Starting phenix.real_space_refine on Sun Jul 5 05:22:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.map" model { file = "/net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgq_53144/07_2026/9qgq_53144.cif" } resolution = 4.5 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= 0.009 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 15843 2.51 5 N 4182 2.21 5 O 4956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24993 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8331 Classifications: {'peptide': 1042} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 1018} Chain breaks: 8 Restraints were copied for chains: B, C Time building chain proxies: 9.81, per 1000 atoms: 0.39 Number of scatterers: 24993 At special positions: 0 Unit cell: (184.92, 182.16, 106.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 4956 8.00 N 4182 7.00 C 15843 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: 2.12 Conformation dependent library (CDL) restraints added in 924.2 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 21 sheets defined 55.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.572A pdb=" N VAL A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.993A pdb=" N GLN A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 61 removed outlier: 3.907A pdb=" N MET A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.697A pdb=" N THR A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 93 removed outlier: 4.018A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 71 " --> pdb=" O LYS A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.755A pdb=" N HIS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 111 through 133 removed outlier: 3.594A pdb=" N LYS A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.844A pdb=" N TYR A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.552A pdb=" N SER A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.638A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 485 through 502 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 564 through 600 removed outlier: 5.723A pdb=" N GLU A 570 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.001A pdb=" N GLU A 606 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.904A pdb=" N TYR A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 693 removed outlier: 3.781A pdb=" N LYS A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 680 " --> pdb=" O ASP A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 3.987A pdb=" N THR A 732 " --> pdb=" O ASN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 748 removed outlier: 3.699A pdb=" N GLN A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 748 " --> pdb=" O TYR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 780 through 797 removed outlier: 3.589A pdb=" N ILE A 785 " --> pdb=" O ASP A 781 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A 786 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.608A pdb=" N ASP A 825 " --> pdb=" O GLU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.690A pdb=" N TYR A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 3.791A pdb=" N GLN A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1019 removed outlier: 3.916A pdb=" N SER A1019 " --> pdb=" O SER A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 Processing helix chain 'A' and resid 1074 through 1078 removed outlier: 4.292A pdb=" N TYR A1077 " --> pdb=" O ASN A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 removed outlier: 4.242A pdb=" N LEU A1090 " --> pdb=" O SER A1086 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A1091 " --> pdb=" O MET A1087 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1112 Processing helix chain 'A' and resid 1126 through 1142 removed outlier: 3.523A pdb=" N LYS A1131 " --> pdb=" O LEU A1127 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1134 " --> pdb=" O GLN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1202 removed outlier: 3.783A pdb=" N SER A1201 " --> pdb=" O ASN A1198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1202 " --> pdb=" O TYR A1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1198 through 1202' Processing helix chain 'A' and resid 1220 through 1225 Processing helix chain 'A' and resid 1228 through 1233 removed outlier: 4.233A pdb=" N LEU A1232 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1233 " --> pdb=" O ASP A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1242 removed outlier: 4.518A pdb=" N ASP A1240 " --> pdb=" O SER A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1259 Processing helix chain 'A' and resid 1260 through 1274 Processing helix chain 'A' and resid 1284 through 1289 Processing helix chain 'B' and resid 6 through 13 removed outlier: 3.571A pdb=" N VAL B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 38 removed outlier: 3.992A pdb=" N GLN B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 61 removed outlier: 3.905A pdb=" N MET B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 52 - end of helix removed outlier: 3.697A pdb=" N THR B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 removed outlier: 4.018A pdb=" N LEU B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.755A pdb=" N HIS B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 111 through 133 removed outlier: 3.595A pdb=" N LYS B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 161 through 165 Processing helix chain 'B' and resid 182 through 201 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.842A pdb=" N TYR B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.552A pdb=" N SER B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 266 Processing helix chain 'B' and