Starting phenix.real_space_refine on Tue Aug 26 22:37:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.map" model { file = "/net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ivq_35759/08_2025/8ivq_35759.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 260 5.16 5 C 26472 2.51 5 N 7360 2.21 5 O 7808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41900 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2921, 20950 Classifications: {'peptide': 2921} Incomplete info: {'truncation_to_alanine': 514} Link IDs: {'PTRANS': 145, 'TRANS': 2775} Chain breaks: 39 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2219 Unresolved non-hydrogen dihedrals: 1417 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'ARG:plan': 21, 'ASP:plan': 34, 'HIS:plan': 18, 'TYR:plan': 16, 'ASN:plan1': 15, 'GLN:plan1': 26, 'PHE:plan': 16, 'GLU:plan': 29, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 824 Chain: "B" Number of atoms: 20950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2921, 20950 Classifications: {'peptide': 2921} Incomplete info: {'truncation_to_alanine': 514} Link IDs: {'PTRANS': 145, 'TRANS': 2775} Chain breaks: 39 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 1721 Unresolved non-hydrogen angles: 2219 Unresolved non-hydrogen dihedrals: 1417 Unresolved non-hydrogen chiralities: 191 Planarities with less than four sites: {'ARG:plan': 21, 'ASP:plan': 34, 'HIS:plan': 18, 'TYR:plan': 16, 'ASN:plan1': 15, 'GLN:plan1': 26, 'PHE:plan': 16, 'GLU:plan': 29, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 824 Time building chain proxies: 9.66, per 1000 atoms: 0.23 Number of scatterers: 41900 At special positions: 0 Unit cell: (212.35, 168.51, 190.43, 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 260 16.00 O 7808 8.00 N 7360 7.00 C 26472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1443 " - pdb=" SG CYS A1447 " distance=2.05 Simple disulfide: pdb=" SG CYS B1443 " - pdb=" SG CYS B1447 " distance=2.05 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: 3.56 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 1.2 microseconds 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11088 Finding SS restraints... Secondary structure from input PDB file: 232 helices and 30 sheets defined 53.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 142 through 155 Processing helix chain 'A' and resid 163 through 183 removed outlier: 3.936A pdb=" N HIS A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.582A pdb=" N TRP A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 218 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.081A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 259 removed outlier: 3.912A pdb=" N TYR A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 259' Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.580A pdb=" N ARG A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 271 removed outlier: 3.530A pdb=" N TRP A 271 " --> pdb=" O PHE A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 271' Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.836A pdb=" N MET A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.537A pdb=" N THR A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'A' and resid 698 through 704 removed outlier: 3.916A pdb=" N GLU A 702 " --> pdb=" O PRO A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.977A pdb=" N ASP A 844 " --> pdb=" O ASP A 841 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN A 845 " --> pdb=" O ILE A 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 841 through 845' Processing helix chain 'A' and resid 994 through 1006 Processing helix chain 'A' and resid 1026 through 1034 removed outlier: 4.063A pdb=" N GLN A1030 " --> pdb=" O GLN A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 removed outlier: 3.897A pdb=" N GLN A1040 " --> pdb=" O GLN A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1049 removed outlier: 3.563A pdb=" N ALA A1046 " --> pdb=" O HIS A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 3.535A pdb=" N HIS A1153 " --> pdb=" O PHE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1186 Processing helix chain 'A' and resid 1290 through 1301 removed outlier: 3.824A pdb=" N GLN A1294 " --> pdb=" O LYS A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.763A pdb=" N HIS A1305 " --> pdb=" O PHE A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1344 removed outlier: 4.388A pdb=" N SER A1344 " --> pdb=" O HIS A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1361 removed outlier: 3.571A pdb=" N CYS A1361 " --> pdb=" O LYS A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1372 Processing helix chain 'A' and resid 1374 through 1393 removed outlier: 4.115A pdb=" N LYS A1393 " --> pdb=" O ILE A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1412 Processing helix chain 'A' and resid 1413 through 1416 Processing helix chain 'A' and resid 1421 through 1436 removed outlier: 3.674A pdb=" N VAL A1425 " --> pdb=" O THR A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1461 removed outlier: 4.566A pdb=" N CYS A1443 " --> pdb=" O ASP A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1473 Processing helix chain 'A' and resid 1510 through 1515 removed outlier: 3.647A pdb=" N LEU A1515 " --> pdb=" O LEU A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1753 through 1757 Processing helix chain 'A' and resid 1895 through 1927 Processing helix chain 'A' and resid 1935 through 1945 Processing helix chain 'A' and resid 1946 through 1985 Processing helix chain 'A' and resid 1996 through 2004 removed outlier: 3.558A pdb=" N SER A2004 " --> pdb=" O LEU A2000 " (cutoff:3.500A) Processing helix chain 'A' and resid 2005 through 2025 Processing helix chain 'A' and resid 2041 through 2054 Processing helix chain 'A' and resid 2057 through 2073 Processing helix chain 'A' and resid 2077 through 2091 Processing helix chain 'A' and resid 2099 through 2114 removed outlier: 3.798A pdb=" N SER A2114 " --> pdb=" O ILE A2110 " (cutoff:3.500A) Processing helix chain 'A' and resid 2118 through 2132 Processing helix chain 'A' and resid 2150 through 2172 removed outlier: 3.991A pdb=" N ILE A2154 " --> pdb=" O ASP A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2327 removed outlier: 4.682A pdb=" N SER A2316 " --> pdb=" O ASP A2312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A2317 " --> pdb=" O ARG A2313 " (cutoff:3.500A) Processing helix chain 'A' and resid 2333 through 2351 removed outlier: 3.624A pdb=" N LEU A2337 " --> pdb=" O HIS A2333 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A2339 " --> pdb=" O ASP A2335 " (cutoff:3.500A) Processing helix chain 'A' and resid 2356 through 2361 removed outlier: 3.767A pdb=" N ILE A2360 " --> pdb=" O HIS A2356 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A2361 " --> pdb=" O LEU A2357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2356 through 2361' Processing helix chain 'A' and resid 2362 through 2374 Processing helix chain 'A' and resid 2386 through 2407 removed outlier: 3.773A pdb=" N ALA A2390 " --> pdb=" O GLY A2386 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A2391 " --> pdb=" O GLY A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2588 removed outlier: 4.395A pdb=" N SER A2588 " --> pdb=" O LEU A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2621 through 2635 Processing helix chain 'A' and resid 2642 through 2658 Processing helix chain 'A' and resid 2683 through 2697 Processing helix chain 'A' and resid 2701 through 2718 Processing helix chain 'A' and resid 2733 through 2741 Processing helix chain 'A' and resid 2742 through 2753 removed outlier: 4.170A pdb=" N HIS A2746 " --> pdb=" O PRO A2742 " (cutoff:3.500A) Processing helix chain 'A' and resid 2767 through 2788 removed outlier: 4.529A pdb=" N ALA A2771 " --> pdb=" O VAL A2767 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A2772 " --> pdb=" O GLY A2768 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER A2788 " --> pdb=" O VAL A2784 " (cutoff:3.500A) Processing helix chain 'A' and resid 2790 through 2807 removed outlier: 3.936A pdb=" N PHE A2794 " --> pdb=" O CYS A2790 " (cutoff:3.500A) Processing helix chain 'A' and resid 2810 through 2815 Processing helix chain 'A' and resid 2818 through 2832 removed outlier: 3.691A pdb=" N GLN A2822 " --> pdb=" O PRO A2818 " (cutoff:3.500A) Processing helix chain 'A' and resid 2838 through 2859 Processing helix chain 'A' and resid 2900 through 2917 removed outlier: 3.612A pdb=" N GLN A2917 " --> pdb=" O ASN A2913 " (cutoff:3.500A) Processing helix chain 'A' and resid 2965 through 2973 removed outlier: 3.976A pdb=" N LEU A2969 " --> pdb=" O CYS A2965 " (cutoff:3.500A) Processing helix chain 'A' and resid 2973 through 2987 removed outlier: 3.510A pdb=" N MET A2977 " --> pdb=" O ASN A2973 " (cutoff:3.500A) Processing helix chain 'A' and resid 2988 through 2993 removed outlier: 3.709A pdb=" N MET A2992 " --> pdb=" O ASN A2988 " (cutoff:3.500A) Processing helix chain 'A' and resid 3017 through 3032 Processing helix chain 'A' and resid 3035 through 3050 removed outlier: 3.807A pdb=" N MET A3039 " --> pdb=" O THR A3035 " (cutoff:3.500A) Proline residue: A3042 - end of helix Processing helix chain 'A' and resid 3064 through 3075 Processing helix chain 'A' and resid 3077 through 3088 Processing helix chain 'A' and resid 3088 through 3104 Processing helix chain 'A' and resid 3109 through 3120 removed outlier: 3.757A pdb=" N THR A3114 " --> pdb=" O SER A3110 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3221 removed outlier: 3.612A pdb=" N THR A3220 " --> pdb=" O SER A3217 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3312 Processing helix chain 'A' and resid 3313 through 3326 removed outlier: 4.263A pdb=" N LEU A3317 " --> pdb=" O SER A3313 " (cutoff:3.500A) Processing helix chain 'A' and resid 3330 through 3339 Processing helix chain 'A' and resid 3343 through 3353 Processing helix chain 'A' and resid 3360 through 3375 removed outlier: 3.614A pdb=" N ILE A3364 " --> pdb=" O HIS A3360 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER A3375 " --> pdb=" O ILE A3371 " (cutoff:3.500A) Processing helix chain 'A' and resid 3375 through 3388 Processing helix chain 'A' and resid 3414 through 3427 Processing helix chain 'A' and resid 3431 through 3456 removed outlier: 3.502A pdb=" N ARG A3435 " --> pdb=" O GLY A3431 " (cutoff:3.500A) Processing helix chain 'A' and resid 3469 through 3474 Processing helix chain 'A' and resid 3476 through 3493 Processing helix chain 'A' and resid 3498 through 3503 Processing helix chain 'A' and resid 3504 through 3518 Processing helix chain 'A' and resid 3522 through 3539 removed outlier: 3.512A pdb=" N LYS A3526 " --> pdb=" O VAL A3522 " (cutoff:3.500A) Processing helix chain 'A' and resid 3539 through 3551 removed outlier: 4.031A pdb=" N PHE A3543 " --> pdb=" O HIS A3539 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A3544 " --> pdb=" O PRO A3540 " (cutoff:3.500A) Processing helix chain 'A' and resid 3592 through 3603 Processing helix chain 'A' and resid 3605 through 3616 Processing helix chain 'A' and resid 3616 through 3632 Processing helix chain 'A' and resid 3668 through 3680 Processing helix chain 'A' and resid 3682 through 3690 removed outlier: 3.546A pdb=" N GLY A3690 " --> pdb=" O LYS A3686 " (cutoff:3.500A) Processing helix chain 'A' and resid 3694 through 3706 removed outlier: 3.745A pdb=" N TRP A3698 " --> pdb=" O VAL A3694 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR A3699 " --> pdb=" O ASN A3695 " (cutoff:3.500A) Processing helix chain 'A' and resid 3738 through 3757 Processing helix chain 'A' and resid 3760 through 3777 Processing helix chain 'A' and resid 3791 through 3803 Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3969 through 3980 Processing helix chain 'A' and resid 4045 through 4051 Processing helix chain 'A' and resid 4056 through 4065 Processing helix chain 'A' and resid 4065 through 4074 removed outlier: 3.774A pdb=" N LEU A4069 " --> pdb=" O GLY A4065 " (cutoff:3.500A) Processing helix chain 'A' and resid 4141 through 4153 removed outlier: 3.610A pdb=" N LEU A4145 " --> pdb=" O PRO A4141 " (cutoff:3.500A) Processing helix chain 'A' and resid 4156 through 4163 removed outlier: 4.178A pdb=" N VAL A4160 " --> pdb=" O GLY A4156 " (cutoff:3.500A) Processing helix chain 'A' and resid 4164 through 4177 Processing helix chain 'A' and resid 4190 through 4195 removed outlier: 4.087A pdb=" N ASN A4194 " --> pdb=" O PRO A4191 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4211 Processing helix chain 'A' and resid 4215 through 4229 Processing helix chain 'A' and resid 4229 through 4242 Processing helix chain 'A' and resid 4292 through 4319 Processing helix chain 'A' and resid 4345 through 4354 removed outlier: 3.920A pdb=" N GLU A4349 " --> pdb=" O SER A4345 " (cutoff:3.500A) Processing helix chain 'A' and resid 4355 through 4364 Processing helix chain 'A' and resid 4368 through 4375 Processing helix chain 'A' and resid 4375 through 4392 Processing helix chain 'A' and resid 4395 through 4399 removed outlier: 3.692A pdb=" N LEU A4399 " --> pdb=" O VAL A4396 " (cutoff:3.500A) Processing helix chain 'A' and resid 4421 through 4442 Processing helix chain 'A' and resid 4464 through 4485 removed outlier: 3.904A pdb=" N ASP A4468 " --> pdb=" O LEU A4464 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 Processing helix chain 'B' and resid 163 through 183 removed outlier: 3.936A pdb=" N HIS B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.582A pdb=" N TRP B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 218 Processing helix chain 'B' and resid 222 through 237 removed outlier: 4.081A pdb=" N VAL B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.912A pdb=" N TYR B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 260 through 267 removed outlier: 3.580A pdb=" N ARG B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 271 removed outlier: 3.530A pdb=" N TRP B 271 " --> pdb=" O PHE B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 271' Processing helix chain 'B' and resid 280 through 287 removed outlier: 3.836A pdb=" N MET B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 327 Processing helix chain 'B' and resid 342 through 349 removed outlier: 3.537A pdb=" N THR B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.915A pdb=" N GLU B 702 " --> pdb=" O PRO B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 830 Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.977A pdb=" N ASP B 844 " --> pdb=" O ASP B 841 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN B 845 " --> pdb=" O ILE B 842 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 841 through 845' Processing helix chain 'B' and resid 994 through 1006 Processing helix chain 'B' and resid 1026 through 1034 removed outlier: 4.063A pdb=" N GLN B1030 " --> pdb=" O GLN B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1040 removed outlier: 3.897A pdb=" N GLN B1040 " --> pdb=" O GLN B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1049 removed outlier: 3.564A pdb=" N ALA B1046 " --> pdb=" O HIS B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1153 removed outlier: 3.535A pdb=" N HIS B1153 " --> pdb=" O PHE B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1186 Processing helix chain 'B' and resid 1290 through 1301 removed outlier: 3.824A pdb=" N GLN B1294 " --> pdb=" O LYS B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1313 removed outlier: 3.764A pdb=" N HIS B1305 " --> pdb=" O PHE B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1322 through 1344 removed outlier: 4.388A pdb=" N SER B1344 " --> pdb=" O HIS B1340 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1361 removed outlier: 3.572A pdb=" N CYS B1361 " --> pdb=" O LYS B1357 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1372 Processing helix chain 'B' and resid 1374 through 1393 removed outlier: 4.115A pdb=" N LYS B1393 " --> pdb=" O ILE B1389 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1412 Processing helix chain 'B' and resid 1413 through 1416 Processing helix chain 'B' and resid 1421 through 1436 removed outlier: 3.674A pdb=" N VAL B1425 " --> pdb=" O THR B1421 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1461 removed outlier: 