Starting phenix.real_space_refine on Fri Sep 11 13:57:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.cif" model { file = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aap_11692/09_2026/7aap_11692.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 26 5.49 5 Mg 3 5.21 5 S 66 5.16 5 C 5919 2.51 5 N 1581 2.21 5 O 1848 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 7345 Classifications: {'peptide': 911} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 880} Chain breaks: 1 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "D" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 221 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNAv2': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNAv2': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' MG': 2, ' ZN': 2, 'POP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GE6': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 42.374 62.670 43.895 1.00 49.57 S ATOM 2487 SG CYS A 306 42.428 61.687 40.192 1.00 46.12 S ATOM 2519 SG CYS A 310 45.719 61.837 42.215 1.00 41.58 S ATOM 3927 SG CYS A 487 24.274 58.627 52.787 1.00 52.25 S ATOM 5180 SG CYS A 645 23.549 58.149 49.031 1.00 57.21 S ATOM 5186 SG CYS A 646 26.332 60.537 50.194 1.00 55.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O POP A1005 " occ=0.50 ... (7 atoms not shown) pdb=" P2 POP A1005 " occ=0.50 Time building chain proxies: 1.70, per 1000 atoms: 0.18 Number of scatterers: 9446 At special positions: 0 Unit cell: (102.7, 92.95, 117.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 26 15.00 Mg 3 11.99 F 1 9.00 O 1848 8.00 N 1581 7.00 C 5919 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 252.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 6 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 54.1% alpha, 18.9% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.613A pdb=" N THR A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.523A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.829A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 3.969A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.301A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.656A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.080A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 384 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.878A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.848A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.538A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.598A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 660 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 790 removed outlier: 3.541A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 851 through 867 removed outlier: 3.515A pdb=" N ILE A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 894 removed outlier: 3.813A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.760A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'B' and resid 79 through 93 removed outlier: 3.631A pdb=" N VAL B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.567A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.521A pdb=" N ALA B 125 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.703A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.841A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 17 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 3.545A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.591A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 66 Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.555A pdb=" N THR D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.963A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 111 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 38 removed outlier: 4.579A pdb=" N CYS A 53 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 31 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR A 51 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A 49 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE A 35 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS A 47 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 