resid 301 through 316 removed outlier: 3.638A pdb=" N GLN B 316 " --> pdb=" O TYR B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 474 through 478 Processing helix chain 'B' and resid 485 through 502 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 564 through 600 removed outlier: 5.723A pdb=" N GLU B 570 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU B 571 " --> pdb=" O ASP B 567 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 596 " --> pdb=" O THR B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 removed outlier: 4.000A pdb=" N GLU B 606 " --> pdb=" O PHE B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.905A pdb=" N TYR B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 641 " --> pdb=" O TYR B 637 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 693 removed outlier: 3.780A pdb=" N LYS B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 733 removed outlier: 3.987A pdb=" N THR B 732 " --> pdb=" O ASN B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 748 removed outlier: 3.698A pdb=" N GLN B 737 " --> pdb=" O SER B 733 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 748 " --> pdb=" O TYR B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 780 through 797 removed outlier: 3.591A pdb=" N ILE B 785 " --> pdb=" O ASP B 781 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 786 " --> pdb=" O ASN B 782 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 797 " --> pdb=" O ASP B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 831 removed outlier: 3.608A pdb=" N ASP B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 855 removed outlier: 3.689A pdb=" N TYR B 845 " --> pdb=" O ASP B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 871 removed outlier: 3.791A pdb=" N GLN B 865 " --> pdb=" O LYS B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1019 removed outlier: 3.917A pdb=" N SER B1019 " --> pdb=" O SER B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1074 through 1078 removed outlier: 4.294A pdb=" N TYR B1077 " --> pdb=" O ASN B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 removed outlier: 4.241A pdb=" N LEU B1090 " --> pdb=" O SER B1086 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS B1091 " --> pdb=" O MET B1087 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B1095 " --> pdb=" O LYS B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1112 Processing helix chain 'B' and resid 1126 through 1142 removed outlier: 3.522A pdb=" N LYS B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B1134 " --> pdb=" O GLN B1130 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1202 removed outlier: 3.783A pdb=" N SER B1201 " --> pdb=" O ASN B1198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B1202 " --> pdb=" O TYR B1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1198 through 1202' Processing helix chain 'B' and resid 1220 through 1225 Processing helix chain 'B' and resid 1228 through 1233 removed outlier: 4.234A pdb=" N LEU B1232 " --> pdb=" O THR B1229 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B1233 " --> pdb=" O ASP B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1242 removed outlier: 4.519A pdb=" N ASP B1240 " --> pdb=" O SER B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1246 through 1259 Processing helix chain 'B' and resid 1260 through 1274 Processing helix chain 'B' and resid 1284 through 1289 Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.572A pdb=" N VAL C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.993A pdb=" N GLN C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 61 removed outlier: 3.907A pdb=" N MET C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Proline residue: C 52 - end of helix removed outlier: 3.696A pdb=" N THR C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 93 removed outlier: 4.018A pdb=" N LEU C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 71 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 removed outlier: 3.754A pdb=" N HIS C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 111 through 133 removed outlier: 3.595A pdb=" N LYS C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 125 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE C 133 " --> pdb=" O ILE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 161 through 165 Processing helix chain 'C' and resid 182 through 201 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.844A pdb=" N TYR C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.552A pdb=" N SER C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 301 through 316 removed outlier: 3.638A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 485 through 502 Processing helix chain 'C' and resid 514 through 524 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 554 through 563 Processing helix chain 'C' and resid 564 through 600 removed outlier: 5.723A pdb=" N GLU C 570 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 581 " --> pdb=" O LYS C 577 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 596 " --> pdb=" O THR C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 608 removed outlier: 4.001A pdb=" N GLU C 606 " --> pdb=" O PHE C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.905A pdb=" N TYR C 637 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR C 638 " --> pdb=" O LEU C 634 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE C 641 " --> pdb=" O TYR C 637 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN C 644 " --> pdb=" O ASP C 640 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 646 " --> pdb=" O ILE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 693 removed outlier: 3.780A pdb=" N LYS