Starting phenix.real_space_refine on Tue Apr 7 06:49:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgq_53144/04_2026/9qgq_53144.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgq_53144/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qgq_53144/04_2026/9qgq_53144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgq_53144/04_2026/9qgq_53144.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qgq_53144/04_2026/9qgq_53144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgq_53144/04_2026/9qgq_53144.map" } 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-2.1rc1-6017/lib/python3.9/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: 8.71, per 1000 atoms: 0.35 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: 2.08 Conformation dependent library (CDL) restraints added in 887.1 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: 0.89 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: 4.13 Time building geometry restraints manager: 2.72 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: 0.05 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: 7.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 24.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1688 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 covalent geometry : bond 0.00371 (25425) covalent geometry : angle 0.56882 (34284) hydrogen bonds : bond 0.17092 ( 1167) hydrogen bonds : angle 7.96558 ( 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 : 0.284 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: 0.0957 time to fit residues: 21.9125 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 : 0.282 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 ASN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 258 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 ASN ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN B 738 ASN ** B 746 GLN ** 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 = 0.5107 r_free = 0.5107 target = 0.211956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.191431 restraints weight = 31806.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.194543 restraints weight = 24805.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.196949 restraints weight = 20019.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.198871 restraints weight = 16629.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.200451 restraints weight = 14043.362| |-----------------------------------------------------------------------------| r_work (final): 0.4977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2942 moved from start: 0.3571 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 : 0.21 % Allowed : 3.44 % 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 covalent geometry : bond 0.00325 (25425) covalent geometry : angle 0.63267 (34284) hydrogen bonds : bond 0.04553 ( 1167) hydrogen bonds : angle 5.80421 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 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: 2 poor density : 116 time to evaluate : 0.237 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 181 ASN cc_start: -0.1821 (OUTLIER) cc_final: -0.2158 (t0) REVERT: B 241 PHE cc_start: 0.1270 (m-80) cc_final: 0.0789 (m-80) REVERT: B 296 MET cc_start: -0.0604 (mmp) cc_final: -0.1028 (mmt) REVERT: B 686 LYS cc_start: 0.9277 (tmmt) cc_final: 0.8951 (tppt) REVERT: B 844 ASP cc_start: 0.6353 (m-30) cc_final: 0.6062 (p0) outliers start: 2 outliers final: 1 residues processed: 118 average time/residue: 0.0967 time to fit residues: 15.5279 Evaluate side-chains 70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.190 ------------------------------------------------------------------------------- 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: 1.9990 chunk 89 optimal weight: 0.3980 chunk 202 optimal weight: 0.3980 chunk 240 optimal weight: 0.0570 chunk 253 optimal weight: 0.1980 overall best weight: 0.1676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 271 GLN B 279 ASN B 316 GLN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 GLN ** B1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1266 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.215001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.196201 restraints weight = 34445.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.199111 restraints weight = 26708.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.201393 restraints weight = 21292.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.203284 restraints weight = 17434.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.5018 r_free = 0.5018 target = 0.204714 restraints weight = 14541.666| |-----------------------------------------------------------------------------| r_work (final): 0.4991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2884 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25425 Z= 0.123 Angle : 0.562 7.132 34284 Z= 0.297 Chirality : 0.040 0.159 3813 Planarity : 0.003 0.044 4464 Dihedral : 4.527 16.007 3300 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % 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: -0.56 (0.15), residues: 3072 helix: -0.22 (0.13), residues: 1464 sheet: -0.46 (0.39), residues: 159 loop : -0.35 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.025 0.002 TYR C 478 PHE 0.032 0.002 PHE A 197 TRP 0.009 0.002 TRP A 854 HIS 0.003 0.001 HIS B1109 Details of bonding type rmsd covalent geometry : bond 0.00261 (25425) covalent geometry : angle 0.56174 (34284) hydrogen bonds : bond 0.03979 ( 1167) hydrogen bonds : angle 5.41776 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.297 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: B 241 PHE cc_start: 0.1118 (m-80) cc_final: 0.0816 (m-80) REVERT: B 845 TYR cc_start: 0.6886 (t80) cc_final: 0.6314 (t80) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0943 time to fit residues: 12.3647 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 : 0.281 ------------------------------------------------------------------------------- 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: 3.9990 chunk 112 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 277 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 chunk 256 optimal weight: 0.8980 chunk 293 optimal weight: 0.0570 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 400 GLN B 575 HIS B 644 ASN B 677 ASN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5098 r_free = 0.5098 target = 0.206466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.185730 restraints weight = 33556.