37 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE A 45 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.041A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.539A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.539A pdb=" N VAL A 335 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL A 341 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 333 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER A 343 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 331 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.505A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.505A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 158 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 757 removed outlier: 4.508A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.611A pdb=" N MET A 818 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.45: 1619 1.45 - 1.57: 5083 1.57 - 1.69: 47 1.69 - 1.81: 99 Bond restraints: 9692 Sorted by residual: bond pdb=" O10 GE6 T1601 " pdb=" P03 GE6 T1601 " ideal model delta sigma weight residual 1.764 1.614 0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C08 GE6 T1601 " pdb=" C10 GE6 T1601 " ideal model delta sigma weight residual 1.454 1.387 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O07 GE6 T1601 " pdb=" P02 GE6 T1601 " ideal model delta sigma weight residual 1.657 1.599 0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" O06 GE6 T1601 " pdb=" P01 GE6 T1601 " ideal model delta sigma weight residual 1.652 1.596 0.056 2.00e-02 2.50e+03 7.91e+00 bond pdb=" N ARG A 553 " pdb=" CA ARG A 553 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.22e-02 6.72e+03 6.30e+00 ... (remaining 9687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12938 1.37 - 2.73: 202 2.73 - 4.10: 90 4.10 - 5.46: 12 5.46 - 6.83: 8 Bond angle restraints: 13250 Sorted by residual: angle pdb=" N ASN A 552 " pdb=" CA ASN A 552 " pdb=" C ASN A 552 " ideal model delta sigma weight residual 113.20 109.15 4.05 1.21e+00 6.83e-01 1.12e+01 angle pdb=" CA GLU A 917 " pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA ALA A 554 " pdb=" C ALA A 554 " pdb=" O ALA A 554 " ideal model delta sigma weight residual 121.05 117.58 3.47 1.14e+00 7.69e-01 9.26e+00 angle pdb=" CA GLU C 50 " pdb=" CB GLU C 50 " pdb=" CG GLU C 50 " ideal model delta sigma weight residual 114.10 119.80 -5.70 2.00e+00 2.50e-01 8.12e+00 angle pdb=" N LEU A 758 " pdb=" CA LEU A 758 " pdb=" C LEU A 758 " ideal model delta sigma weight residual 109.96 106.40 3.56 1.58e+00 4.01e-01 5.08e+00 ... (remaining 13245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 5535 26.36 - 52.73: 198 52.73 - 79.09: 16 79.09 - 105.45: 6 105.45 - 131.82: 2 Dihedral angle restraints: 5757 sinusoidal: 2436 harmonic: 3321 Sorted by residual: dihedral pdb=" O4 POP A1005 " pdb=" O POP A1005 " pdb=" P2 POP A1005 " pdb=" P1 POP A1005 " ideal model delta sinusoidal sigma weight residual -57.41 70.19 -127.61 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O2 POP A1005 " pdb=" O POP A1005 " pdb=" P1 POP A1005 " pdb=" P2 POP A1005 " ideal model delta sinusoidal sigma weight residual -88.77 -176.80 88.04 1 2.00e+01 2.50e-03 2.32e+01 dihedral pdb=" O10 GE6 T1601 " pdb=" O07 GE6 T1601 " pdb=" P02 GE6 T1601 " pdb=" P01 GE6 T1601 " ideal model delta sinusoidal sigma weight residual 198.44 66.62 131.82 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 5754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1287 0.058 - 0.115: 177 0.115 - 0.173: 12 0.173 - 0.231: 13 0.231 - 0.289: 12 Chirality restraints: 1501 Sorted by residual: chirality pdb=" P U P 20 " pdb=" OP1 U P 20 " pdb=" OP2 U P 20 " pdb=" O5' U P 20 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" P A T 18 " pdb=" OP1 A T 18 " pdb=" OP2 A T 18 " pdb=" O5' A T 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" P U P 18 " pdb=" OP1 U P 18 " pdb=" OP2 U P 18 " pdb=" O5' U P 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1498 not shown) Planarity restraints: 1614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.035 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 927 