C 675 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS C 680 " --> pdb=" O ASP C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 733 removed outlier: 3.986A pdb=" N THR C 732 " --> pdb=" O ASN C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 748 removed outlier: 3.698A pdb=" N GLN C 737 " --> pdb=" O SER C 733 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 748 " --> pdb=" O TYR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 753 Processing helix chain 'C' and resid 780 through 797 removed outlier: 3.591A pdb=" N ILE C 785 " --> pdb=" O ASP C 781 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE C 786 " --> pdb=" O ASN C 782 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 797 " --> pdb=" O ASP C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 831 removed outlier: 3.608A pdb=" N ASP C 825 " --> pdb=" O GLU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 855 removed outlier: 3.690A pdb=" N TYR C 845 " --> pdb=" O ASP C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 871 removed outlier: 3.791A pdb=" N GLN C 865 " --> pdb=" O LYS C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1019 removed outlier: 3.917A pdb=" N SER C1019 " --> pdb=" O SER C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1032 Processing helix chain 'C' and resid 1074 through 1078 removed outlier: 4.292A pdb=" N TYR C1077 " --> pdb=" O ASN C1074 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1095 removed outlier: 4.241A pdb=" N LEU C1090 " --> pdb=" O SER C1086 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS C1091 " --> pdb=" O MET C1087 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN C1095 " --> pdb=" O LYS C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1112 Processing helix chain 'C' and resid 1126 through 1142 removed outlier: 3.522A pdb=" N LYS C1131 " --> pdb=" O LEU C1127 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C1134 " --> pdb=" O GLN C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1198 through 1202 removed outlier: 3.784A pdb=" N SER C1201 " --> pdb=" O ASN C1198 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C1202 " --> pdb=" O TYR C1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1198 through 1202' Processing helix chain 'C' and resid 1220 through 1225 Processing helix chain 'C' and resid 1228 through 1233 removed outlier: 4.233A pdb=" N LEU C1232 " --> pdb=" O THR C1229 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C1233 " --> pdb=" O ASP C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1235 through 1242 removed outlier: 4.519A pdb=" N ASP C1240 " --> pdb=" O SER C1237 " (cutoff:3.500A) Processing helix chain 'C' and resid 1246 through 1259 Processing helix chain 'C' and resid 1260 through 1274 Processing helix chain 'C' and resid 1284 through 1289 Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 142 Processing sheet with id=AA2, first strand: chain 'A' and resid 287 through 291 removed outlier: 3.669A pdb=" N GLY A 287 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 204 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 323 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS A 449 " --> pdb=" O ASP A 323 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS A 325 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 Processing sheet with id=AA5, first strand: chain 'A' and resid 1010 through 1014 removed outlier: 5.388A pdb=" N PHE A1010 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A 882 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A1012 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 880 " --> pdb=" O GLY A1012 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 877 " --> pdb=" O VAL A1219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A1214 " --> pdb=" O ILE A1189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1010 through 1014 removed outlier: 5.388A pdb=" N PHE A1010 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A 882 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A1012 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 880 " --> pdb=" O GLY A1012 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA A 877 " --> pdb=" O VAL A1219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1280 through 1282 Processing sheet with id=AA8, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 287 through 291 removed outlier: 3.669A pdb=" N GLY B 287 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN B 204 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 323 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS B 449 " --> pdb=" O ASP B 323 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 325 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 480 Processing sheet with id=AB3, first strand: chain 'B' and resid 1010 through 1014 removed outlier: 5.386A pdb=" N PHE B1010 " --> pdb=" O SER B 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER B 882 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B1012 " --> pdb=" O VAL B 880 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 880 " --> pdb=" O GLY B1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 877 " --> pdb=" O VAL B1219 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B1214 " --> pdb=" O ILE B1189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1010 through 1014 removed outlier: 5.386A pdb=" N PHE B1010 " --> pdb=" O SER B 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER B 882 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY B1012 " --> pdb=" O VAL B 880 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 880 " --> pdb=" O GLY B1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA B 877 " --> pdb=" O VAL B1219 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1280 through 1282 Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain 'C' and resid 287 through 291 removed outlier: 3.669A pdb=" N GLY C 287 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN C 204 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP C 323 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LYS C 449 " --> pdb=" O ASP C 323 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LYS C 325 " --> pdb=" O LYS C 449 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 268 through 269 Processing sheet with id=AB9, first strand: chain 'C' and resid 479 through 480 Processing sheet with id=AC1, first strand: chain 'C' and resid 1010 through 1014 removed outlier: 5.387A pdb=" N PHE C1010 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER C 882 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C1012 " --> pdb=" O VAL C 880 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 880 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 877 " --> pdb=" O VAL C1219 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR C1214 " --> pdb=" O ILE C1189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1010 through 1014 removed outlier: 5.387A pdb=" N PHE C1010 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER C 882 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C1012 " --> pdb=" O VAL C 880 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 880 " --> pdb=" O GLY C1012 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 877 " --> pdb=" O VAL C1219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1280 through 1282 1200 hydrogen bonds defined for protein. 3411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 4380 1.30 - 1.42: 6438 1.42 - 1.55: 14579 1.55 - 1.67: 4 1.67 - 1.80: 24 Bond restraints: 25425 Sorted by residual: bond pdb=" C SER B 305 " pdb=" O SER B 305 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.73e+01 bond pdb=" C SER A 305 " pdb=" O SER A 305 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C SER C 305 " pdb=" O SER C 305 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.69e+01 bond pdb=" C SER B 305 " pdb=" N ALA B 306 " ideal model delta sigma weight residual 1.335 1.279 0.056 1.36e-02 5.41e+03 1.69e+01 bond pdb=" C SER A 305 " pdb=" N ALA A 306 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.36e-02 5.41e+03 1.64e+01 ... (remaining 25420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 33319 1.40 - 2.80: 762 2.80 - 4.20: 139 4.20 - 5.60: 49 5.60 - 7.00: 15 Bond angle restraints: 34284 Sorted by residual: angle pdb=" N SER C 305 " pdb=" CA SER C 305 " pdb=" CB SER C 305 " ideal model delta sigma weight residual 110.12 104.67 5.45 1.47e+00 4.63e-01 1.37e+01 angle pdb=" N SER B 305 " pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 110.12 104.69 5.43 1.47e+00 4.63e-01 1.36e+01 angle pdb=" N SER A 305 " pdb=" CA SER A 305 " pdb=" CB SER A 305 " ideal model delta sigma weight residual 110.12 104.71 5.41 1.47e+00 4.63e-01 1.36e+01 angle pdb=" C THR A 710 " pdb=" CA THR A 710 " pdb=" CB THR A 710 " ideal model delta sigma weight residual 111.17 104.62 6.55 1.96e+00 2.60e-01 1.12e+01 angle pdb=" C THR C 710 " pdb=" CA THR C 710 " pdb=" CB THR C 710 " ideal model delta sigma weight residual 111.17 104.63 6.54 1.96e+00 2.60e-01 1.11e+01 ... (remaining 34279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 12622 17.34 - 34.69: 2006 34.69 - 52.03: 565 52.03 - 69.38: 95 69.38 - 86.72: 42 Dihedral angle restraints: 15330 sinusoidal: 6177 harmonic: 9153 Sorted by residual: dihedral pdb=" CA ASP A 756 " pdb=" C ASP A 756 " pdb=" N ILE A 757 " pdb=" CA ILE A 757 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP C 756 " pdb=" C ASP C 756 " pdb=" N ILE C 757 " pdb=" CA ILE C 757 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ARG B1007 " pdb=" C ARG B1007 " pdb=" N TYR B1008 " pdb=" CA TYR B1008 " ideal model delta harmonic sigma weight residual -180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 15327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2161 0.029 - 0.057: 1101 0.057 - 0.086: 402 0.086 - 0.115: 135 0.115 - 0.143: 14 Chirality restraints: 3813 Sorted by residual: chirality pdb=" CA ILE A 459 " pdb=" N ILE A 459 " pdb=" C ILE A 459 " pdb=" CB ILE A 459 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE B 459 " pdb=" N ILE B 459 " pdb=" C ILE B 459 " pdb=" CB ILE B 459 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 697 " pdb=" N ILE A 697 " pdb=" C ILE A 697 " pdb=" CB ILE A 697 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 3810 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 301 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO C 302 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 301 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO B 302 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 301 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 302 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " 0.027 5.00e-02 4.00e+02 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2533 2.74 - 3.28: 26417 3.28 - 3.82: 44039 3.82 - 4.36: 55298 4.36 - 4.90: 90925 Nonbonded interactions: 219212 Sorted by model distance: nonbonded pdb=" OG SER C1086 " pdb=" OD1 ASN C1089 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A1086 " pdb=" OD1 ASN A1089 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B1086 " pdb=" OD1 ASN B1089 " model vdw 2.202 3.040 nonbonded pdb=" ND2 ASN B 200 " pdb=" OH TYR B 522 " model vdw 2.213 3.120 nonbonded pdb=" ND2 ASN C 200 " pdb=" OH TYR C 522 " model vdw 2.213 3.120 ... (remaining 219207 