4.565A pdb=" N CYS B1443 " --> pdb=" O ASP B1439 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1473 Processing helix chain 'B' and resid 1510 through 1515 removed outlier: 3.648A pdb=" N LEU B1515 " --> pdb=" O LEU B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1753 through 1757 Processing helix chain 'B' and resid 1895 through 1927 Processing helix chain 'B' and resid 1935 through 1945 Processing helix chain 'B' and resid 1946 through 1985 Processing helix chain 'B' and resid 1996 through 2004 removed outlier: 3.557A pdb=" N SER B2004 " --> pdb=" O LEU B2000 " (cutoff:3.500A) Processing helix chain 'B' and resid 2005 through 2025 Processing helix chain 'B' and resid 2041 through 2054 Processing helix chain 'B' and resid 2057 through 2073 Processing helix chain 'B' and resid 2077 through 2091 Processing helix chain 'B' and resid 2099 through 2114 removed outlier: 3.798A pdb=" N SER B2114 " --> pdb=" O ILE B2110 " (cutoff:3.500A) Processing helix chain 'B' and resid 2118 through 2132 Processing helix chain 'B' and resid 2150 through 2172 removed outlier: 3.990A pdb=" N ILE B2154 " --> pdb=" O ASP B2150 " (cutoff:3.500A) Processing helix chain 'B' and resid 2310 through 2327 removed outlier: 4.682A pdb=" N SER B2316 " --> pdb=" O ASP B2312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B2317 " --> pdb=" O ARG B2313 " (cutoff:3.500A) Processing helix chain 'B' and resid 2333 through 2351 removed outlier: 3.624A pdb=" N LEU B2337 " --> pdb=" O HIS B2333 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B2339 " --> pdb=" O ASP B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2356 through 2361 removed outlier: 3.768A pdb=" N ILE B2360 " --> pdb=" O HIS B2356 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B2361 " --> pdb=" O LEU B2357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2356 through 2361' Processing helix chain 'B' and resid 2362 through 2374 Processing helix chain 'B' and resid 2386 through 2407 removed outlier: 3.773A pdb=" N ALA B2390 " --> pdb=" O GLY B2386 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B2391 " --> pdb=" O GLY B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2588 removed outlier: 4.395A pdb=" N SER B2588 " --> pdb=" O LEU B2584 " (cutoff:3.500A) Processing helix chain 'B' and resid 2621 through 2635 Processing helix chain 'B' and resid 2642 through 2658 Processing helix chain 'B' and resid 2683 through 2697 Processing helix chain 'B' and resid 2701 through 2718 Processing helix chain 'B' and resid 2733 through 2741 Processing helix chain 'B' and resid 2742 through 2753 removed outlier: 4.170A pdb=" N HIS B2746 " --> pdb=" O PRO B2742 " (cutoff:3.500A) Processing helix chain 'B' and resid 2767 through 2788 removed outlier: 4.530A pdb=" N ALA B2771 " --> pdb=" O VAL B2767 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B2772 " --> pdb=" O GLY B2768 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER B2788 " --> pdb=" O VAL B2784 " (cutoff:3.500A) Processing helix chain 'B' and resid 2790 through 2807 removed outlier: 3.935A pdb=" N PHE B2794 " --> pdb=" O CYS B2790 " (cutoff:3.500A) Processing helix chain 'B' and resid 2810 through 2815 Processing helix chain 'B' and resid 2818 through 2832 removed outlier: 3.691A pdb=" N GLN B2822 " --> pdb=" O PRO B2818 " (cutoff:3.500A) Processing helix chain 'B' and resid 2838 through 2859 Processing helix chain 'B' and resid 2900 through 2917 removed outlier: 3.613A pdb=" N GLN B2917 " --> pdb=" O ASN B2913 " (cutoff:3.500A) Processing helix chain 'B' and resid 2965 through 2973 removed outlier: 3.975A pdb=" N LEU B2969 " --> pdb=" O CYS B2965 " (cutoff:3.500A) Processing helix chain 'B' and resid 2973 through 2987 removed outlier: 3.510A pdb=" N MET B2977 " --> pdb=" O ASN B2973 " (cutoff:3.500A) Processing helix chain 'B' and resid 2988 through 2993 removed outlier: 3.710A pdb=" N MET B2992 " --> pdb=" O ASN B2988 " (cutoff:3.500A) Processing helix chain 'B' and resid 3017 through 3032 Processing helix chain 'B' and resid 3035 through 3050 removed outlier: 3.807A pdb=" N MET B3039 " --> pdb=" O THR B3035 " (cutoff:3.500A) Proline residue: B3042 - end of helix Processing helix chain 'B' and resid 3064 through 3075 Processing helix chain 'B' and resid 3077 through 3088 Processing helix chain 'B' and resid 3088 through 3104 Processing helix chain 'B' and resid 3109 through 3120 removed outlier: 3.756A pdb=" N THR B3114 " --> pdb=" O SER B3110 " (cutoff:3.500A) Processing helix chain 'B' and resid 3217 through 3221 removed outlier: 3.613A pdb=" N THR B3220 " --> pdb=" O SER B3217 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3312 Processing helix chain 'B' and resid 3313 through 3326 removed outlier: 4.263A pdb=" N LEU B3317 " --> pdb=" O SER B3313 " (cutoff:3.500A) Processing helix chain 'B' and resid 3330 through 3339 Processing helix chain 'B' and resid 3343 through 3353 Processing helix chain 'B' and resid 3360 through 3375 removed outlier: 3.615A pdb=" N ILE B3364 " --> pdb=" O HIS B3360 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B3375 " --> pdb=" O ILE B3371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3375 through 3388 Processing helix chain 'B' and resid 3414 through 3427 Processing helix chain 'B' and resid 3431 through 3456 removed outlier: 3.502A pdb=" N ARG B3435 " --> pdb=" O GLY B3431 " (cutoff:3.500A) Processing helix chain 'B' and resid 3469 through 3474 Processing helix chain 'B' and resid 3476 through 3493 Processing helix chain 'B' and resid 3498 through 3503 Processing helix chain 'B' and resid 3504 through 3518 Processing helix chain 'B' and resid 3522 through 3539 removed outlier: 3.512A pdb=" N LYS B3526 " --> pdb=" O VAL B3522 " (cutoff:3.500A) Processing helix chain 'B' and resid 3539 through 3551 removed outlier: 4.031A pdb=" N PHE B3543 " --> pdb=" O HIS B3539 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B3544 " --> pdb=" O PRO B3540 " (cutoff:3.500A) Processing helix chain 'B' and resid 3592 through 3603 Processing helix chain 'B' and resid 3605 through 3616 Processing helix chain 'B' and resid 3616 through 3632 Processing helix chain 'B' and resid 3668 through 3680 Processing helix chain 'B' and resid 3682 through 3690 removed outlier: 3.546A pdb=" N GLY B3690 " --> pdb=" O LYS B3686 " (cutoff:3.500A) Processing helix chain 'B' and resid 3694 through 3706 removed outlier: 3.744A pdb=" N TRP B3698 " --> pdb=" O VAL B3694 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B3699 " --> pdb=" O ASN B3695 " (cutoff:3.500A) Processing helix chain 'B' and resid 3738 through 3757 Processing helix chain 'B' and resid 3760 through 3777 Processing helix chain 'B' and resid 3791 through 3803 Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3969 through 3980 Processing helix chain 'B' and resid 4045 through 4051 Processing helix chain 'B' and resid 4056 through 4065 Processing helix chain 'B' and resid 4065 through 4074 removed outlier: 3.774A pdb=" N LEU B4069 " --> pdb=" O GLY B4065 " (cutoff:3.500A) Processing helix chain 'B' and resid 4141 through 4153 removed outlier: 3.610A pdb=" N LEU B4145 " --> pdb=" O PRO B4141 " (cutoff:3.500A) Processing helix chain 'B' and resid 4156 through 4163 removed outlier: 4.177A pdb=" N VAL B4160 " --> pdb=" O GLY B4156 " (cutoff:3.500A) Processing helix chain 'B' and resid 4164 through 4177 Processing helix chain 'B' and resid 4190 through 4195 removed outlier: 4.087A pdb=" N ASN B4194 " --> pdb=" O PRO B4191 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4211 Processing helix chain 'B' and resid 4215 through 4229 Processing helix chain 'B' and resid 4229 through 4242 Processing helix chain 'B' and resid 4292 through 4319 Processing helix chain 'B' and resid 4345 through 4354 removed outlier: 3.920A pdb=" N GLU B4349 " --> pdb=" O SER B4345 " (cutoff:3.500A) Processing helix chain 'B' and resid 4355 through 4364 Processing helix chain 'B' and resid 4368 through 4375 Processing helix chain 'B' and resid 4375 through 4392 Processing helix chain 'B' and resid 4395 through 4399 removed outlier: 3.692A pdb=" N LEU B4399 " --> pdb=" O VAL B4396 " (cutoff:3.500A) Processing