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.188721 restraints weight = 26119.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.191194 restraints weight = 20955.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.193118 restraints weight = 17277.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.194710 restraints weight = 14560.145| |-----------------------------------------------------------------------------| r_work (final): 0.4960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3049 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25425 Z= 0.129 Angle : 0.565 8.271 34284 Z= 0.300 Chirality : 0.040 0.220 3813 Planarity : 0.003 0.045 4464 Dihedral : 4.441 16.206 3300 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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: -0.56 (0.15), residues: 3072 helix: -0.08 (0.13), residues: 1443 sheet: -0.37 (0.41), residues: 156 loop : -0.53 (0.18), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 131 TYR 0.024 0.002 TYR A 848 PHE 0.028 0.001 PHE B1084 TRP 0.006 0.001 TRP A1295 HIS 0.003 0.001 HIS A 853 Details of bonding type rmsd covalent geometry : bond 0.00273 (25425) covalent geometry : angle 0.56537 (34284) hydrogen bonds : bond 0.03745 ( 1167) hydrogen bonds : angle 5.19383 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.310 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: B 62 TYR cc_start: 0.6494 (t80) cc_final: 0.5921 (m-80) REVERT: B 241 PHE cc_start: 0.1263 (m-80) cc_final: 0.0950 (m-80) REVERT: B 296 MET cc_start: -0.1012 (mmt) cc_final: -0.1643 (mmt) REVERT: B 735 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 845 TYR cc_start: 0.6926 (t80) cc_final: 0.6455 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1065 time to fit residues: 11.9983 Evaluate side-chains 59 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 181 optimal weight: 0.0170 chunk 80 optimal weight: 0.0270 chunk 99 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** 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 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 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 = 0.5100 r_free = 0.5100 target = 0.206797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.185898 restraints weight = 32914.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.189188 restraints weight = 25256.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.191596 restraints weight = 20059.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.193650 restraints weight = 16407.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.195189 restraints weight = 13696.998| |-----------------------------------------------------------------------------| r_work (final): 0.4993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3058 moved from start: 0.5436 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= 0.112 Angle : 0.535 7.831 34284 Z= 0.284 Chirality : 0.039 0.167 3813 Planarity : 0.003 0.035 4464 Dihedral : 4.358 17.191 3300 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % 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: -0.59 (0.15), residues: 3072 helix: 0.01 (0.13), residues: 1491 sheet: -0.22 (0.41), residues: 156 loop : -0.73 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 39 TYR 0.028 0.002 TYR A 848 PHE 0.029 0.001 PHE C 581 TRP 0.022 0.002 TRP B1295 HIS 0.006 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00240 (25425) covalent geometry : angle 0.53476 (34284) hydrogen bonds : bond 0.03525 ( 1167) hydrogen bonds : angle 4.95663 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6734 (t80) cc_final: 0.6153 (m-80) REVERT: B 296 MET cc_start: -0.0712 (mmt) cc_final: -0.1494 (mmt) REVERT: B 845 TYR cc_start: 0.6874 (t80) cc_final: 0.6412 (t80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0884 time to fit residues: 10.2059 Evaluate side-chains 59 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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: 0.0670 chunk 184 optimal weight: 0.0050 chunk 164 optimal weight: 0.1980 chunk 245 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 290 optimal weight: 0.0000 chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 160 optimal weight: 0.0980 chunk 87 optimal weight: 0.0970 overall best weight: 0.0534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 271 GLN B 489 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: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5103 r_free = 0.5103 target = 0.207425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.186756 restraints weight = 33463.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.189744 restraints weight = 26275.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.192229 restraints weight = 21151.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.194145 restraints weight = 17314.