Starting phenix.real_space_refine on Tue Mar 19 00:31:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8urb_42488/03_2024/8urb_42488.pdb" } resolution = 3.4 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= 0.002 sd= 0.049 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 41 5.49 5 S 82 5.16 5 C 7239 2.51 5 N 1974 2.21 5 O 2316 1.98 5 H 11060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22714 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 14521 Classifications: {'peptide': 921} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 895} Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2901 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} Chain: "C" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1072 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2909 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 178} Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 639 Classifications: {'RNA': 20} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "J" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 670 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 9} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4641 SG CYS A 296 33.356 94.490 113.706 1.00 58.21 S ATOM 4707 SG CYS A 301 35.192 97.441 115.219 1.00 43.72 S ATOM 4771 SG CYS A 305 35.279 94.028 116.947 1.00 43.40 S ATOM 7554 SG CYS A 482 32.799 95.250 91.808 1.00 41.59 S ATOM 10058 SG CYS A 640 33.477 98.838 92.934 1.00 58.82 S ATOM 10069 SG CYS A 641 31.431 96.466 95.177 1.00 46.50 S Time building chain proxies: 10.41, per 1000 atoms: 0.46 Number of scatterers: 22714 At special positions: 0 Unit cell: (92.568, 122.36, 169.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 82 16.00 P 41 15.00 O 2316 8.00 N 1974 7.00 C 7239 6.00 H 11060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.68 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 290 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 296 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 305 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 637 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 482 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 641 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 640 " Number of angles added : 6 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 56.8% alpha, 12.2% beta 18 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 10.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.760A pdb=" N ARG A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.578A pdb=" N ARG A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.720A pdb=" N LEU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.733A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.592A pdb=" N LYS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.828A pdb=" N MET A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.678A pdb=" N GLU A 267 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.690A pdb=" N PHE A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 372 through 379 removed outlier: 4.491A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 460 through 474 removed outlier: 4.797A pdb=" N VAL A 466 " --> pdb=" O CYS A 462 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.711A pdb=" N VAL A 488 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 506 through 514 removed outlier: 4.022A pdb=" N TYR A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 556 through 577 removed outlier: 3.513A pdb=" N THR A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A 570 " --> pdb=" O TYR A 566 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 642 through 657 removed outlier: 3.571A pdb=" N GLU A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 703 removed outlier: 4.040A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 728 Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.734A pdb=" N VAL A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 746 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 773 through 785 removed outlier: 3.911A pdb=" N ALA A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.649A pdb=" N CYS A 794 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 removed outlier: 4.055A pdb=" N LYS A 802 " --> pdb=" O ASP A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 837 removed outlier: 3.737A pdb=" N ILE A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 4.322A pdb=" N ALA A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 848 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 849 " --> pdb=" O ASP A 846 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 852 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 853 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 867 Processing helix chain 'A' and resid 869 through 899 removed outlier: 3.589A pdb=" N VAL A 875 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.237A pdb=" N TYR A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 31 through 96 removed outlier: 3.975A pdb=" N GLN B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 removed outlier: 3.565A pdb=" N THR B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.901A pdb=" N ARG