helix chain 'B' and resid 4421 through 4442 Processing helix chain 'B' and resid 4464 through 4485 removed outlier: 3.904A pdb=" N ASP B4468 " --> pdb=" O LEU B4464 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 39 removed outlier: 4.653A pdb=" N PHE A 939 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N CYS A 37 " --> pdb=" O LEU A 937 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU A 937 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG A 927 " --> pdb=" O TYR A 921 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR A 921 " --> pdb=" O ARG A 927 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 929 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 919 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS A 931 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 51 removed outlier: 3.538A pdb=" N SER A 47 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP A 70 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR A 76 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 95 removed outlier: 3.590A pdb=" N ARG A 112 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 135 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291 removed outlier: 3.650A pdb=" N MET A 302 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 367 removed outlier: 3.691A pdb=" N ALA A 376 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP A 388 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 395 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 488 removed outlier: 6.253A pdb=" N GLY A 545 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU A 485 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU A 543 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 487 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 541 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG A 696 " --> pdb=" O PRO A 603 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 605 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS A 694 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 607 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 706 through 713 removed outlier: 6.469A pdb=" N GLY A 723 " --> pdb=" O ASP A 709 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 711 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 721 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS A 719 " --> pdb=" O PRO A 713 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 832 through 838 removed outlier: 6.748A pdb=" N THR A 882 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 835 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL A 880 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU A 837 " --> pdb=" O HIS A 878 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS A 878 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 888 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS A 901 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 890 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 897 " --> pdb=" O ASP A 892 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1007 through 1009 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1007 through 1009 current: chain 'A' and resid 1051 through 1055 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1051 through 1055 current: chain 'A' and resid 1174 through 1179 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1015 through 1017 removed outlier: 3.840A pdb=" N THR A1017 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A1068 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS A1065 " --> pdb=" O VAL A1200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1555 through 1556 removed outlier: 3.684A pdb=" N ARG A1555 " --> pdb=" O ILE A1765 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A1857 " --> pdb=" O ILE A1766 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1774 through 1792 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1774 through 1792 current: chain 'A' and resid 1815 through 1820 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 2863 through 2865 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2863 through 2865 current: chain 'A' and resid 3237 through 3238 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 3841 through 3847 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 39 removed outlier: 4.653A pdb=" N PHE B 939 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS B 37 " --> pdb=" O LEU B 937 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B 937 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 927 " --> pdb=" O TYR B 921 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR B 921 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS B 929 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 919 " --> pdb=" O CYS B 929 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N CYS B 931 " --> pdb=" O VAL B 917 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.537A pdb=" N SER B 47 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 70 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR B 76 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 91 through 95 removed outlier: 3.589A pdb=" N ARG B 112 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 135 through 141 Processing sheet with id=AC2, first strand: chain 'B' and resid 289 through 291 removed outlier: 3.650A pdb=" N MET B 302 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 363 through 367 removed outlier: 3.690A pdb=" N ALA B 376 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 388 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 395 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 478 through 488 removed outlier: 6.252A pdb=" N GLY B 545 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU B 485 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU B 543 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE B 487 " --> pdb=" O CYS B 541 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS B 541 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG B 696 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 605 " --> pdb=" O CYS B 694 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS B 694 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 607 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 706 through 713 removed outlier: 6.469A pdb=" N GLY B 723 " --> pdb=" O ASP B 709 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE B 711 " --> pdb=" O LEU B 721 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU B 721 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS B 719 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 832 through 838 removed outlier: 6.749A pdb=" N THR B 882 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 835 " --> pdb=" O VAL B 880 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 880 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU B 837 " --> pdb=" O HIS B 878 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS B 878 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 888 " --> pdb=" O LYS B 901 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS B 901 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 890 " --> pdb=" O LEU B 899 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 897 " --> pdb=" O ASP B 892 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1007 through 1009 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1007 through 1009 current: chain 'B' and resid 1051 through 1055 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1051 through 1055 current: chain 'B' and resid 1174 through 1179 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 1015 through 1017 removed outlier: 3.840A pdb=" N THR B1017 " --> pdb=" O GLU B1068 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B1068 " --> pdb=" O THR B1017 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS B1065 " --> pdb=" O VAL B1200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1555 through 1556 removed outlier: 3.684A pdb=" N ARG B1555 " --> pdb=" O ILE B1765 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B1857 " --> pdb=" O ILE B1766 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1774 through 1792 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1774 through 1792 current: chain 'B' and resid 1815 through 1820 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 2863 through 2865 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2863 through 2865 current: chain 'B' and resid 3237 through 3238 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 3841 through 3847 2310 hydrogen bonds defined for protein. 