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.195324 restraints weight = 14523.220| |-----------------------------------------------------------------------------| r_work (final): 0.4961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3021 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 25425 Z= 0.106 Angle : 0.539 7.487 34284 Z= 0.286 Chirality : 0.039 0.198 3813 Planarity : 0.003 0.037 4464 Dihedral : 4.283 16.450 3300 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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: -0.63 (0.15), residues: 3072 helix: -0.06 (0.13), residues: 1506 sheet: -0.07 (0.41), residues: 156 loop : -0.74 (0.18), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1028 TYR 0.030 0.002 TYR A 848 PHE 0.017 0.001 PHE C 581 TRP 0.012 0.002 TRP A1295 HIS 0.004 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00215 (25425) covalent geometry : angle 0.53910 (34284) hydrogen bonds : bond 0.03479 ( 1167) hydrogen bonds : angle 4.93154 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 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 : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6697 (t80) cc_final: 0.6226 (m-80) REVERT: B 296 MET cc_start: -0.0684 (mmt) cc_final: -0.1652 (mmt) REVERT: B 845 TYR cc_start: 0.6749 (t80) cc_final: 0.6215 (t80) REVERT: B 1034 PHE cc_start: 0.5419 (t80) cc_final: 0.5200 (t80) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.0894 time to fit residues: 10.2908 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 : 0.283 ------------------------------------------------------------------------------- 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: 0.0980 chunk 102 optimal weight: 0.0000 chunk 294 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 264 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 304 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 644 ASN B 868 GLN ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.206378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.184376 restraints weight = 33459.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.187567 restraints weight = 26071.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.190064 restraints weight = 20875.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.192266 restraints weight = 17283.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.193898 restraints weight = 14491.893| |-----------------------------------------------------------------------------| r_work (final): 0.4941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3116 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25425 Z= 0.108 Angle : 0.537 7.006 34284 Z= 0.284 Chirality : 0.039 0.212 3813 Planarity : 0.003 0.036 4464 Dihedral : 4.222 16.705 3300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -0.60 (0.15), residues: 3072 helix: 0.02 (0.13), residues: 1497 sheet: -0.38 (0.39), residues: 162 loop : -0.75 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 836 TYR 0.032 0.001 TYR C 848 PHE 0.015 0.001 PHE B 171 TRP 0.013 0.002 TRP C1295 HIS 0.005 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00229 (25425) covalent geometry : angle 0.53720 (34284) hydrogen bonds : bond 0.03370 ( 1167) hydrogen bonds : angle 4.90909 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 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 : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.6828 (t80) cc_final: 0.6361 (m-80) REVERT: B 296 MET cc_start: -0.0804 (mmt) cc_final: -0.1602 (mmt) REVERT: B 845 TYR cc_start: 0.6664 (t80) cc_final: 0.6177 (t80) REVERT: B 1034 PHE cc_start: 0.5416 (t80) cc_final: 0.5159 (t80) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0936 time to fit residues: 10.5445 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 : 0.316 ------------------------------------------------------------------------------- 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: 0.9980 chunk 212 optimal weight: 0.9980 chunk 285 optimal weight: 0.0030 chunk 50 optimal weight: 0.4980 chunk 297 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 237 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 293 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN B 271 GLN B 644 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 = 0.5122 r_free = 0.5122 target = 0.207336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.182770 restraints weight = 33127.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.186109 restraints weight = 25579.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.188917 restraints weight = 20484.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.190748 restraints weight = 16801.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.192528 restraints weight = 14350.012| |-----------------------------------------------------------------------------| r_work (final): 0.4913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3207 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25425 Z= 0.108 Angle : 0.548 7.820 34284 Z= 0.287 Chirality : 0.039 0.211 3813 Planarity : 0.003 0.037 4464 Dihedral : 4.172 16.944 3300 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.51 (0.15), residues: 3072 helix: 0.12 (0.13), residues: 1461 sheet: -0.30 (0.39), residues: 162 loop : -0.72 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 873 TYR 0.033 0.001 TYR C 848 PHE 0.051 0.001 PHE B 581 TRP 0.018 0.002 TRP B1295 HIS 0.003 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00228 (25425) covalent geometry : angle 0.54785 (34284) hydrogen bonds : bond 0.03349 ( 1167) hydrogen bonds : angle 4.84162 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 TYR cc_start: 0.7033 (t80) cc_final: 0.6439 (m-10) REVERT: B 296 MET cc_start: -0.0519 (mmt) cc_final: -0.1384 (mmt) REVERT: B 749 GLU cc_start: 0.9002 (pm20) cc_final: 0.8799 (mp0) REVERT: B 845 TYR cc_start: 0.6576 (t80) cc_final: 0.6052 (t80) REVERT: B 1034 PHE cc_start: 0.5812 (t80) cc_final: 0.5439 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0863 time to fit residues: 9.5225 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 : 0.303 ------------------------------------------------------------------------------- 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: 0.8980 chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 293 optimal weight: 0.4980 chunk 192 optimal weight: 0.4980 chunk 265 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 644 ASN ** 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 = 0.5091 r_free = 0.5091 target = 0.205553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.184444 restraints weight = 34592.