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.100 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 28.530 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1651 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 : 0.004 0.061 25425 Z= 0.203 Angle : 0.569 7.003 34284 Z= 0.318 Chirality : 0.039 0.143 3813 Planarity : 0.003 0.048 4464 Dihedral : 18.425 86.721 9396 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.69 % Allowed : 29.75 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.15), residues: 3072 helix: -0.59 (0.13), residues: 1506 sheet: 0.08 (0.40), residues: 159 loop : -0.71 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 39 TYR 0.017 0.002 TYR B 312 PHE 0.019 0.002 PHE C 57 TRP 0.020 0.002 TRP B 854 HIS 0.004 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.20 (25425) covalent geometry : angle 0.56882 / 0.32 (34284) hydrogen bonds : bond 0.17092 / 11.22 ( 1167) hydrogen bonds : angle 7.96558 / 5.63 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 THR cc_start: 0.3660 (OUTLIER) cc_final: 0.2136 (p) REVERT: A 486 VAL cc_start: 0.4998 (t) cc_final: 0.4754 (t) REVERT: A 761 THR cc_start: 0.5912 (m) cc_final: 0.5698 (m) REVERT: A 1007 ARG cc_start: 0.4540 (mmm160) cc_final: 0.3618 (pmt-80) REVERT: A 1027 SER cc_start: 0.5054 (OUTLIER) cc_final: 0.4278 (t) outliers start: 43 outliers final: 9 residues processed: 172 average time/residue: 0.1026 time to fit residues: 23.4079 Evaluate side-chains 81 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.0270 chunk 298 optimal weight: 0.8980 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 181 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 258 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 737 GLN A 738 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1294 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.211973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.191464 restraints weight = 31884.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.194628 restraints weight = 24859.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.197082 restraints weight = 20031.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.198934 restraints weight = 16553.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.200517 restraints weight = 13993.487| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2966 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25425 Z= 0.150 Angle : 0.633 8.253 34284 Z= 0.336 Chirality : 0.042 0.269 3813 Planarity : 0.004 0.058 4464 Dihedral : 4.746 23.679 3300 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.66 (0.15), residues: 3072 helix: -0.25 (0.13), residues: 1506 sheet: -0.36 (0.39), residues: 159 loop : -0.49 (0.18), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.023 0.002 TYR C 638 PHE 0.024 0.002 PHE C1215 TRP 0.013 0.003 TRP C1295 HIS 0.005 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (25425) covalent geometry : angle 0.63267 / 0.34 (34284) hydrogen bonds : bond 0.04553 / 3.00 ( 1167) hydrogen bonds : angle 5.80421 / 4.13 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 PHE cc_start: 0.1260 (m-80) cc_final: 0.0829 (m-80) REVERT: B 296 MET cc_start: -0.0611 (mmp) cc_final: -0.1042 (mmt) REVERT: B 686 LYS cc_start: 0.9280 (tmmt) cc_final: 0.8951 (tppt) REVERT: B 844 ASP cc_start: 0.6346 (m-30) cc_final: 0.6059 (p0) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.0895 time to fit residues: 14.5609 Evaluate side-chains 68 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 302 optimal weight: 0.0870 chunk 23 optimal weight: 0.1980 chunk 263 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 250 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 202 optimal weight: 0.9980 chunk 240 optimal weight: 0.0570 chunk 253 optimal weight: 0.5980 overall best weight: 0.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 255 ASN B 271 GLN B 279 ASN B 316 GLN B 575 HIS ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 738 ASN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1266 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.214720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.196382 restraints weight = 34395.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.199144 restraints weight = 26973.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.201301 restraints weight = 21865.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.203110 restraints weight = 17964.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.204430 restraints weight = 15074.489| |-----------------------------------------------------------------------------| r_work (final): 0.4988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2888 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25425 Z= 0.124 Angle : 0.568 7.418 34284 Z= 0.301 Chirality : 0.040 0.164 3813 Planarity : 0.004 0.050 4464 Dihedral : 4.530 15.956 3300 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.21 (0.16), residues: 3072 helix: 0.07 (0.14), residues: 1464 sheet: -0.21 (0.40), residues: 159 loop : -0.19 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.026 0.002 TYR A 848 PHE 0.036 0.002 PHE A 197 TRP 0.009 0.002 TRP A 854 HIS 0.004 0.001 HIS C1212 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (25425) covalent geometry : angle 0.56846 / 0.30 (34284) hydrogen bonds : bond 0.04005 / 2.67 ( 1167) hydrogen bonds : angle 5.36558 / 3.85 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 PHE cc_start: 0.1109 (m-80) cc_final: 0.0814 (m-80) REVERT: B 845 TYR cc_start: 0.6913 (t80) cc_final: 0.6322 (t80) REVERT: B 1033 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7886 (tm-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0927 time to fit residues: 11.8851 Evaluate side-chains 65 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 143 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 chunk 195 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 240 optimal weight: 0.0050 chunk 256 optimal weight: 0.6980 chunk 293 optimal weight: 0.0870 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 575 HIS ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5108 r_free = 0.5108 target = 0.207808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.187692 restraints weight = 33265.