6828 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: 14.21 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 14068 1.35 - 1.48: 9706 1.48 - 1.62: 18392 1.62 - 1.75: 0 1.75 - 1.88: 386 Bond restraints: 42552 Sorted by residual: bond pdb=" CG LEU B1330 " pdb=" CD1 LEU B1330 " ideal model delta sigma weight residual 1.521 1.412 0.109 3.30e-02 9.18e+02 1.08e+01 bond pdb=" CG LEU A1330 " pdb=" CD1 LEU A1330 " ideal model delta sigma weight residual 1.521 1.413 0.108 3.30e-02 9.18e+02 1.07e+01 bond pdb=" N THR B2755 " pdb=" CA THR B2755 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.31e+00 bond pdb=" N THR A2755 " pdb=" CA THR A2755 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.15e+00 bond pdb=" CG PRO B1396 " pdb=" CD PRO B1396 " ideal model delta sigma weight residual 1.503 1.407 0.096 3.40e-02 8.65e+02 7.99e+00 ... (remaining 42547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 57029 3.31 - 6.62: 755 6.62 - 9.94: 146 9.94 - 13.25: 24 13.25 - 16.56: 6 Bond angle restraints: 57960 Sorted by residual: angle pdb=" CA PRO B1396 " pdb=" N PRO B1396 " pdb=" CD PRO B1396 " ideal model delta sigma weight residual 112.00 103.67 8.33 1.40e+00 5.10e-01 3.54e+01 angle pdb=" CA PRO A1396 " pdb=" N PRO A1396 " pdb=" CD PRO A1396 " ideal model delta sigma weight residual 112.00 103.70 8.30 1.40e+00 5.10e-01 3.51e+01 angle pdb=" CA MET A4321 " pdb=" CB MET A4321 " pdb=" CG MET A4321 " ideal model delta sigma weight residual 114.10 124.79 -10.69 2.00e+00 2.50e-01 2.85e+01 angle pdb=" CA MET B4321 " pdb=" CB MET B4321 " pdb=" CG MET B4321 " ideal model delta sigma weight residual 114.10 124.75 -10.65 2.00e+00 2.50e-01 2.83e+01 angle pdb=" CA GLU A4305 " pdb=" CB GLU A4305 " pdb=" CG GLU A4305 " ideal model delta sigma weight residual 114.10 124.57 -10.47 2.00e+00 2.50e-01 2.74e+01 ... (remaining 57955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 23716 17.88 - 35.77: 1566 35.77 - 53.65: 202 53.65 - 71.54: 124 71.54 - 89.42: 24 Dihedral angle restraints: 25632 sinusoidal: 8704 harmonic: 16928 Sorted by residual: dihedral pdb=" CA PRO A1396 " pdb=" C PRO A1396 " pdb=" N CYS A1397 " pdb=" CA CYS A1397 " ideal model delta harmonic sigma weight residual 180.00 148.14 31.86 0 5.00e+00 4.00e-02 4.06e+01 dihedral pdb=" CA PRO B1396 " pdb=" C PRO B1396 " pdb=" N CYS B1397 " pdb=" CA CYS B1397 " ideal model delta harmonic sigma weight residual 180.00 148.19 31.81 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA ILE A1834 " pdb=" C ILE A1834 " pdb=" N PRO A1835 " pdb=" CA PRO A1835 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 25629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 6281 0.078 - 0.157: 781 0.157 - 0.235: 58 0.235 - 0.313: 24 0.313 - 0.392: 8 Chirality restraints: 7152 Sorted by residual: chirality pdb=" CG LEU B4385 " pdb=" CB LEU B4385 " pdb=" CD1 LEU B4385 " pdb=" CD2 LEU B4385 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" CG LEU A4385 " pdb=" CB LEU A4385 " pdb=" CD1 LEU A4385 " pdb=" CD2 LEU A4385 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CB VAL A4396 " pdb=" CA VAL A4396 " pdb=" CG1 VAL A4396 " pdb=" CG2 VAL A4396 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 7149 not shown) Planarity restraints: 7414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A4151 " 0.002 2.00e-02 2.50e+03 2.85e-02 1.42e+01 pdb=" CG PHE A4151 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A4151 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A4151 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A4151 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A4151 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A4151 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B4151 " -0.002 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE B4151 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B4151 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE B4151 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE B4151 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE B4151 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B4151 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1395 " -0.062 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO A1396 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A1396 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1396 " -0.050 5.00e-02 4.00e+02 ... (remaining 7411 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6851 2.77 - 3.30: 39107 3.30 - 3.83: 70238 3.83 - 4.37: 77226 4.37 - 4.90: 134655 Nonbonded interactions: 328077 Sorted by model distance: nonbonded pdb=" OG1 THR A1017 " pdb=" OE2 GLU A1068 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR B1017 " pdb=" OE2 GLU B1068 " model vdw 2.234 3.040 nonbonded pdb=" OE1 GLN B2070 " pdb=" OG1 THR B2587 " model vdw 2.284 3.040 nonbonded pdb=" OE1 GLN A2070 " pdb=" OG1 THR A2587 " model vdw 2.284 3.040 nonbonded pdb=" O HIS B2051 " pdb=" OG SER B2055 " model vdw 2.307 3.040 ... (remaining 328072 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.240 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 45.280 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 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 : 0.005 0.109 42554 Z= 0.236 Angle : 0.998 16.561 57964 Z= 0.517 Chirality : 0.053 0.392 7152 Planarity : 0.007 0.104 7414 Dihedral : 13.289 89.424 14538 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -1.01 (0.10), residues: 5682 helix: -0.58 (0.08), residues: 2868 sheet: 0.43 (0.19), residues: 764 loop : -1.01 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B3796 TYR 0.026 0.002 TYR B1193 PHE 0.049 0.003 PHE A4151 TRP 0.060 0.003 TRP B2696 HIS 0.032 0.002 HIS B1340 Details of bonding type rmsd covalent geometry : bond 0.00482 (42552) covalent geometry : angle 0.99643 (57960) SS BOND : bond 0.01504 ( 2) SS BOND : angle 5.75386 ( 4) hydrogen bonds : bond 0.14388 ( 2310) hydrogen bonds : angle 6.34840 ( 6828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1406 LEU cc_start: 0.7741 (tp) cc_final: 0.7411 (tp) REVERT: A 1489 MET cc_start: 0.6853 (tpp) cc_final: 0.6605 (mmt) REVERT: A 2076 ARG cc_start: 0.7173 (mtp85) cc_final: 0.6912 (ttp80) REVERT: A 2130 ASN cc_start: 0.8662 (m-40) cc_final: 0.8279 (m110) REVERT: A 2572 MET cc_start: 0.7810 (ttm) cc_final: 0.7526 (mtt) REVERT: A 2761 ASN cc_start: 0.5617 (t0) cc_final: 0.5338 (t0) REVERT: A 2905 MET cc_start: 0.8479 (mmt) cc_final: 0.8251 (mmp) REVERT: A 2926 TYR cc_start: 0.8075 (m-80) cc_final: 0.7824 (m-10) REVERT: A 3492 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7710 (tm-30) REVERT: A 3794 VAL cc_start: 0.7944 (t) cc_final: 0.7740 (t) REVERT: A 3804 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 1406 LEU cc_start: 0.7740 (tp) cc_final: 0.7421 (tp) REVERT: B 1489 MET cc_start: 0.6866 (tpp) cc_final: 0.6611 (mmt) REVERT: B 2076 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6909 (ttp80) REVERT: B 2105 MET cc_start: 0.7720 (mtp) cc_final: 0.7486 (mtt) REVERT: B 2130 ASN cc_start: 0.8670 (m-40) cc_final: 0.8286 (m110) REVERT: B 2572 MET cc_start: 0.7804 (ttm) cc_final: 0.7524 (mtt) REVERT: B 2761 ASN cc_start: 0.5644 (t0) cc_final: 0.5364 (t0) REVERT: B 2905 MET cc_start: 0.8475 (mmt) cc_final: 0.8254 (mmp) REVERT: B 2926 TYR cc_start: 0.8055 (m-80) cc_final: 0.7806 (m-10) REVERT: B 3492 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 3794 VAL cc_start: 0.7944 (t) cc_final: 0.7739 (t) REVERT: B 3804 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7392 (mm-30) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.2546 time to fit residues: 262.1336 Evaluate side-chains 338 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 7.9990 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 10.0000 chunk 223 optimal weight: 0.0470 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1030 GLN A1031 GLN A1056 GLN ** A1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 HIS A1867 HIS A1898 GLN A1975 ASN A2761 ASN A2903 GLN A2974 GLN A3212 GLN ** A3374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3831 GLN A3839 HIS B1030 GLN B1031 GLN B1056 GLN ** B1199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1826 HIS B1867 HIS B1898 GLN B1975 ASN B2761 ASN B2903 GLN B2973 ASN B2974 GLN B3212 GLN ** B3374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3747 ASN ** B3800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3839 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.161932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.121695 restraints weight = 91453.