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A P 19 " -0.021 2.00e-02 2.50e+03 9.33e-03 2.39e+00 pdb=" N9 A P 19 " 0.005 2.00e-02 2.50e+03 pdb=" C8 A P 19 " 0.013 2.00e-02 2.50e+03 pdb=" N7 A P 19 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A P 19 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A P 19 " -0.010 2.00e-02 2.50e+03 pdb=" N6 A P 19 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A P 19 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A P 19 " 0.008 2.00e-02 2.50e+03 pdb=" N3 A P 19 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A P 19 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 50 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" CD GLU C 50 " -0.026 2.00e-02 2.50e+03 pdb=" OE1 GLU C 50 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 50 " 0.009 2.00e-02 2.50e+03 ... (remaining 1611 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 119 2.66 - 3.22: 8743 3.22 - 3.78: 14756 3.78 - 4.34: 21626 4.34 - 4.90: 33690 Nonbonded interactions: 78934 Sorted by model distance: nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1004 " model vdw 2.097 2.170 nonbonded pdb="MG MG A1004 " pdb=" O3 POP A1005 " model vdw 2.159 2.170 nonbonded pdb="MG MG A1004 " pdb=" O5 POP A1005 " model vdw 2.216 2.170 nonbonded pdb=" OG1 THR A 120 " pdb=" OD1 ASP A 211 " model vdw 2.225 3.040 nonbonded pdb=" OG SER B 173 " pdb=" OD1 ASP B 175 " model vdw 2.250 3.040 ... (remaining 78929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.610 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.950 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 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 : 0.003 0.150 9700 Z= 0.163 Angle : 0.520 6.827 13256 Z= 0.267 Chirality : 0.049 0.289 1501 Planarity : 0.002 0.054 1614 Dihedral : 13.136 131.817 3611 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1110 helix: 0.54 (0.23), residues: 504 sheet: 0.89 (0.48), residues: 112 loop : 0.31 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 80 TYR 0.014 0.001 TYR A 80 PHE 0.007 0.001 PHE A 741 TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 9692) covalent geometry : angle 0.51946 / 0.27 (13250) hydrogen bonds : bond 0.24964 / 16.79 ( 429) hydrogen bonds : angle 7.29375 / 5.28 ( 1226) metal coordination : bond 0.00384 / 0.26 ( 8) metal coordination : angle 0.65128 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 82 HIS cc_start: 0.8674 (t70) cc_final: 0.8472 (t-90) REVERT: A 98 LYS cc_start: 0.8405 (tttt) cc_final: 0.8101 (tttm) REVERT: A 196 MET cc_start: 0.8759 (mtp) cc_final: 0.8448 (mtp) REVERT: A 806 THR cc_start: 0.8299 (p) cc_final: 0.7425 (p) REVERT: A 855 MET cc_start: 0.7963 (mtm) cc_final: 0.7677 (mtt) REVERT: A 875 GLN cc_start: 0.8955 (tp40) cc_final: 0.8628 (tp40) REVERT: C 28 LEU cc_start: 0.8239 (mm) cc_final: 0.7726 (mt) REVERT: D 94 MET cc_start: 0.6740 (mtt) cc_final: 0.6086 (mpt) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.4967 time to fit residues: 93.4166 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS A 414 ASN A 416 ASN A 713 ASN B 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.084110 restraints weight = 13252.280| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.28 r_work: 0.2904 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9700 Z= 0.189 Angle : 0.580 6.181 13256 Z= 0.306 Chirality : 0.045 0.199 1501 Planarity : 0.004 0.039 1614 Dihedral : 8.803 129.063 1527 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.82 % Allowed : 8.17 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.25), residues: 1110 helix: 1.01 (0.23), residues: 511 sheet: 0.46 (0.45), residues: 122 loop : 0.34 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 914 TYR 0.018 0.002 TYR A 69 PHE 0.022 0.001 PHE A 652 TRP 0.019 0.002 TRP A 916 HIS 0.008 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9692) covalent geometry : angle 0.57831 / 0.31 (13250) hydrogen bonds : bond 0.04722 / 3.25 ( 429) hydrogen bonds : angle 4.81082 / 3.47 ( 1226) metal coordination : bond 0.00520 / 0.34 ( 8) metal coordination : angle 1.97300 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8575 (tttt) cc_final: 0.8190 (tttm) REVERT: A 541 GLN cc_start: 0.8578 (tt0) cc_final: 0.8304 (tt0) REVERT: A 855 MET cc_start: 0.8280 (mtm) cc_final: 0.7946 (mtt) REVERT: A 889 ARG cc_start: 0.8105 (mpt-90) cc_final: 0.7479 (mpt-90) REVERT: B 174 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7910 (tpp) REVERT: C 26 SER cc_start: 0.7964 (t) cc_final: 0.7717 (p) REVERT: D 94 MET cc_start: 0.6576 (mtt) cc_final: 0.5979 (mpt) outliers start: 18 outliers final: 5 residues processed: 144 average time/residue: 0.5009 time to fit residues: 77.4179 Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 174 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 0.0370 chunk 102 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN B 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.086263 restraints weight = 13400.474| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.27 r_work: 0.2938 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9700 Z= 0.110 Angle : 0.491 6.036 13256 Z= 0.256 Chirality : 0.042 0.199 1501 Planarity : 0.003 0.037 1614 Dihedral : 8.455 124.674 1527 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.72 % Allowed : 10.70 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1110 helix: 1.24 (0.24), residues: 510 sheet: 0.26 (0.45), residues: 122 loop : 0.32 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 914 TYR 0.011 0.001 TYR A 788 PHE 0.016 0.001 PHE A 652 TRP 0.019 0.001 TRP A 916 HIS 0.005 0.000 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 9692) covalent geometry : angle 0.49007 / 0.26 (13250) hydrogen bonds : bond 0.03886 / 2.68 ( 429) hydrogen bonds : angle 4.36513 / 3.15 ( 1226) metal coordination : bond 0.00531 / 0.37 ( 8) metal coordination : angle 1.41013 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8568 (tttt) cc_final: 0.8162 (tttm) REVERT: A 414 ASN cc_start: 0.8348 (m110) cc_final: 0.8114 (m-40) REVERT: A 541 GLN cc_start: 0.8532 (tt0) cc_final: 0.8319 (tt0) REVERT: A 736 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8356 (p0) REVERT: A 796 GLU cc_start: 0.8009 (tt0) cc_final: 0.7520 (tm-30) REVERT: A 855 MET cc_start: 0.8306 (mtm) cc_final: 0.8010 (ttm) REVERT: B 163 ASP cc_start: 0.8457 (m-30) cc_final: 0.8220 (m-30) REVERT: B 171 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7816 (mt-10) REVERT: C 26 SER cc_start: 0.7884 (t) cc_final: 0.7670 (p) REVERT: D 94 MET cc_start: 0.6556 (mtt) cc_final: 0.6004 (mpt) outliers start: 17 outliers final: 6 residues processed: 136 average time/residue: 0.5126 time to fit residues: 75.0147 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 892 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.131133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085658 restraints weight = 13455.594| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.29 r_work: 0.2929 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9700 Z= 0.110 Angle : 0.485 5.908 13256 Z= 0.252 Chirality : 0.042 0.201 1501 Planarity : 0.003 0.028 1614 Dihedral : 8.176 126.873 1527 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.41 % Allowed : 12.01 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1110 helix: 1.35 (0.24), residues: 510 sheet: 0.19 (0.45), residues: 122 loop : 0.25 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 914 TYR 0.011 0.001 TYR A 149 PHE 0.015 0.001 PHE A 652 TRP 0.019 0.001 TRP A 916 HIS 0.005 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9692) covalent geometry : angle 0.48408 / 0.25 (13250) hydrogen bonds : bond 0.03608 / 2.50 ( 429) hydrogen bonds : angle 4.19713 / 3.04 ( 1226) metal coordination : bond 0.00431 / 0.29 ( 8) metal coordination : angle 1.34603 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8540 (tttt) cc_final: 0.8208 (tttm) REVERT: A 541 GLN cc_start: 0.8524 (tt0) cc_final: 0.8303 (tt0) REVERT: A 668 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8099 (tpp) REVERT: A 736 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8403 (p0) REVERT: A 796 GLU cc_start: 0.8006 (tt0) cc_final: 0.7484 (tm-30) REVERT: A 855 MET cc_start: 0.8327 (mtm) cc_final: 0.8020 (ttm) REVERT: A 889 ARG