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.190760 restraints weight = 25685.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.193109 restraints weight = 20477.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.195126 restraints weight = 16690.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.196563 restraints weight = 13973.365| |-----------------------------------------------------------------------------| r_work (final): 0.4975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2969 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25425 Z= 0.117 Angle : 0.542 7.651 34284 Z= 0.288 Chirality : 0.040 0.249 3813 Planarity : 0.003 0.033 4464 Dihedral : 4.399 16.075 3300 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.11 (0.16), residues: 3072 helix: 0.27 (0.14), residues: 1446 sheet: 0.50 (0.44), residues: 138 loop : -0.35 (0.18), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 131 TYR 0.026 0.002 TYR A 848 PHE 0.011 0.001 PHE B 308 TRP 0.007 0.001 TRP A1295 HIS 0.003 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (25425) covalent geometry : angle 0.54196 / 0.29 (34284) hydrogen bonds : bond 0.03694 / 2.44 ( 1167) hydrogen bonds : angle 5.09867 / 3.66 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6352 (t80) cc_final: 0.5860 (m-80) REVERT: B 296 MET cc_start: -0.1376 (mmt) cc_final: -0.1925 (mmt) REVERT: B 845 TYR cc_start: 0.6841 (t80) cc_final: 0.6334 (t80) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1081 time to fit residues: 12.6414 Evaluate side-chains 63 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 282 optimal weight: 0.0010 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 181 optimal weight: 0.0470 chunk 80 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 156 optimal weight: 0.0570 overall best weight: 0.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 271 GLN B 400 GLN B 489 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 ASN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1294 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.224303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.213830 restraints weight = 50800.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5127 r_free = 0.5127 target = 0.215522 restraints weight = 37562.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5144 r_free = 0.5144 target = 0.216803 restraints weight = 28693.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.217676 restraints weight = 22476.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.5166 r_free = 0.5166 target = 0.218513 restraints weight = 18396.886| |-----------------------------------------------------------------------------| r_work (final): 0.5045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3011 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25425 Z= 0.116 Angle : 0.556 8.473 34284 Z= 0.296 Chirality : 0.039 0.173 3813 Planarity : 0.003 0.033 4464 Dihedral : 4.377 16.501 3300 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.11 % Allowed : 2.04 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.04 (0.16), residues: 3072 helix: 0.42 (0.14), residues: 1470 sheet: 0.01 (0.41), residues: 156 loop : -0.39 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1184 TYR 0.028 0.002 TYR A 848 PHE 0.054 0.002 PHE C 581 TRP 0.019 0.002 TRP C1295 HIS 0.008 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (25425) covalent geometry : angle 0.55612 / 0.30 (34284) hydrogen bonds : bond 0.03710 / 2.45 ( 1167) hydrogen bonds : angle 5.01621 / 3.60 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6387 (t80) cc_final: 0.5922 (m-80) REVERT: B 296 MET cc_start: -0.1128 (mmt) cc_final: -0.1742 (mmt) REVERT: B 845 TYR cc_start: 0.6797 (t80) cc_final: 0.6281 (t80) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.0948 time to fit residues: 10.7523 Evaluate side-chains 60 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 0.9980 chunk 184 optimal weight: 0.0070 chunk 164 optimal weight: 0.7980 chunk 245 optimal weight: 0.0030 chunk 76 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 290 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 160 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 overall best weight: 0.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5104 r_free = 0.5104 target = 0.207691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.186595 restraints weight = 33750.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.189893 restraints weight = 26224.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.192322 restraints weight = 20955.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.194467 restraints weight = 17130.