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118623 restraints weight = 101414.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.119779 restraints weight = 80385.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120005 restraints weight = 62502.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120088 restraints weight = 60086.513| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 42554 Z= 0.192 Angle : 0.643 9.835 57964 Z= 0.321 Chirality : 0.043 0.202 7152 Planarity : 0.005 0.053 7414 Dihedral : 4.359 25.073 6046 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 7.36 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.11), residues: 5682 helix: 1.07 (0.09), residues: 2920 sheet: 0.38 (0.19), residues: 750 loop : -0.58 (0.12), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1816 TYR 0.015 0.002 TYR A1869 PHE 0.041 0.002 PHE B4151 TRP 0.027 0.002 TRP B2696 HIS 0.009 0.001 HIS A1049 Details of bonding type rmsd covalent geometry : bond 0.00452 (42552) covalent geometry : angle 0.64286 (57960) SS BOND : bond 0.01430 ( 2) SS BOND : angle 2.73536 ( 4) hydrogen bonds : bond 0.04546 ( 2310) hydrogen bonds : angle 4.43081 ( 6828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1076 MET cc_start: 0.3494 (mtt) cc_final: 0.3290 (mtt) REVERT: A 1163 TRP cc_start: 0.4436 (m100) cc_final: 0.3366 (m-90) REVERT: A 1489 MET cc_start: 0.6996 (tpp) cc_final: 0.6684 (mmt) REVERT: A 2571 MET cc_start: 0.8211 (ppp) cc_final: 0.7981 (ppp) REVERT: A 2572 MET cc_start: 0.7832 (ttm) cc_final: 0.7595 (ttm) REVERT: A 2905 MET cc_start: 0.8673 (mmt) cc_final: 0.8363 (mmt) REVERT: B 1076 MET cc_start: 0.3088 (mtt) cc_final: 0.2856 (mtt) REVERT: B 1163 TRP cc_start: 0.4410 (m100) cc_final: 0.3349 (m-90) REVERT: B 1489 MET cc_start: 0.6989 (tpp) cc_final: 0.6621 (mmt) REVERT: B 2571 MET cc_start: 0.8218 (ppp) cc_final: 0.7988 (ppp) REVERT: B 2572 MET cc_start: 0.7831 (ttm) cc_final: 0.7588 (ttm) REVERT: B 2905 MET cc_start: 0.8669 (mmt) cc_final: 0.8356 (mmt) REVERT: B 3474 MET cc_start: 0.8507 (mmm) cc_final: 0.8277 (tpt) outliers start: 64 outliers final: 38 residues processed: 386 average time/residue: 0.2205 time to fit residues: 145.6402 Evaluate side-chains 318 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1340 HIS Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1863 PHE Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2060 ILE Chi-restraints excluded: chain A residue 2166 ASP Chi-restraints excluded: chain A residue 2190 ILE Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2635 MET Chi-restraints excluded: chain A residue 2638 VAL Chi-restraints excluded: chain A residue 2900 THR Chi-restraints excluded: chain A residue 3259 GLU Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3330 LEU Chi-restraints excluded: chain A residue 3522 VAL Chi-restraints excluded: chain A residue 3810 MET Chi-restraints excluded: chain A residue 4070 ILE Chi-restraints excluded: chain A residue 4187 ILE Chi-restraints excluded: chain B residue 1173 HIS Chi-restraints excluded: chain B residue 1340 HIS Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1863 PHE Chi-restraints excluded: chain B residue 1869 TYR Chi-restraints excluded: chain B residue 2060 ILE Chi-restraints excluded: chain B residue 2166 ASP Chi-restraints excluded: chain B residue 2190 ILE Chi-restraints excluded: chain B residue 2568 MET Chi-restraints excluded: chain B residue 2635 MET Chi-restraints excluded: chain B residue 2638 VAL Chi-restraints excluded: chain B residue 2900 THR Chi-restraints excluded: chain B residue 3259 GLU Chi-restraints excluded: chain B residue 3276 THR Chi-restraints excluded: chain B residue 3330 LEU Chi-restraints excluded: chain B residue 3522 VAL Chi-restraints excluded: chain B residue 3810 MET Chi-restraints excluded: chain B residue 4070 ILE Chi-restraints excluded: chain B residue 4187 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 483 optimal weight: 4.9990 chunk 325 optimal weight: 50.0000 chunk 29 optimal weight: 0.0040 chunk 235 optimal weight: 0.8980 chunk 291 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 565 optimal weight: 20.0000 chunk 475 optimal weight: 1.9990 chunk 279 optimal weight: 7.9990 chunk 313 optimal weight: 50.0000 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2333 HIS A2640 HIS A3212 GLN ** B1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2333 HIS B3212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.159529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.117200 restraints weight = 89224.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112685 restraints weight = 66894.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112898 restraints weight = 63249.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.113263 restraints weight = 60938.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.113362 restraints weight = 53303.322| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 42554 Z= 0.181 Angle : 0.601 8.468 57964 Z= 0.298 Chirality : 0.042 0.175 7152 Planarity : 0.004 0.041 7414 Dihedral : 4.116 23.007 6046 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.88 % Allowed : 9.73 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.11), residues: 5682 helix: 1.77 (0.09), residues: 2912 sheet: 0.24 (0.19), residues: 786 loop : -0.27 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A3109 TYR 0.015 0.002 TYR B1434 PHE 0.032 0.002 PHE B4151 TRP 0.026 0.002 TRP B2696 HIS 0.010 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00427 (42552) covalent geometry : angle 0.60004 (57960) SS BOND : bond 0.01480 ( 2) SS BOND : angle 3.05246 ( 4) hydrogen bonds : bond 0.04137 ( 2310) hydrogen bonds : angle 4.15473 ( 6828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 319 time to evaluate : 1.571 Fit side-chains REVERT: A 996 GLU cc_start: 0.8741 (tp30) cc_final: 0.8460 (tp30) REVERT: A 1298 MET cc_start: 0.5925 (tpp) cc_final: 0.5638 (tpp) REVERT: A 1557 GLU cc_start: 0.4533 (mt-10) cc_final: 0.4324 (mm-30) REVERT: A 1776 PHE cc_start: 0.4451 (p90) cc_final: 0.3805 (p90) REVERT: A 1903 MET cc_start: 0.7170 (mmp) cc_final: 0.6870 (mmp) REVERT: A 2571 MET cc_start: 0.8058 (ppp) cc_final: 0.7850 (ppp) REVERT: A 2905 MET cc_start: 0.8721 (mmt) cc_final: 0.8379 (mmt) REVERT: A 2994 MET cc_start: 0.6071 (mtt) cc_final: 0.5583 (ttm) REVERT: A 3535 MET cc_start: 0.8292 (mtp) cc_final: 0.8015 (mtp) REVERT: A 3767 MET cc_start: 0.7823 (tmm) cc_final: 0.7514 (tpt) REVERT: A 3950 PRO cc_start: 0.4669 (Cg_exo) cc_final: 0.4441 (Cg_endo) REVERT: B 996 GLU cc_start: 0.8780 (tp30) cc_final: 0.8500 (tp30) REVERT: B 1298 MET cc_start: 0.5941 (tpp) cc_final: 0.5645 (tpp) REVERT: B 1776 PHE cc_start: 0.4457 (p90) cc_final: 0.3798 (p90) REVERT: B 1903 MET cc_start: 0.7180 (mmp) cc_final: 0.6878 (mmp) REVERT: B 2571 MET cc_start: 0.8049 (ppp) cc_final: 0.7848 (ppp) REVERT: B 2905 MET cc_start: 0.8708 (mmt) cc_final: 0.8367 (mmt) REVERT: B 2994 MET cc_start: 0.6082 (mtt) cc_final: 0.5591 (ttm) REVERT: B 3535 MET cc_start: 0.8301 (mtp) cc_final: 0.8018 (mtp) REVERT: B 3767 MET cc_start: 0.7823 (tmm) cc_final: 0.7516 (tpt) REVERT: B 3950 PRO cc_start: 0.4383 (Cg_exo) cc_final: 0.4091 (Cg_endo) outliers start: 77 outliers final: 47 