cc_start: 0.8241 (mpt-90) cc_final: 0.8019 (mtm-85) REVERT: B 163 ASP cc_start: 0.8430 (m-30) cc_final: 0.7945 (m-30) REVERT: B 171 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7960 (mt-10) REVERT: D 94 MET cc_start: 0.6575 (mtt) cc_final: 0.6014 (mpt) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 0.5093 time to fit residues: 69.4669 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 916 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084709 restraints weight = 13427.625| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.25 r_work: 0.2900 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9700 Z= 0.135 Angle : 0.506 10.208 13256 Z= 0.263 Chirality : 0.042 0.200 1501 Planarity : 0.003 0.025 1614 Dihedral : 8.110 125.408 1527 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.31 % Allowed : 13.52 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1110 helix: 1.38 (0.23), residues: 518 sheet: 0.14 (0.44), residues: 132 loop : 0.16 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 914 TYR 0.016 0.001 TYR B 135 PHE 0.017 0.001 PHE A 652 TRP 0.017 0.001 TRP A 916 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 9692) covalent geometry : angle 0.50524 / 0.26 (13250) hydrogen bonds : bond 0.03881 / 2.70 ( 429) hydrogen bonds : angle 4.21693 / 3.06 ( 1226) metal coordination : bond 0.00417 / 0.26 ( 8) metal coordination : angle 1.43147 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8536 (tttt) cc_final: 0.8134 (tttm) REVERT: A 541 GLN cc_start: 0.8578 (tt0) cc_final: 0.8278 (tt0) REVERT: A 648 LEU cc_start: 0.9022 (mm) cc_final: 0.8745 (tp) REVERT: A 668 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8065 (tpp) REVERT: A 796 GLU cc_start: 0.7938 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 855 MET cc_start: 0.8406 (mtm) cc_final: 0.8097 (ttm) REVERT: A 879 ASP cc_start: 0.8730 (m-30) cc_final: 0.8523 (m-30) REVERT: A 889 ARG cc_start: 0.8309 (mpt-90) cc_final: 0.8108 (mtm-85) REVERT: B 163 ASP cc_start: 0.8138 (m-30) cc_final: 0.7919 (m-30) REVERT: B 171 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 27 LYS cc_start: 0.8097 (mmpt) cc_final: 0.7825 (mmtm) REVERT: D 94 MET cc_start: 0.6511 (mtt) cc_final: 0.6079 (ttm) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.5374 time to fit residues: 67.7677 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 758 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 0.0970 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.128874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083504 restraints weight = 13421.981| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.25 r_work: 0.2886 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9700 Z= 0.164 Angle : 0.524 6.346 13256 Z= 0.276 Chirality : 0.043 0.199 1501 Planarity : 0.003 0.024 1614 Dihedral : 8.105 122.480 1527 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.61 % Allowed : 13.93 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1110 helix: 1.39 (0.23), residues: 514 sheet: 0.10 (0.44), residues: 132 loop : 0.10 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 914 TYR 0.014 0.001 TYR A 149 PHE 0.019 0.001 PHE A 652 TRP 0.020 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9692) covalent geometry : angle 0.52333 / 0.28 (13250) hydrogen bonds : bond 0.04142 / 2.88 ( 429) hydrogen bonds : angle 4.26262 / 3.09 ( 1226) metal coordination : bond 0.00527 / 0.33 ( 8) metal coordination : angle 1.63887 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8516 (tttt) cc_final: 0.8134 (tttm) REVERT: A 541 GLN cc_start: 0.8610 (tt0) cc_final: 0.8313 (tt0) REVERT: A 668 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8065 (tpp) REVERT: A 736 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8577 (p0) REVERT: A 796 GLU cc_start: 0.7909 (tt0) cc_final: 0.7419 (tm-30) REVERT: A 855 MET cc_start: 0.8460 (mtm) cc_final: 0.8122 (ttm) REVERT: A 889 ARG cc_start: 0.8375 (mpt-90) cc_final: 0.8172 (mtm-85) REVERT: B 163 ASP cc_start: 0.8083 (m-30) cc_final: 0.7855 (m-30) REVERT: D 90 MET cc_start: 0.6669 (ppp) cc_final: 0.6429 (tmm) outliers start: 16 outliers final: 7 