 " model vdw 1.673 2.520 nonbonded pdb=" N GLN B 462 " pdb=" O GLN B 462 " model vdw 1.881 2.496 ... (remaining 68938 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: 0.990 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: 5.180 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.830 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 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 : 0.041 2.661 8786 Z= 2.567 Angle : 1.858 88.232 11889 Z= 0.933 Chirality : 0.079 0.727 1334 Planarity : 0.009 0.092 1508 Dihedral : 17.272 129.678 3243 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.66 % Favored : 89.95 % Rotamer: Outliers : 2.09 % Allowed : 11.31 % Favored : 86.61 % Cbeta Deviations : 1.07 % 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: -5.56 (0.18), residues: 1035 helix: -3.42 (0.12), residues: 673 sheet: -4.64 (0.68), residues: 35 loop : -3.70 (0.27), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 686 HIS 0.013 0.002 HIS B 473 PHE 0.079 0.004 PHE A 43 TYR 0.027 0.003 TYR A 42 ARG 0.006 0.001 ARG B 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 229 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 210 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 670 ASP cc_start: 0.4363 (OUTLIER) cc_final: 0.3952 (t70) REVERT: B 906 ASP cc_start: 0.4825 (m-30) cc_final: 0.4400 (m-30) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.2524 time to fit residues: 73.8302 Evaluate side-chains 115 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain B residue 670 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 ASN B 387 GLN B 428 HIS ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 ASN B 605 ASN B 766 ASN B 868 ASN B 898 GLN B 914 HIS B 951 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8786 Z= 0.217 Angle : 0.697 10.893 11889 Z= 0.346 Chirality : 0.041 0.187 1334 Planarity : 0.006 0.070 1508 Dihedral : 9.668 128.126 1203 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.50 % Favored : 91.40 % Rotamer: Outliers : 2.85 % Allowed : 16.25 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -3.62 (0.23), residues: 1035 helix: -1.77 (0.18), residues: 661 sheet: -3.80 (0.79), residues: 36 loop : -3.28 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 281 HIS 0.004 0.001 HIS B 414 PHE 0.026 0.002 PHE A 107 TYR 0.016 0.002 TYR A 42 ARG 0.004 0.001 ARG B 548 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 163 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: B 142 ILE cc_start: 0.8041 (mp) cc_final: 0.7691 (mt) REVERT: B 236 MET cc_start: 0.7624 (mmm) cc_final: 0.7312 (tpt) REVERT: B 279 GLU cc_start: 0.4648 (OUTLIER) cc_final: 0.4173 (pt0) REVERT: B 653 ARG cc_start: 0.6084 (mmp80) cc_final: 0.5637 (mmm-85) REVERT: B 799 GLU cc_start: 0.6949 (pp20) cc_final: 0.6528 (pt0) REVERT: B 883 MET cc_start: 0.6827 (tpp) cc_final: 0.6567 (tpp) outliers start: 26 outliers final: 17 residues processed: 158 average time/residue: 0.2661 time to fit residues: 56.3525 Evaluate side-chains 123 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 537 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 914 HIS Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.0270 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 85 optimal weight: 0.0770 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 473 HIS B 501 HIS B 573 ASN B 898 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4258 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= 0.186 Angle : 0.618 12.046 11889 Z= 0.311 Chirality : 0.040 0.180 1334 Planarity : 0.005 0.065 1508 Dihedral : 8.375 107.435 1196 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.31 % Favored : 91.59 % Rotamer: Outliers : 2.63 % Allowed : 18.99 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.71 (0.25), residues: 1035 helix: -1.01 (0.19), residues: 659 sheet: -3.77 (0.77), residues: 36 loop : -2.99 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 686 HIS 0.019 0.001 HIS B 914 PHE 0.025 0.002 PHE A 107 TYR 0.018 0.001 TYR A 42 ARG 0.005 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 155 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 653 ARG cc_start: 0.6156 (mmp80) cc_final: 0.5728 (mmm-85) outliers start: 24 outliers final: 20 residues processed: 152 average time/residue: 0.2081 time to fit residues: 44.0844 Evaluate side-chains 133 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 817 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** B 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 771 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4936 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= 0.186 Angle : 0.618 12.915 11889 Z= 0.309 Chirality : 0.040 0.227 1334 Planarity : 0.005 0.063 1508 Dihedral : 7.856 112.369 1194 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 3.40 % Allowed : 21.51 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -2.21 (0.26), residues: 1035 helix: -0.56 (0.20), residues: 660 sheet: -3.58 (0.81), residues: 36 loop : -2.92 