residues processed: 376 average time/residue: 0.2400 time to fit residues: 156.4158 Evaluate side-chains 320 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1340 HIS Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2120 VAL Chi-restraints excluded: chain A residue 2166 ASP Chi-restraints excluded: chain A residue 2190 ILE Chi-restraints excluded: chain A residue 2340 VAL Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2636 LEU Chi-restraints excluded: chain A residue 2656 ASN Chi-restraints excluded: chain A residue 2782 LEU Chi-restraints excluded: chain A residue 2900 THR Chi-restraints excluded: chain A residue 3113 SER Chi-restraints excluded: chain A residue 3167 VAL Chi-restraints excluded: chain A residue 3259 GLU Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3353 MET Chi-restraints excluded: chain A residue 3522 VAL Chi-restraints excluded: chain A residue 3969 THR Chi-restraints excluded: chain A residue 4187 ILE Chi-restraints excluded: chain A residue 4234 ILE Chi-restraints excluded: chain B residue 1173 HIS Chi-restraints excluded: chain B residue 1340 HIS Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2120 VAL Chi-restraints excluded: chain B residue 2166 ASP Chi-restraints excluded: chain B residue 2190 ILE Chi-restraints excluded: chain B residue 2340 VAL Chi-restraints excluded: chain B residue 2568 MET Chi-restraints excluded: chain B residue 2636 LEU Chi-restraints excluded: chain B residue 2656 ASN Chi-restraints excluded: chain B residue 2782 LEU Chi-restraints excluded: chain B residue 2900 THR Chi-restraints excluded: chain B residue 3113 SER Chi-restraints excluded: chain B residue 3167 VAL Chi-restraints excluded: chain B residue 3259 GLU Chi-restraints excluded: chain B residue 3276 THR Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3522 VAL Chi-restraints excluded: chain B residue 3810 MET Chi-restraints excluded: chain B residue 3969 THR Chi-restraints excluded: chain B residue 4187 ILE Chi-restraints excluded: chain B residue 4234 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 412 optimal weight: 0.8980 chunk 411 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 275 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 228 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN ** A1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2030 HIS A2349 ASN A2803 HIS A3326 HIS A3831 GLN ** B1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2349 ASN B2803 HIS B2973 ASN B3326 HIS B3831 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.160595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117813 restraints weight = 89113.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114356 restraints weight = 63569.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114367 restraints weight = 59481.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114806 restraints weight = 56140.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.114836 restraints weight = 49370.253| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42554 Z= 0.120 Angle : 0.526 7.393 57964 Z= 0.261 Chirality : 0.039 0.158 7152 Planarity : 0.003 0.039 7414 Dihedral : 3.871 22.472 6046 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.91 % Allowed : 11.83 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.11), residues: 5682 helix: 2.17 (0.09), residues: 2912 sheet: 0.35 (0.19), residues: 766 loop : -0.15 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1816 TYR 0.014 0.001 TYR B1434 PHE 0.021 0.001 PHE A4151 TRP 0.019 0.001 TRP B2696 HIS 0.007 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00274 (42552) covalent geometry : angle 0.52600 (57960) SS BOND : bond 0.01388 ( 2) SS BOND : angle 2.59839 ( 4) hydrogen bonds : bond 0.03537 ( 2310) hydrogen bonds : angle 3.92772 ( 6828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 996 GLU cc_start: 0.8612 (tp30) cc_final: 0.8411 (tp30) REVERT: A 1163 TRP cc_start: 0.4805 (m100) cc_final: 0.3637 (m100) REVERT: A 1413 MET cc_start: 0.8168 (tpp) cc_final: 0.7948 (tpp) REVERT: A 1776 PHE cc_start: 0.4304 (p90) cc_final: 0.3667 (p90) REVERT: A 1903 MET cc_start: 0.7308 (mmp) cc_final: 0.6928 (mmp) REVERT: A 2153 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7216 (tmm) REVERT: A 2905 MET cc_start: 0.8655 (mmt) cc_final: 0.8354 (mmt) REVERT: A 2994 MET cc_start: 0.5780 (mtt) cc_final: 0.5329 (ttm) REVERT: A 4299 LYS cc_start: 0.3491 (OUTLIER) cc_final: 0.3236 (ttmm) REVERT: B 996 GLU cc_start: 0.8634 (tp30) cc_final: 0.8419 (tp30) REVERT: B 1413 MET cc_start: 0.8167 (tpp) cc_final: 0.7947 (tpp) REVERT: B 1776 PHE cc_start: 0.4310 (p90) cc_final: 0.3661 (p90) REVERT: B 1903 MET cc_start: 0.7310 (mmp) cc_final: 0.6924 (mmp) REVERT: B 2153 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7205 (tmm) REVERT: B 2905 MET cc_start: 0.8669 (mmt) cc_final: 0.8366 (mmt) REVERT: B 2994 MET cc_start: 0.5781 (mtt) cc_final: 0.5328 (ttm) outliers start: 78 outliers final: 45 residues processed: 360 average time/residue: 0.2384 time to fit residues: 149.1282 Evaluate side-chains 330 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1340 HIS Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1869 TYR Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2166 ASP Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2190 ILE Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2635 MET Chi-restraints excluded: chain A residue 2638 VAL Chi-restraints excluded: chain A residue 2656 ASN Chi-restraints excluded: chain A residue 2696 TRP Chi-restraints excluded: chain A residue 2782 LEU Chi-restraints excluded: chain A residue 2819 LEU Chi-restraints excluded: chain A residue 2900 THR Chi-restraints excluded: chain A residue 3237 LEU Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3353 MET Chi-restraints excluded: chain A residue 4187 ILE Chi-restraints excluded: chain A residue 4234 ILE Chi-restraints excluded: chain A residue 4299 LYS Chi-restraints excluded: chain B residue 1173 HIS Chi-restraints excluded: chain B residue 1340 HIS Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2153 MET Chi-restraints excluded: chain B residue 2166 ASP Chi-restraints excluded: chain B residue 2170 THR Chi-restraints excluded: chain B residue 2190 ILE Chi-restraints excluded: chain B residue 2568 MET Chi-restraints excluded: chain B residue 2635 MET Chi-restraints excluded: chain B residue 2638 VAL Chi-restraints excluded: chain B residue 2656 ASN Chi-restraints excluded: chain B residue 2696 TRP Chi-restraints excluded: chain B residue 2782 LEU Chi-restraints excluded: chain B residue 2819 LEU Chi-restraints excluded: chain B residue 2900 THR Chi-restraints excluded: chain B residue 3276 THR Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3522 VAL Chi-restraints excluded: chain B residue 4187 ILE Chi-restraints excluded: chain B residue 4234 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 197 optimal weight: 0.5980 chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 329 optimal weight: 30.0000 chunk 303 optimal weight: 10.0000 chunk 382 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 269 optimal weight: 0.2980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1342 ASN A1938 ASN ** A1975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3831 GLN ** B1274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1938 ASN ** B1975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2030 HIS B3831 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.158530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.118314 restraints weight = 88545.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.115624 restraints weight = 79527.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.116586 restraints weight = 67495.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117069 restraints weight = 50227.