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.196108 restraints weight = 14322.245| |-----------------------------------------------------------------------------| r_work (final): 0.4968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2989 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25425 Z= 0.110 Angle : 0.543 7.452 34284 Z= 0.287 Chirality : 0.039 0.197 3813 Planarity : 0.003 0.035 4464 Dihedral : 4.274 16.949 3300 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.06 (0.16), residues: 3072 helix: 0.42 (0.14), residues: 1494 sheet: 0.12 (0.41), residues: 156 loop : -0.46 (0.18), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1028 TYR 0.030 0.002 TYR B 848 PHE 0.055 0.001 PHE C 581 TRP 0.010 0.002 TRP B1295 HIS 0.005 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (25425) covalent geometry : angle 0.54277 / 0.29 (34284) hydrogen bonds : bond 0.03589 / 2.39 ( 1167) hydrogen bonds : angle 4.92698 / 3.52 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6561 (t80) cc_final: 0.6097 (m-80) REVERT: B 296 MET cc_start: -0.0837 (mmt) cc_final: -0.1735 (mmt) REVERT: B 845 TYR cc_start: 0.6712 (t80) cc_final: 0.6084 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0933 time to fit residues: 10.3924 Evaluate side-chains 61 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 25 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 264 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 304 optimal weight: 0.3980 chunk 229 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN B 204 ASN B 258 ASN B 271 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 GLN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.205851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.184990 restraints weight = 35111.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.188090 restraints weight = 27397.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.190468 restraints weight = 21895.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.192364 restraints weight = 18091.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.193923 restraints weight = 15210.991| |-----------------------------------------------------------------------------| r_work (final): 0.4947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3155 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25425 Z= 0.116 Angle : 0.548 7.225 34284 Z= 0.290 Chirality : 0.039 0.200 3813 Planarity : 0.003 0.035 4464 Dihedral : 4.302 17.072 3300 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.11 % Allowed : 1.40 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.01 (0.16), residues: 3072 helix: 0.52 (0.14), residues: 1497 sheet: -0.24 (0.40), residues: 162 loop : -0.41 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 873 TYR 0.030 0.002 TYR C 848 PHE 0.040 0.001 PHE A 581 TRP 0.008 0.001 TRP A1295 HIS 0.004 0.001 HIS A 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (25425) covalent geometry : angle 0.54782 / 0.29 (34284) hydrogen bonds : bond 0.03492 / 2.31 ( 1167) hydrogen bonds : angle 4.92430 / 3.51 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6829 (t80) cc_final: 0.6286 (m-80) REVERT: B 181 ASN cc_start: -0.1280 (OUTLIER) cc_final: -0.1881 (t0) REVERT: B 296 MET cc_start: -0.0712 (mmt) cc_final: -0.1589 (mmt) REVERT: B 845 TYR cc_start: 0.6634 (t80) cc_final: 0.6129 (t80) REVERT: B 1034 PHE cc_start: 0.5418 (t80) cc_final: 0.5158 (t80) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0865 time to fit residues: 9.8301 Evaluate side-chains 60 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 12 optimal weight: 0.6980 chunk 212 optimal weight: 0.6980 chunk 285 optimal weight: 0.0030 chunk 50 optimal weight: 0.9980 chunk 297 optimal weight: 0.0010 chunk 74 optimal weight: 0.3980 chunk 112 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 293 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 271 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5172 r_free = 0.5172 target = 0.222783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5128 r_free = 0.5128 target = 0.213404 restraints weight = 50848.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5125 r_free = 0.5125 target = 0.215457 restraints weight = 35691.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.216327 restraints weight = 24315.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.217478 restraints weight = 19681.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5161 r_free = 0.5161 target = 0.218031 restraints weight = 14052.432| |-----------------------------------------------------------------------------| r_work (final): 0.5054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3082 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25425 Z= 0.106 Angle : 0.550 7.902 34284 Z= 0.287 Chirality : 0.039 0.155 3813 Planarity : 0.003 0.036 4464 Dihedral : 4.238 17.274 3300 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.07 (0.16), residues: 3072 helix: 0.58 (0.14), residues: 1482 sheet: -0.10 (0.41), residues: 162 loop : -0.39 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 873 TYR 0.032 0.001 TYR C 848 PHE 0.045 0.001 PHE A 581 TRP 0.011 0.002 TRP A1295 HIS 0.003 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (25425) covalent geometry : angle 0.54962 / 0.29 (34284) hydrogen bonds : bond 0.03453 / 2.28 ( 1167) hydrogen bonds : angle 4.85657 / 3.47 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 GLN cc_start: 0.8389 (mm110) cc_final: 0.8187 (mm-40) REVERT: B 62 TYR cc_start: 0.6643 (t80) cc_final: 0.6281 (m-80) REVERT: B 296 MET cc_start: -0.1182 (mmt) cc_final: -0.1829 (mmt) REVERT: B 845 TYR cc_start: 0.6571 (t80) cc_final: 0.6018 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0912 time to fit residues: 10.2790 Evaluate side-chains 58 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 293 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 55 optimal weight: 0.0030 chunk 70 optimal weight: 0.4980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.205983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.185935 restraints weight = 33153.