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 686 HIS 0.004 0.001 HIS A 38 PHE 0.024 0.002 PHE A 107 TYR 0.017 0.001 TYR B 269 ARG 0.005 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 161 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 142 ILE cc_start: 0.7905 (mp) cc_final: 0.7634 (mt) REVERT: B 172 MET cc_start: 0.7132 (mmt) cc_final: 0.6897 (mmt) REVERT: B 795 MET cc_start: 0.5989 (ppp) cc_final: 0.5330 (ptm) outliers start: 31 outliers final: 22 residues processed: 155 average time/residue: 0.2040 time to fit residues: 43.6905 Evaluate side-chains 140 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 380 GLN Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 87 optimal weight: 0.0770 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8786 Z= 0.156 Angle : 0.573 11.307 11889 Z= 0.288 Chirality : 0.039 0.178 1334 Planarity : 0.004 0.063 1508 Dihedral : 7.332 109.561 1194 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.54 % Favored : 92.27 % Rotamer: Outliers : 3.07 % Allowed : 22.06 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.68 (0.26), residues: 1035 helix: -0.08 (0.21), residues: 663 sheet: -3.73 (0.87), residues: 30 loop : -2.89 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 686 HIS 0.002 0.001 HIS A 38 PHE 0.023 0.001 PHE A 107 TYR 0.019 0.001 TYR B 269 ARG 0.004 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 160 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: B 172 MET cc_start: 0.7133 (mmt) cc_final: 0.6895 (mmt) REVERT: B 653 ARG cc_start: 0.5976 (mmp80) cc_final: 0.5581 (mmm-85) REVERT: B 795 MET cc_start: 0.6030 (ppp) cc_final: 0.5285 (ptm) REVERT: B 891 GLN cc_start: 0.6806 (tm-30) cc_final: 0.6580 (tm-30) outliers start: 28 outliers final: 15 residues processed: 152 average time/residue: 0.2059 time to fit residues: 43.3084 Evaluate side-chains 133 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8786 Z= 0.222 Angle : 0.636 10.278 11889 Z= 0.317 Chirality : 0.042 0.243 1334 Planarity : 0.005 0.065 1508 Dihedral : 7.672 104.711 1194 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.79 % Favored : 91.11 % Rotamer: Outliers : 3.51 % Allowed : 22.28 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.62 (0.26), residues: 1035 helix: -0.06 (0.21), residues: 667 sheet: -3.50 (0.82), residues: 37 loop : -2.84 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 686 HIS 0.007 0.001 HIS B 907 PHE 0.025 0.002 PHE A 107 TYR 0.023 0.002 TYR A 42 ARG 0.003 0.000 ARG B 690 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 151 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 0.980 Fit side-chains REVERT: B 157 ILE cc_start: 0.7371 (mt) cc_final: 0.7007 (mt) REVERT: B 795 MET cc_start: 0.5824 (ppp) cc_final: 0.5245 (ptm) REVERT: B 802 GLU cc_start: 0.6505 (tt0) cc_final: 0.6039 (tt0) REVERT: B 963 ARG cc_start: 0.7174 (tpp-160) cc_final: 0.5557 (ttm-80) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.1981 time to fit residues: 40.5994 Evaluate side-chains 136 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 HIS 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: 3.9990 chunk 74 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.5942 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= 0.181 Angle : 0.615 10.961 11889 Z= 0.303 Chirality : 0.040 0.209 1334 Planarity : 0.004 0.063 1508 Dihedral : 7.403 102.036 1194 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.02 % Favored : 91.88 % Rotamer: Outliers : 3.18 % Allowed : 23.16 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.35 (0.27), residues: 1035 helix: 0.22 (0.21), residues: 662 sheet: -3.55 (0.86), residues: 30 loop : -2.85 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 686 HIS 0.003 0.001 HIS A 38 PHE 0.024 0.001 PHE A 107 TYR 0.032 0.001 TYR B 239 ARG 0.003 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 148 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.979 Fit side-chains REVERT: A 43 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: A 151 ASP cc_start: 0.6860 (t0) cc_final: 0.6518 (t70) REVERT: B 157 ILE cc_start: 0.7303 (mt) cc_final: 0.6906 (mt) REVERT: B 653 ARG cc_start: 0.6145 (mmp80) cc_final: 0.5768 (mmm-85) REVERT: B 795 MET cc_start: 0.5899 (ppp) cc_final: 0.5230 (ptm) REVERT: B 802 GLU cc_start: 0.6529 (tt0) cc_final: 0.6067 (tt0) outliers start: 29 outliers final: 23 residues processed: 143 average time/residue: 0.2005 time to fit residues: 40.3900 Evaluate side-chains 137 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8786 Z= 0.231 Angle : 0.657 10.433 11889 Z= 0.324 Chirality : 0.042 0.215 1334 Planarity : 0.005 0.064 1508 Dihedral : 7.614 103.711 1194 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.70 % Favored : 91.21 % Rotamer: Outliers : 3.40 % Allowed : 22.83 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.38 (0.26), residues: 1035 helix: 0.21 (0.20), residues: 663 sheet: -3.47 (0.80), residues: 37 loop : -2.90 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 686 HIS 0.014 0.001 HIS