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117036 restraints weight = 46293.422| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 42554 Z= 0.167 Angle : 0.574 10.749 57964 Z= 0.282 Chirality : 0.041 0.182 7152 Planarity : 0.004 0.038 7414 Dihedral : 3.880 22.067 6046 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.42 % Allowed : 12.49 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.11), residues: 5682 helix: 2.24 (0.09), residues: 2908 sheet: 0.30 (0.19), residues: 764 loop : -0.13 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A4153 TYR 0.018 0.001 TYR B1434 PHE 0.019 0.002 PHE A3290 TRP 0.018 0.001 TRP A2696 HIS 0.008 0.001 HIS A1049 Details of bonding type rmsd covalent geometry : bond 0.00398 (42552) covalent geometry : angle 0.57331 (57960) SS BOND : bond 0.01438 ( 2) SS BOND : angle 2.94836 ( 4) hydrogen bonds : bond 0.03827 ( 2310) hydrogen bonds : angle 3.99798 ( 6828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11364 Ramachandran restraints generated. 5682 Oldfield, 0 Emsley, 5682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 288 time to evaluate : 1.629 Fit side-chains REVERT: A 1434 TYR cc_start: 0.6940 (t80) cc_final: 0.6688 (t80) REVERT: A 1842 MET cc_start: 0.7272 (mmt) cc_final: 0.7026 (mmm) REVERT: A 1903 MET cc_start: 0.7314 (mmp) cc_final: 0.7020 (mmp) REVERT: A 2153 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7250 (tmm) REVERT: A 2714 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (mp) REVERT: A 2905 MET cc_start: 0.8719 (mmt) cc_final: 0.8414 (mmt) REVERT: A 3474 MET cc_start: 0.8063 (tpt) cc_final: 0.7817 (tpt) REVERT: A 3767 MET cc_start: 0.7236 (tmm) cc_final: 0.7015 (tpt) REVERT: B 1413 MET cc_start: 0.7961 (tpp) cc_final: 0.7759 (tpp) REVERT: B 1434 TYR cc_start: 0.6959 (t80) cc_final: 0.6660 (t80) REVERT: B 1842 MET cc_start: 0.7230 (mmt) cc_final: 0.7015 (mmm) REVERT: B 1903 MET cc_start: 0.7299 (mmp) cc_final: 0.7005 (mmp) REVERT: B 2153 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7291 (tmm) REVERT: B 2714 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8865 (mp) REVERT: B 2905 MET cc_start: 0.8685 (mmt) cc_final: 0.8377 (mmt) REVERT: B 3767 MET cc_start: 0.7227 (tmm) cc_final: 0.6998 (tpt) outliers start: 99 outliers final: 73 residues processed: 367 average time/residue: 0.2400 time to fit residues: 153.2767 Evaluate side-chains 347 residues out of total 5120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 270 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1173 HIS Chi-restraints excluded: chain A residue 1340 HIS Chi-restraints excluded: chain A residue 1342 ASN Chi-restraints excluded: chain A residue 1362 LEU Chi-restraints excluded: chain A residue 1421 THR Chi-restraints excluded: chain A residue 1867 HIS Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2120 VAL Chi-restraints excluded: chain A residue 2153 MET Chi-restraints excluded: chain A residue 2166 ASP Chi-restraints excluded: chain A residue 2170 THR Chi-restraints excluded: chain A residue 2190 ILE Chi-restraints excluded: chain A residue 2335 ASP Chi-restraints excluded: chain A residue 2340 VAL Chi-restraints excluded: chain A residue 2568 MET Chi-restraints excluded: chain A residue 2635 MET Chi-restraints excluded: chain A residue 2636 LEU Chi-restraints excluded: chain A residue 2638 VAL Chi-restraints excluded: chain A residue 2656 ASN Chi-restraints excluded: chain A residue 2696 TRP Chi-restraints excluded: chain A residue 2714 LEU Chi-restraints excluded: chain A residue 2782 LEU Chi-restraints excluded: chain A residue 2819 LEU Chi-restraints excluded: chain A residue 2837 VAL Chi-restraints excluded: chain A residue 2900 THR Chi-restraints excluded: chain A residue 3074 VAL Chi-restraints excluded: chain A residue 3237 LEU Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3288 THR Chi-restraints excluded: chain A residue 3331 GLU Chi-restraints excluded: chain A residue 3353 MET Chi-restraints excluded: chain A residue 3522 VAL Chi-restraints excluded: chain A residue 3699 THR Chi-restraints excluded: chain A residue 3810 MET Chi-restraints excluded: chain A residue 4187 ILE Chi-restraints excluded: chain A residue 4234 ILE Chi-restraints excluded: chain A residue 4299 LYS Chi-restraints excluded: chain B residue 1100 LEU Chi-restraints excluded: chain B residue 1173 HIS Chi-restraints excluded: chain B residue 1340 HIS Chi-restraints excluded: chain B residue 1362 LEU Chi-restraints excluded: chain B residue 1421 THR Chi-restraints excluded: chain B residue 1867 HIS Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2120 VAL Chi-restraints excluded: chain B residue 2153 MET Chi-restraints excluded: chain B residue 2166 ASP Chi-restraints excluded: chain B residue 2170 THR Chi-restraints excluded: chain B residue 2190 ILE Chi-restraints excluded: chain B residue 2335 ASP Chi-restraints excluded: chain B residue 2340 VAL Chi-restraints excluded: chain B residue 2568 MET Chi-restraints excluded: chain B residue 2635 MET Chi-restraints excluded: chain B residue 2636 LEU Chi-restraints excluded: chain B residue 2638 VAL Chi-restraints excluded: chain B residue 2656 ASN Chi-restraints excluded: chain B residue 2696 TRP Chi-restraints excluded: chain B residue 2714 LEU Chi-restraints excluded: chain B residue 2782 LEU Chi-restraints excluded: chain B residue 2819 LEU Chi-restraints excluded: chain B residue 2837 VAL Chi-restraints excluded: chain B residue 2900 THR Chi-restraints excluded: chain B residue 3074 VAL Chi-restraints excluded: chain B residue 3276 THR Chi-restraints excluded: chain B residue 3288 THR Chi-restraints excluded: chain B residue 3331 GLU Chi-restraints excluded: chain B residue 3353 MET Chi-restraints excluded: chain B residue 3522 VAL Chi-restraints excluded: chain B residue 3699 THR Chi-restraints excluded: chain B residue 3810 MET Chi-restraints excluded: chain B residue 4070 ILE Chi-restraints excluded: chain B residue 4187 ILE Chi-restraints excluded: chain B residue 4234 ILE Chi-restraints excluded: chain B residue 4299 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5035 > 50: distance: 27 - 107: 31.246 distance: 30 - 104: 23.777 distance: 65 - 69: 20.855 distance: 69 - 70: 17.412 distance: 70 - 71: 18.841 distance: 70 - 73: 17.658 distance: 71 - 72: 9.036 distance: 71 - 76: 17.117 distance: 73 - 74: 18.688 distance: 73 - 75: 26.965 distance: 76 - 77: 18.898 distance: 76 - 204: 23.957 distance: 77 - 78: 22.375 distance: 77 - 80: 24.085 distance: 78 - 79: 6.051 distance: 78 - 87: 17.703 distance: 79 - 201: 21.217 distance: 80 - 81: 15.497 distance: 81 - 82: 6.060 distance: 81 - 83: 13.491 distance: 82 - 84: 9.268 distance: 83 - 85: 7.874 distance: 84 - 86: 11.480 distance: 85 - 86: 6.329 distance: 87 - 88: 15.733 distance: 88 - 89: 19.078 distance: 88 - 91: 20.451 distance: 89 - 90: 32.423 distance: 89 - 96: 15.391 distance: 91 - 92: 23.753 distance: 92 - 93: 14.496 distance: 93 - 94: 11.697 distance: 93 - 95: 8.159 distance: 96 - 97: 27.179 distance: 96 - 190: 22.540 distance: 97 - 98: 15.466 distance: 97 - 100: 26.958 distance: 98 - 99: 35.041 distance: 98 - 104: 53.446 distance: 99 - 187: 14.218 distance: 100 - 101: 13.190 distance: 101 - 102: 35.953 distance: 101 - 103: 17.072 distance: 104 - 105: 20.390 distance: 105 - 106: 30.657 distance: 105 - 108: 7.351 distance: 106 - 107: 48.996 distance: 106 - 111: 14.156 distance: 108 - 109: 17.610 distance: 108 - 110: 9.751 distance: 112 - 113: 43.715 distance: 112 - 115: 53.960 distance: 113 - 114: 31.528 distance: 113 - 119: 21.110 distance: 115 - 116: 30.843 distance: 116 - 117: 20.340 distance: 116 - 118: 12.888 distance: 119 - 120: 19.243 distance: 119 - 125: 29.981 distance: 120 - 121: 30.523 distance: 120 - 123: 19.193 distance: 121 - 122: 40.271 distance: 121 - 126: 20.140 distance: 123 - 124: 22.172 distance: 124 - 125: 27.401 distance: 126 - 127: 28.323 distance: 127 - 128: 27.557 distance: 127 - 130: 29.946 distance: 128 - 129: 43.703 distance: 128 - 135: 11.045 distance: 130 - 131: 42.687 distance: 131 - 132: 31.413 distance: 132 - 133: 40.348 distance: 133 - 134: 26.248 distance: 135 - 136: 21.803 distance: 136 - 137: 45.353 distance: 136 - 139: 23.333 distance: 137 - 138: 38.430 distance: 137 - 140: 25.340 distance: 140 - 141: 12.287 distance: 141 - 142: 7.289 distance: 141 - 144: 26.058 distance: 142 - 143: 22.459 distance: 142 - 146: 9.048 distance: 144 - 145: 18.741