residues processed: 125 average time/residue: 0.5011 time to fit residues: 67.6946 Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 88 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082674 restraints weight = 13308.054| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.24 r_work: 0.2879 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9700 Z= 0.179 Angle : 0.538 7.461 13256 Z= 0.282 Chirality : 0.044 0.198 1501 Planarity : 0.003 0.024 1614 Dihedral : 8.150 119.644 1527 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.51 % Allowed : 14.23 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1110 helix: 1.35 (0.23), residues: 514 sheet: 0.22 (0.45), residues: 123 loop : 0.07 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 914 TYR 0.014 0.002 TYR A 515 PHE 0.019 0.001 PHE A 652 TRP 0.022 0.002 TRP B 182 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9692) covalent geometry : angle 0.53715 / 0.28 (13250) hydrogen bonds : bond 0.04261 / 2.96 ( 429) hydrogen bonds : angle 4.30706 / 3.12 ( 1226) metal coordination : bond 0.00593 / 0.37 ( 8) metal coordination : angle 1.62943 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8526 (tttt) cc_final: 0.8249 (tttm) REVERT: A 668 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8076 (tpp) REVERT: A 796 GLU cc_start: 0.7906 (tt0) cc_final: 0.7416 (tm-30) REVERT: A 855 MET cc_start: 0.8493 (mtm) cc_final: 0.8145 (ttm) REVERT: C 27 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7889 (tptt) REVERT: D 94 MET cc_start: 0.6510 (mtt) cc_final: 0.5801 (mpt) outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 0.4778 time to fit residues: 63.0196 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 16 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.085592 restraints weight = 13376.218| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.24 r_work: 0.2929 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9700 Z= 0.102 Angle : 0.498 11.724 13256 Z= 0.259 Chirality : 0.041 0.186 1501 Planarity : 0.003 0.025 1614 Dihedral : 8.030 122.534 1527 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.11 % Allowed : 14.63 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1110 helix: 1.47 (0.24), residues: 516 sheet: 0.24 (0.45), residues: 122 loop : 0.08 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 914 TYR 0.012 0.001 TYR A 788 PHE 0.015 0.001 PHE A 652 TRP 0.024 0.002 TRP B 182 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9692) covalent geometry : angle 0.49716 / 0.26 (13250) hydrogen bonds : bond 0.03390 / 2.34 ( 429) hydrogen bonds : angle 4.13293 / 3.00 ( 1226) metal coordination : bond 0.00424 / 0.29 ( 8) metal coordination : angle 1.29347 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8489 (tttt) cc_final: 0.8202 (tttm) REVERT: A 452 ASP cc_start: 0.8794 (t70) cc_final: 0.8440 (t70) REVERT: A 668 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8041 (tpp) REVERT: A 796 GLU cc_start: 0.7883 (tt0) cc_final: 0.7365 (tm-30) REVERT: A 855 MET cc_start: 0.8477 (mtm) cc_final: 0.8151 (ttm) REVERT: A 875 GLN cc_start: 0.8614 (tp40) cc_final: 0.8141 (tp-100) REVERT: C 27 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7787 (tptt) outliers start: 11 outliers final: 6 residues processed: 123 average time/residue: 0.4960 time to fit residues: 66.0648 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain C residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 552 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.129782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.084365 restraints weight = 13272.033| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.24 r_work: 0.2899 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9700 Z= 0.129 Angle : 0.502 6.079 13256 Z= 0.263 Chirality : 0.042 0.183 1501 Planarity : 0.003 0.025 1614 Dihedral : 7.967 122.656 1527 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 14.33 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1110 helix: 1.47 (0.24), residues: 516 sheet: 0.31 (0.47), residues: 112 loop : 0.04 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 889 TYR 0.024 0.001 