B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.626A pdb=" N VAL B 172 " --> pdb=" O VAL B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.744A pdb=" N GLU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.739A pdb=" N ALA C 24 " --> pdb=" O ASN C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.501A pdb=" N GLU C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 80 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.598A pdb=" N SER D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 97 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.792A pdb=" N ILE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.796A pdb=" N VAL D 169 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.603A pdb=" N GLU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 5.279A pdb=" N PHE A 63 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP A 112 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 65 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.988A pdb=" N VAL A 29 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 48 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 218 removed outlier: 3.557A pdb=" N ILE A 225 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 227 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 338 removed outlier: 9.864A pdb=" N SER A 358 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP A 329 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 338 removed outlier: 3.518A pdb=" N VAL B 115 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 343 Processing sheet with id=AA8, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.670A pdb=" N ALA A 382 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N VAL B 131 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL A 384 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 156 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 3.685A pdb=" N GLN A 536 " --> pdb=" O GLY A 554 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR A 535 " --> pdb=" O TYR A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 753 Processing sheet with id=AB3, first strand: chain 'A' and resid 811 through 817 Processing sheet with id=AB4, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.810A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP D 158 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D 156 " --> pdb=" O GLU D 189 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 40 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 9.46 Time building geometry restraints manager: 18.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11004 1.03 - 1.23: 77 1.23 - 1.42: 5214 1.42 - 1.62: 6624 1.62 - 1.81: 120 Bond restraints: 23039 Sorted by residual: bond pdb=" N ASP A 331 " pdb=" H ASP A 331 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" N ASP B 24 " pdb=" H ASP B 24 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.76e+01 bond pdb=" N ASN B 28 " pdb=" H ASN B 28 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" ND2 ASN B 28 " pdb="HD22 ASN B 28 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" ND2 ASN B 28 " pdb="HD21 ASN B 28 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 ... (remaining 23034 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.71: 485 106.71 - 113.55: 26548 113.55 - 120.39: 8101 120.39 - 127.23: 6161 127.23 - 134.06: 184 Bond angle restraints: 41479 Sorted by residual: angle pdb=" CA GLU B 144 " pdb=" CB GLU B 144 " pdb=" CG GLU B 144 " ideal model delta sigma weight residual 114.10 122.43 -8.33 2.00e+00 2.50e-01 1.73e+01 angle pdb=" N ASP A 331 " pdb=" CA ASP A 331 " pdb=" C ASP A 331 " ideal model delta sigma weight residual 112.86 109.31 3.55 1.22e+00 6.72e-01 8.46e+00 angle pdb=" CA ASP A 331 " pdb=" C ASP A 331 " pdb=" O ASP A 331 " ideal model delta sigma weight residual 120.32 117.02 3.30 1.18e+00 7.18e-01 7.82e+00 angle pdb=" CA ARG D 96 " pdb=" CB ARG D 96 " pdb=" CG ARG D 96 " ideal model delta sigma weight residual 114.10 119.60 -5.50 2.00e+00 2.50e-01 7.57e+00 angle pdb=" N VAL A 393 " pdb=" CA VAL A 393 " pdb=" C VAL A 393 " ideal model delta sigma weight residual 106.42 110.54 -4.12 1.51e+00 4.39e-01 7.43e+00 ... (remaining 41474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 10017 21.39 - 42.78: 627 42.78 - 64.17: 200 64.17 - 85.56: 53 85.56 - 106.95: 5 Dihedral angle restraints: 10902 sinusoidal: 6133 harmonic: 4769 Sorted by residual: dihedral pdb=" CA TYR A 854 " pdb=" C TYR A 854 " pdb=" N VAL A 855 " pdb=" CA VAL A 855 " ideal model delta harmonic sigma weight residual 180.00 155.02 24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLU D 171 " pdb=" C GLU D 171 " pdb=" N VAL D 172 " pdb=" CA VAL D 172 " ideal model delta harmonic sigma weight residual -180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ASP A 860 " pdb=" CB ASP A 860 " pdb=" CG ASP A 860 " pdb=" OD1 ASP A 860 " ideal model delta sinusoidal sigma weight residual -30.00 -88.33 58.33 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1237 0.027 - 0.054: 428 0.054 - 0.081: 106 0.081 - 0.108: 69 0.108 - 0.135: 28 Chirality restraints: 1868 Sorted by residual: chirality pdb=" CA VAL A 52 " pdb=" N VAL A 52 " pdb=" C VAL