B 289 PHE 0.023 0.002 PHE A 107 TYR 0.033 0.002 TYR B 239 ARG 0.003 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 141 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 0.945 Fit side-chains REVERT: A 151 ASP cc_start: 0.6903 (t0) cc_final: 0.6614 (t0) REVERT: B 142 ILE cc_start: 0.7880 (mt) cc_final: 0.7660 (mt) REVERT: B 157 ILE cc_start: 0.7316 (mt) cc_final: 0.6944 (mt) REVERT: B 653 ARG cc_start: 0.6190 (mmp80) cc_final: 0.5802 (mmm-85) REVERT: B 802 GLU cc_start: 0.6613 (tt0) cc_final: 0.6091 (tt0) outliers start: 31 outliers final: 26 residues processed: 134 average time/residue: 0.1975 time to fit residues: 37.6384 Evaluate side-chains 131 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 888 THR Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 914 HIS 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: 0.7980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 86 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 HIS ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8786 Z= 0.193 Angle : 0.629 9.510 11889 Z= 0.309 Chirality : 0.040 0.207 1334 Planarity : 0.005 0.063 1508 Dihedral : 7.400 112.563 1194 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.60 % Favored : 91.30 % Rotamer: Outliers : 2.74 % Allowed : 23.93 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.14 (0.26), residues: 1035 helix: 0.39 (0.20), residues: 665 sheet: -2.83 (1.19), residues: 20 loop : -2.92 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 686 HIS 0.003 0.001 HIS A 38 PHE 0.023 0.002 PHE A 107 TYR 0.036 0.001 TYR B 239 ARG 0.004 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 140 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: A 67 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.8118 (mmm160) REVERT: B 137 MET cc_start: 0.6742 (mmm) cc_final: 0.6450 (mmt) REVERT: B 142 ILE cc_start: 0.8006 (mt) cc_final: 0.7787 (mt) REVERT: B 157 ILE cc_start: 0.7269 (mt) cc_final: 0.6872 (mt) REVERT: B 653 ARG cc_start: 0.6122 (mmp80) cc_final: 0.5707 (mmm-85) REVERT: B 802 GLU cc_start: 0.6602 (tt0) cc_final: 0.6033 (tt0) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.2293 time to fit residues: 43.9947 Evaluate side-chains 127 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.0000 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8786 Z= 0.179 Angle : 0.629 9.777 11889 Z= 0.308 Chirality : 0.040 0.206 1334 Planarity : 0.004 0.062 1508 Dihedral : 7.406 119.534 1194 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.89 % Favored : 91.01 % Rotamer: Outliers : 2.85 % Allowed : 24.04 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -0.91 (0.27), residues: 1035 helix: 0.64 (0.21), residues: 655 sheet: -2.73 (1.19), residues: 20 loop : -2.90 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 686 HIS 0.003 0.001 HIS B 907 PHE 0.022 0.001 PHE A 107 TYR 0.035 0.001 TYR B 239 ARG 0.004 0.000 ARG B 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 144 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 43 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: A 67 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8100 (mmm160) REVERT: B 137 MET cc_start: 0.6849 (mmm) cc_final: 0.6646 (mmt) REVERT: B 142 ILE cc_start: 0.8006 (mt) cc_final: 0.7777 (mt) REVERT: B 157 ILE cc_start: 0.7263 (mt) cc_final: 0.6877 (mt) REVERT: B 211 GLU cc_start: 0.7163 (tp30) cc_final: 0.6849 (tp30) REVERT: B 653 ARG cc_start: 0.6147 (mmp80) cc_final: 0.5935 (mmp80) REVERT: B 747 LYS cc_start: 0.5923 (pttt) cc_final: 0.5619 (ttpt) REVERT: B 802 GLU cc_start: 0.6541 (tt0) cc_final: 0.5984 (tt0) outliers start: 26 outliers final: 24 residues processed: 137 average time/residue: 0.1919 time to fit residues: 37.5658 Evaluate side-chains 138 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 817 SER Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 894 VAL Chi-restraints excluded: chain B residue 899 THR Chi-restraints excluded: chain B residue 914 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 30.0000 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.177817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.142197 restraints weight = 9022.750| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.79 r_work: 0.3724 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8786 Z= 0.301 Angle : 0.719 9.866 11889 Z= 0.352 Chirality : 0.044 0.204 1334 Planarity : 0.005 0.063 1508 Dihedral : 8.270 147.887 1194 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.66 % Favored : 90.24 % Rotamer: Outliers : 2.96 % Allowed : 24.48 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: -1.40 (0.26), residues: 1035 helix: 0.16 (0.20), residues: 669 sheet: -3.70 (0.75), residues: 37 loop : -2.83 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 686 HIS 0.007 0.001 HIS B 907 PHE 0.024 0.002 PHE A 107 TYR 0.038 0.002 TYR B 239 ARG 0.005 0.001 ARG B 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2584.87 seconds wall clock time: 47 minutes 18.12 seconds (2838.12 seconds total)