TYR B 135 PHE 0.016 0.001 PHE A 652 TRP 0.029 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9692) covalent geometry : angle 0.50149 / 0.26 (13250) hydrogen bonds : bond 0.03720 / 2.58 ( 429) hydrogen bonds : angle 4.16071 / 3.02 ( 1226) metal coordination : bond 0.00455 / 0.30 ( 8) metal coordination : angle 1.41969 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8217 (t) cc_final: 0.7885 (p) REVERT: A 98 LYS cc_start: 0.8481 (tttt) cc_final: 0.8199 (tttm) REVERT: A 541 GLN cc_start: 0.8531 (tt0) cc_final: 0.8245 (tt0) REVERT: A 668 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8033 (tpp) REVERT: A 796 GLU cc_start: 0.7885 (tt0) cc_final: 0.7388 (tm-30) REVERT: A 855 MET cc_start: 0.8492 (mtm) cc_final: 0.8169 (ttm) REVERT: A 875 GLN cc_start: 0.8609 (tp40) cc_final: 0.8144 (tp-100) REVERT: B 135 TYR cc_start: 0.8206 (t80) cc_final: 0.7992 (t80) REVERT: C 27 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7812 (tptt) REVERT: D 94 MET cc_start: 0.6248 (mtp) cc_final: 0.5924 (mtt) outliers start: 15 outliers final: 7 residues processed: 128 average time/residue: 0.5188 time to fit residues: 71.5767 Evaluate side-chains 123 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain C residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084594 restraints weight = 13239.243| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.24 r_work: 0.2908 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9700 Z= 0.128 Angle : 0.522 11.970 13256 Z= 0.269 Chirality : 0.042 0.179 1501 Planarity : 0.003 0.025 1614 Dihedral : 7.945 122.602 1527 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.11 % Allowed : 14.93 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1110 helix: 1.46 (0.23), residues: 516 sheet: 0.33 (0.47), residues: 112 loop : 0.03 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 889 TYR 0.023 0.001 TYR B 135 PHE 0.016 0.001 PHE A 652 TRP 0.030 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9692) covalent geometry : angle 0.52082 / 0.27 (13250) hydrogen bonds : bond 0.03682 / 2.55 ( 429) hydrogen bonds : angle 4.15061 / 3.01 ( 1226) metal coordination : bond 0.00451 / 0.29 ( 8) metal coordination : angle 1.40897 / 0.86 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8476 (tttt) cc_final: 0.8192 (tttm) REVERT: A 541 GLN cc_start: 0.8507 (tt0) cc_final: 0.8233 (tt0) REVERT: A 668 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8011 (tpp) REVERT: A 796 GLU cc_start: 0.7885 (tt0) cc_final: 0.7381 (tm-30) REVERT: A 855 MET cc_start: 0.8509 (mtm) cc_final: 0.8182 (ttm) REVERT: A 875 GLN cc_start: 0.8607 (tp40) cc_final: 0.8136 (tp-100) REVERT: C 27 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7829 (tptt) outliers start: 11 outliers final: 9 residues processed: 124 average time/residue: 0.5469 time to fit residues: 72.9537 Evaluate side-chains 134 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 19 optimal weight: 0.0970 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.130715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085473 restraints weight = 13202.374| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.24 r_work: 0.2913 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9700 Z= 0.111 Angle : 0.505 8.302 13256 Z= 0.263 Chirality : 0.042 0.170 1501 Planarity : 0.003 0.061 1614 Dihedral : 7.906 123.478 1527 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.11 % Allowed : 15.04 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.26), residues: 1110 helix: 1.53 (0.24), residues: 507 sheet: 0.35 (0.48), residues: 112 loop : 0.08 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 914 TYR 0.014 0.001 TYR B 135 PHE 0.015 0.001 PHE A 652 TRP 0.033 0.002 TRP B 182 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9692) covalent geometry : angle 0.50384 / 0.26 (13250) hydrogen bonds : bond 0.03458 / 2.38 ( 429) hydrogen bonds : angle 4.10005 / 2.98 ( 1226) metal coordination : bond 0.00412 / 0.27 ( 8) metal coordination : angle 1.32647 / 0.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4241.12 seconds wall clock time: 72 minutes 45.23 seconds (4365.23 seconds total)