A 52 " pdb=" CB VAL A 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL A 661 " pdb=" N VAL A 661 " pdb=" C VAL A 661 " pdb=" CB VAL A 661 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 104 " pdb=" N ILE A 104 " pdb=" C ILE A 104 " pdb=" CB ILE A 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1865 not shown) Planarity restraints: 3294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 28 " 0.089 2.00e-02 2.50e+03 8.39e-02 1.06e+02 pdb=" CG ASN B 28 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN B 28 " -0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN B 28 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 28 " -0.115 2.00e-02 2.50e+03 pdb="HD22 ASN B 28 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 24 " -0.021 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" N ALA B 25 " 0.069 2.00e-02 2.50e+03 pdb=" CA ALA B 25 " -0.018 2.00e-02 2.50e+03 pdb=" H ALA B 25 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.84e+00 pdb=" C ASP B 24 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 24 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA B 25 " -0.018 2.00e-02 2.50e+03 ... (remaining 3291 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1317 2.21 - 2.81: 44949 2.81 - 3.40: 57451 3.40 - 4.00: 75372 4.00 - 4.60: 117376 Nonbonded interactions: 296465 Sorted by model distance: nonbonded pdb=" O ARG A 83 " pdb="HE21 GLN A 193 " model vdw 1.612 1.850 nonbonded pdb=" HG1 THR D 132 " pdb=" O LEU D 184 " model vdw 1.622 1.850 nonbonded pdb=" OE1 GLN A 204 " pdb=" HH TYR A 231 " model vdw 1.632 1.850 nonbonded pdb=" O PHE A 910 " pdb=" HH TYR A 916 " model vdw 1.634 1.850 nonbonded pdb=" H ASP D 161 " pdb=" O GLY D 164 " model vdw 1.648 1.850 ... (remaining 296460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 11 through 192) selection = (chain 'D' and resid 11 through 192) } 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: 0.790 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: 0.310 Extract box with map and model: 4.780 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 87.220 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.002 0.034 11979 Z= 0.155 Angle : 0.518 8.326 16414 Z= 0.303 Chirality : 0.035 0.135 1868 Planarity : 0.003 0.058 1949 Dihedral : 15.021 106.954 4603 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.17 % Allowed : 7.56 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1351 helix: -0.16 (0.21), residues: 620 sheet: -0.38 (0.42), residues: 137 loop : -0.50 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 911 HIS 0.002 0.001 HIS A 567 PHE 0.011 0.001 PHE A 898 TYR 0.012 0.001 TYR A 854 ARG 0.009 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 157 ILE cc_start: 0.8421 (mt) cc_final: 0.8202 (mt) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.7327 time to fit residues: 107.9298 Evaluate side-chains 107 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11979 Z= 0.344 Angle : 0.587 5.649 16414 Z= 0.328 Chirality : 0.040 0.156 1868 Planarity : 0.004 0.036 1949 Dihedral : 11.065 106.995 2075 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.09 % Allowed : 7.47 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.40 (0.22), residues: 1351 helix: 0.28 (0.20), residues: 670 sheet: -0.33 (0.44), residues: 128 loop : -0.79 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 911 HIS 0.005 0.001 HIS A 747 PHE 0.015 0.002 PHE A 736 TYR 0.021 0.002 TYR A 743 ARG 0.005 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.7577 (tp30) cc_final: 0.6998 (tp30) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.5647 time to fit residues: 92.3055 Evaluate side-chains 107 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain D residue 15 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 101 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: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11979 Z= 0.228 Angle : 0.500 5.699 16414 Z= 0.275 Chirality : 0.037 0.148 1868 Planarity : 0.004 0.032 1949 Dihedral : 10.954 106.367 2073 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.26 % Allowed : 8.82 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.13 (0.22), residues: 1351 helix: 0.66 (0.20), residues: 670 sheet: -0.47 (0.40), residues: 138 loop : -0.83 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 911 HIS 0.007 0.001 HIS C 36 PHE 0.011 0.001 PHE D 92 TYR 0.016 0.001 TYR A 743 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8192 (ptp-170) REVERT: B 153 ILE cc_start: 0.8156 (tt) cc_final: 0.7908 (tt) REVERT: B 154 TRP cc_start: 0.9048 (OUTLIER) cc_final: 0.8725 (m100) REVERT: D 96 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7733 (tpt170) outliers start: 15 outliers final: 7 residues processed: 116 average time/residue: 0.5633 time to fit residues: 91.4682 Evaluate side-chains 109 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11979 Z= 0.205 Angle : 0.486 4.929 16414 Z= 0.266 Chirality : 0.037 0.149 1868 Planarity : 0.003 0.030 1949 Dihedral : 10.891 106.731 2073 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.76 % Allowed : 10.24 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.01 (0.23), residues: 1351 helix: 0.86 (0.21), residues: 670 sheet: -0.60 (0.41), residues: 140 loop : -0.81 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.005 0.001 HIS C 36 PHE 0.011 0.001 PHE A 736 TYR 0.016 0.001 TYR A 743 ARG 0.003 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.8327 (ptm) cc_final: 0.8087 (ptm) REVERT: A 511 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: A 745 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7584 (mtm110) REVERT: A 919 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7831 (mtt) REVERT: B 62 MET cc_start: 0.7903 (tpp) cc_final: 0.7666 (tpp) REVERT: D 96 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7774 (tpt170) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.5922 time to fit residues: 97.4721 Evaluate side-chains 116 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 0.1980 chunk 92 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11979 Z= 0.315 Angle : 0.529 4.774 16414 Z= 0.291 Chirality : 0.039 0.147 1868 Planarity : 0.004 0.034 1949 Dihedral : 10.942 107.198 2073 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.35 % Allowed : 10.41 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.23 (0.23), residues: 1351 helix: 0.75 (0.21), residues: 676 sheet: -0.68 (0.41), residues: 140 loop : -1.10 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 911 HIS 0.005 0.001 HIS A 747 PHE 0.013 0.001 PHE A 736 TYR 0.023 0.002 TYR A 743 ARG 0.004 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8651 (p) cc_final: 0.8408 (p) REVERT: A 239 MET cc_start: 0.8501 (ptm) cc_final: 0.8131 (ptm) REVERT: A 511 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: A 564 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8196 (ptp-170) REVERT: A 745 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7564 (mtm110) REVERT: A 919 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: B 62 MET cc_start: 0.7875 (tpp) cc_final: 0.7672 (tpp) REVERT: B 154 TRP cc_start: 0.9087 (OUTLIER) cc_final: 0.8705 (m100) REVERT: C 13 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8020 (tt) outliers start: 28 outliers final: 16 residues processed: 127 average time/residue: 0.5741 time to fit residues: 103.2118 Evaluate side-chains 122 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11979 Z= 0.220 Angle : 0.486 4.823 16414 Z= 0.266 Chirality : 0.037 0.146 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.922 106.936 2073 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.27 % Allowed : 10.83 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.07 (0.23), residues: 1351 helix: 0.89 (0.21), residues: 670 sheet: -0.69 (0.41), residues: 140 loop : -0.99 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 736 TYR 0.016 0.001 TYR A 743 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8637 (p) cc_final: 0.8394 (p) REVERT: A 239 MET cc_start: 0.8524 (ptm) cc_final: 0.8208 (ptm) REVERT: A 511 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: A 745 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7608 (mtm110) REVERT: A 919 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7927 (mtt) REVERT: B 62 MET cc_start: 0.7806 (tpp) cc_final: 0.7584 (tpp) REVERT: B 154 TRP cc_start: 0.9080 (OUTLIER) cc_final: 0.8698 (m100) REVERT: C 13 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8033 (tt) outliers start: 27 outliers final: 20 residues processed: 127 average time/residue: 0.5699 time to fit residues: 101.5531 Evaluate side-chains 129 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11979 Z= 0.229 Angle : 0.484 4.645 16414 Z= 0.265 Chirality : 0.037 0.143 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.907 106.978 2073 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.60 % Allowed : 11.00 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.02 (0.23), residues: 1351 helix: 0.97 (0.21), residues: 670 sheet: -0.70 (0.41), residues: 140 loop : -1.00 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 213 TYR 0.018 0.001 TYR A 743 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8623 (p) cc_final: 0.8383 (p) REVERT: A 239 MET cc_start: 0.8531 (ptm) cc_final: 0.8276 (ptm) REVERT: A 511 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: A 745 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7606 (mtm110) REVERT: A 919 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: B 62 MET cc_start: 0.7771 (tpp) cc_final: 0.7479 (tpp) REVERT: B 154 TRP cc_start: 0.9091 (OUTLIER) cc_final: 0.8703 (m100) REVERT: C 13 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8081 (tt) outliers start: 31 outliers final: 23 residues processed: 129 average time/residue: 0.5625 time to fit residues: 101.7419 Evaluate side-chains 130 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 400 MET Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 161 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11979 Z= 0.254 Angle : 0.498 4.876 16414 Z= 0.273 Chirality : 0.037 0.142 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.909 107.232 2073 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.69 % Allowed : 11.00 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: -0.09 (0.23), residues: 1351 helix: 0.93 (0.21), residues: 