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.188978 restraints weight = 25665.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.191447 restraints weight = 20393.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.193382 restraints weight = 16490.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.194917 restraints weight = 13695.769| |-----------------------------------------------------------------------------| r_work (final): 0.4953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3208 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25425 Z= 0.104 Angle : 0.542 7.619 34284 Z= 0.283 Chirality : 0.039 0.224 3813 Planarity : 0.003 0.035 4464 Dihedral : 4.158 17.801 3300 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.11 % Allowed : 0.64 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.17 (0.16), residues: 3072 helix: 0.64 (0.14), residues: 1485 sheet: 0.10 (0.40), residues: 159 loop : -0.35 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.034 0.002 TYR B 848 PHE 0.039 0.001 PHE C 581 TRP 0.013 0.002 TRP B1295 HIS 0.003 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (25425) covalent geometry : angle 0.54150 / 0.28 (34284) hydrogen bonds : bond 0.03311 / 2.19 ( 1167) hydrogen bonds : angle 4.75383 / 3.39 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.7000 (t80) cc_final: 0.6436 (m-10) REVERT: B 296 MET cc_start: -0.0637 (mmt) cc_final: -0.1387 (mmt) REVERT: B 749 GLU cc_start: 0.9052 (pm20) cc_final: 0.8851 (mp0) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0831 time to fit residues: 9.7062 Evaluate side-chains 55 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 275 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 248 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 644 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5088 r_free = 0.5088 target = 0.204169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.183486 restraints weight = 35863.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.186416 restraints weight = 28236.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.188768 restraints weight = 22738.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.190502 restraints weight = 18677.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.192106 restraints weight = 15799.404| |-----------------------------------------------------------------------------| r_work (final): 0.4932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3466 moved from start: 0.6952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25425 Z= 0.117 Angle : 0.572 7.665 34284 Z= 0.300 Chirality : 0.039 0.161 3813 Planarity : 0.003 0.044 4464 Dihedral : 4.281 19.857 3300 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.15 (0.16), residues: 3072 helix: 0.66 (0.14), residues: 1467 sheet: -0.00 (0.40), residues: 159 loop : -0.38 (0.18), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 873 TYR 0.032 0.002 TYR A 848 PHE 0.040 0.002 PHE C 581 TRP 0.018 0.002 TRP A1295 HIS 0.005 0.001 HIS B 575 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (25425) covalent geometry : angle 0.57216 / 0.30 (34284) hydrogen bonds : bond 0.03442 / 2.27 ( 1167) hydrogen bonds : angle 4.86654 / 3.46 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.7213 (t80) cc_final: 0.6608 (m-10) REVERT: B 296 MET cc_start: -0.0306 (mmt) cc_final: -0.1117 (mmt) REVERT: B 675 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8436 (mmmm) REVERT: B 749 GLU cc_start: 0.9154 (pm20) cc_final: 0.8901 (mp0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0859 time to fit residues: 9.7865 Evaluate side-chains 62 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.7980 chunk 234 optimal weight: 0.7980 chunk 67 optimal weight: 0.0020 chunk 306 optimal weight: 2.9990 chunk 279 optimal weight: 0.1980 chunk 252 optimal weight: 0.9990 chunk 230 optimal weight: 0.0970 chunk 305 optimal weight: 6.9990 chunk 231 optimal weight: 0.0870 chunk 16 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 overall best weight: 0.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 271 GLN B 644 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.221531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.211772 restraints weight = 51241.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5115 r_free = 0.5115 target = 0.213281 restraints weight = 38653.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5132 r_free = 0.5132 target = 0.214622 restraints weight = 27650.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5145 r_free = 0.5145 target = 0.215510 restraints weight = 21669.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.216410 restraints weight = 16729.342| |-----------------------------------------------------------------------------| r_work (final): 0.5052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3297 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25425 Z= 0.106 Angle : 0.551 7.599 34284 Z= 0.287 Chirality : 0.039 0.145 3813 Planarity : 0.003 0.044 4464 Dihedral : 4.145 17.501 3300 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.23 (0.16), residues: 3072 helix: 0.77 (0.14), residues: 1470 sheet: -0.11 (0.40), residues: 162 loop : -0.37 (0.18), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1297 TYR 0.034 0.001 TYR B 848 PHE 0.032 0.001 PHE B 581 TRP 0.011 0.002 TRP C1295 HIS 0.003 0.001 HIS B 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (25425) covalent geometry : angle 0.55130 / 0.29 (34284) hydrogen bonds : bond 0.03295 / 2.15 ( 1167) hydrogen bonds : angle 4.74175 / 3.38 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.59 seconds wall clock time: 42 minutes 45.60 seconds (2565.60 seconds total)