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.187476 restraints weight = 27363.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.189922 restraints weight = 21943.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.191892 restraints weight = 18012.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.193347 restraints weight = 15217.517| |-----------------------------------------------------------------------------| r_work (final): 0.4937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3242 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25425 Z= 0.105 Angle : 0.543 7.434 34284 Z= 0.286 Chirality : 0.038 0.143 3813 Planarity : 0.003 0.037 4464 Dihedral : 4.105 17.238 3300 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % 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: -0.51 (0.15), residues: 3072 helix: 0.11 (0.13), residues: 1479 sheet: -0.20 (0.39), residues: 159 loop : -0.73 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1184 TYR 0.034 0.001 TYR A 848 PHE 0.051 0.001 PHE A 581 TRP 0.015 0.002 TRP C1295 HIS 0.002 0.001 HIS B1109 Details of bonding type rmsd covalent geometry : bond 0.00221 (25425) covalent geometry : angle 0.54348 (34284) hydrogen bonds : bond 0.03290 ( 1167) hydrogen bonds : angle 4.83052 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.286 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: 0.7004 (t80) cc_final: 0.6461 (m-10) REVERT: B 296 MET cc_start: -0.0897 (mmt) cc_final: -0.1534 (mmt) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0893 time to fit residues: 9.9858 Evaluate side-chains 59 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0170 chunk 134 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 146 optimal weight: 0.2980 chunk 271 optimal weight: 0.5980 chunk 121 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 overall best weight: 0.3018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 271 GLN B 644 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 = 0.5098 r_free = 0.5098 target = 0.205923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.184841 restraints weight = 34894.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.187761 restraints weight = 27368.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.190266 restraints weight = 22056.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4927 r_free = 0.4927 target = 0.192217 restraints weight = 18096.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.193912 restraints weight = 15182.353| |-----------------------------------------------------------------------------| r_work (final): 0.4944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3241 moved from start: 0.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 25425 Z= 0.102 Angle : 0.539 8.180 34284 Z= 0.282 Chirality : 0.039 0.219 3813 Planarity : 0.003 0.038 4464 Dihedral : 4.088 17.308 3300 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.44 (0.15), residues: 3072 helix: 0.24 (0.13), residues: 1464 sheet: -0.20 (0.39), residues: 162 loop : -0.78 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 873 TYR 0.034 0.001 TYR B 848 PHE 0.049 0.001 PHE B 581 TRP 0.015 0.002 TRP C1295 HIS 0.002 0.001 HIS C 575 Details of bonding type rmsd covalent geometry : bond 0.00209 (25425) covalent geometry : angle 0.53930 (34284) hydrogen bonds : bond 0.03233 ( 1167) hydrogen bonds : angle 4.76005 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4096 Ramachandran restraints generated. 2048 Oldfield, 0 Emsley, 2048 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 : 0.304 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: 0.6941 (t80) cc_final: 0.6499 (m-10) REVERT: B 296 MET cc_start: -0.0730 (mmt) cc_final: -0.1404 (mmt) REVERT: B 749 GLU cc_start: 0.9149 (pm20) cc_final: 0.8932 (mp0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.0860 time to fit residues: 9.8485 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 : 0.370 ------------------------------------------------------------------------------- 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: 0.0570 chunk 234 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 306 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 252 optimal weight: 0.0970 chunk 230 optimal weight: 0.5980 chunk 305 optimal weight: 2.9990 chunk 231 optimal weight: 0.1980 chunk 16 optimal weight: 0.0670 chunk 108 optimal weight: 0.9990 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 644 ASN ** 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 = 0.5105 r_free = 0.5105 target = 0.206514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.185550 restraints weight = 34717.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.188510 restraints weight = 27141.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.190972 restraints weight = 21847.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.192988 restraints weight = 17862.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4955 r_free = 0.4955 target = 0.194624 restraints weight = 14898.265| |-----------------------------------------------------------------------------| r_work (final): 0.4951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3205 moved from start: 0.6792 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= 0.099 Angle : 0.533 7.321 34284 Z= 0.279 Chirality : 0.038 0.142 3813 Planarity : 0.003 0.037 4464 Dihedral : 4.055 22.524 3300 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.42 (0.15), residues: 3072 helix: 0.35 (0.13), residues: 1446 sheet: -0.21 (0.40), residues: 162 loop : -0.86 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1286 TYR 0.034 0.001 TYR A 848 PHE 0.013 0.001 PHE C 745 TRP 0.027 0.003 TRP B 881 HIS 0.003 0.001 HIS A 575 Details of bonding type rmsd covalent geometry : bond 0.00206 (25425) covalent geometry : angle 0.53332 (34284) hydrogen bonds : bond 0.03182 ( 1167) hydrogen bonds : angle 4.74679 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.62 seconds wall clock time: 41 minutes 37.05 seconds (2497.05 seconds total)