677 sheet: -0.69 (0.41), residues: 140 loop : -1.12 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.004 0.001 HIS C 36 PHE 0.011 0.001 PHE A 736 TYR 0.019 0.001 TYR A 743 ARG 0.002 0.000 ARG A 831 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 CYS cc_start: 0.8619 (p) cc_final: 0.8384 (p) REVERT: A 239 MET cc_start: 0.8548 (ptm) cc_final: 0.8300 (ptm) REVERT: A 511 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8472 (m-80) REVERT: A 739 GLU cc_start: 0.8281 (tp30) cc_final: 0.7719 (tt0) REVERT: A 745 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7610 (mtm110) REVERT: A 919 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7923 (mtt) REVERT: B 62 MET cc_start: 0.7765 (tpp) cc_final: 0.7465 (tpp) REVERT: B 154 TRP cc_start: 0.9108 (OUTLIER) cc_final: 0.8668 (m100) REVERT: C 13 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8101 (tt) outliers start: 32 outliers final: 23 residues processed: 128 average time/residue: 0.5762 time to fit residues: 104.4600 Evaluate side-chains 130 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11979 Z= 0.185 Angle : 0.467 5.586 16414 Z= 0.255 Chirality : 0.036 0.140 1868 Planarity : 0.003 0.030 1949 Dihedral : 10.898 107.065 2073 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.02 % Allowed : 11.84 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.17 (0.23), residues: 1351 helix: 1.15 (0.21), residues: 667 sheet: -0.58 (0.41), residues: 145 loop : -0.96 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.003 0.001 HIS B 148 PHE 0.010 0.001 PHE D 49 TYR 0.015 0.001 TYR A 743 ARG 0.002 0.000 ARG A 831 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7847 (mttp) REVERT: A 69 CYS cc_start: 0.8594 (p) cc_final: 0.8360 (p) REVERT: A 85 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: A 239 MET cc_start: 0.8546 (ptm) cc_final: 0.8260 (ptm) REVERT: A 511 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: A 739 GLU cc_start: 0.8218 (tp30) cc_final: 0.7609 (tt0) REVERT: A 745 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7642 (mtm110) REVERT: A 919 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7950 (mtt) REVERT: B 62 MET cc_start: 0.7779 (tpp) cc_final: 0.7460 (tpp) REVERT: B 154 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8651 (m100) REVERT: C 13 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7981 (tt) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.5935 time to fit residues: 109.3629 Evaluate side-chains 132 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11979 Z= 0.201 Angle : 0.469 6.470 16414 Z= 0.256 Chirality : 0.036 0.139 1868 Planarity : 0.003 0.031 1949 Dihedral : 10.884 107.371 2073 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.18 % Allowed : 11.75 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.16 (0.23), residues: 1351 helix: 1.16 (0.21), residues: 671 sheet: -0.55 (0.41), residues: 145 loop : -1.02 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.006 0.001 HIS C 36 PHE 0.010 0.001 PHE A 213 TYR 0.016 0.001 TYR A 743 ARG 0.002 0.000 ARG A 831 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8301 (mtpp) cc_final: 0.7894 (mttp) REVERT: A 69 CYS cc_start: 0.8589 (p) cc_final: 0.8360 (p) REVERT: A 239 MET cc_start: 0.8530 (ptm) cc_final: 0.8292 (ptm) REVERT: A 511 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8396 (m-80) REVERT: A 739 GLU cc_start: 0.8209 (tp30) cc_final: 0.7615 (tt0) REVERT: A 745 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7585 (mtm110) REVERT: A 919 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: B 62 MET cc_start: 0.7789 (tpp) cc_final: 0.7483 (tpp) REVERT: B 154 TRP cc_start: 0.9094 (OUTLIER) cc_final: 0.8638 (m100) REVERT: C 13 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7978 (tt) outliers start: 26 outliers final: 20 residues processed: 129 average time/residue: 0.5570 time to fit residues: 101.8757 Evaluate side-chains 130 residues out of total 1191 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 161 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 564 ARG Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 786 ASN Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 154 TRP Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.167917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119769 restraints weight = 41400.865| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.23 r_work: 0.3294 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11979 Z= 0.238 Angle : 0.486 6.284 16414 Z= 0.266 Chirality : 0.037 0.138 1868 Planarity : 0.003 0.033 1949 Dihedral : 10.886 107.676 2073 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.35 % Allowed : 11.59 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % 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: 0.06 (0.23), residues: 1351 helix: 1.10 (0.21), residues: 678 sheet: -0.53 (0.41), residues: 145 loop : -1.15 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 911 HIS 0.006 0.001 HIS C 36 PHE 0.012 0.001 PHE A 213 TYR 0.018 0.001 TYR A 743 ARG 0.002 0.000 ARG A 831 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.59 seconds wall clock time: 84 minutes 56.50 seconds (5096.50 seconds total)