Starting phenix.real_space_refine on Sat Sep 12 23:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ylf_10837/09_2026/6ylf_10837.map" } resolution = 4.2 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= 0.004 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: 3 Type Number sf(0) Gaussians C 10962 2.51 5 N 3700 2.21 5 O 3700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18362 Number of models: 1 Model: "" Number of chains: 2 Chain: "AP1" Number of atoms: 18010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3629, 18010 Classifications: {'peptide': 3629} Incomplete info: {'truncation_to_alanine': 3296} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 110, 'TRANS': 3516} Chain breaks: 39 Unresolved chain link angles: 111 Unresolved non-hydrogen bonds: 11778 Unresolved non-hydrogen angles: 15065 Unresolved non-hydrogen dihedrals: 9774 Unresolved non-hydrogen chiralities: 1169 Planarities with less than four sites: {'GLN:plan1': 113, 'ASP:plan': 210, 'ARG:plan': 157, 'ASN:plan1': 196, 'PHE:plan': 189, 'GLU:plan': 251, 'HIS:plan': 62, 'TYR:plan': 116, 'TRP:plan': 46} Unresolved non-hydrogen planarities: 6129 Chain: "xP1" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 352 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 6, 'TRANS': 64} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 95 Time building chain proxies: 4.56, per 1000 atoms: 0.25 Number of scatterers: 18362 At special positions: 0 Unit cell: (121.785, 223.449, 231.921, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3700 8.00 N 3700 7.00 C 10962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7124 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 17 sheets defined 60.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'AP1' and resid 10 through 24 removed outlier: 3.830A pdb=" N ALAAP1 23 " --> pdb=" O LEUAP1 19 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHEAP1 24 " --> pdb=" O PHEAP1 20 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 42 through 55 Processing helix chain 'AP1' and resid 60 through 65 Processing helix chain 'AP1' and resid 68 through 79 removed outlier: 3.973A pdb=" N ILEAP1 72 " --> pdb=" O ILEAP1 68 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 84 through 96 Processing helix chain 'AP1' and resid 102 through 122 removed outlier: 3.761A pdb=" N ASPAP1 111 " --> pdb=" O GLUAP1 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYSAP1 112 " --> pdb=" O ASPAP1 108 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASPAP1 115 " --> pdb=" O ASPAP1 111 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N HISAP1 116 " --> pdb=" O LYSAP1 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHEAP1 117 " --> pdb=" O GLUAP1 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILEAP1 120 " --> pdb=" O HISAP1 116 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 129 through 146 removed outlier: 4.626A pdb=" N ILEAP1 135 " --> pdb=" O ASPAP1 131 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASNAP1 146 " --> pdb=" O LEUAP1 142 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 155 through 169 removed outlier: 3.717A pdb=" N LEUAP1 159 " --> pdb=" O GLNAP1 155 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 174 through 187 Processing helix chain 'AP1' and resid 191 through 202 Processing helix chain 'AP1' and resid 223 through 236 removed outlier: 4.054A pdb=" N GLUAP1 227 " --> pdb=" O LEUAP1 223 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALAAP1 228 " --> pdb=" O GLUAP1 224 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYSAP1 229 " --> pdb=" O LEUAP1 225 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 256 through 260 removed outlier: 3.524A pdb=" N ASPAP1 260 " --> pdb=" O GLUAP1 257 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 294 through 307 removed outlier: 3.930A pdb=" N ASNAP1 307 " --> pdb=" O ARGAP1 303 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 320 through 333 removed outlier: 3.918A pdb=" N LEUAP1 324 " --> pdb=" O GLYAP1 320 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILEAP1 325 " --> pdb=" O LYSAP1 321 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYSAP1 330 " --> pdb=" O ASNAP1 326 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYRAP1 331 " --> pdb=" O GLUAP1 327 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 370 through 379 Processing helix chain 'AP1' and resid 387 through 390 Processing helix chain 'AP1' and resid 391 through 402 removed outlier: 3.751A pdb=" N ILEAP1 397 " --> pdb=" O ASPAP1 393 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SERAP1 400 " --> pdb=" O SERAP1 396 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 446 through 453 Processing helix chain 'AP1' and resid 464 through 472 removed outlier: 4.726A pdb=" N LEUAP1 470 " --> pdb=" O LEUAP1 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLNAP1 472 " --> pdb=" O HISAP1 468 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 480 through 501 removed outlier: 4.069A pdb=" N ILEAP1 485 " --> pdb=" O ILEAP1 481 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASPAP1 486 " --> pdb=" O PROAP1 482 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N METAP1 496 " --> pdb=" O LYSAP1 492 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASNAP1 497 " --> pdb=" O SERAP1 493 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYSAP1 499 " --> pdb=" O TYRAP1 495 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHEAP1 500 " --> pdb=" O METAP1 496 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 512 through 529 removed outlier: 3.665A pdb=" N ASPAP1 516 " --> pdb=" O VALAP1 512 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASPAP1 525 " --> pdb=" O CYSAP1 521 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEUAP1 527 " --> pdb=" O ARGAP1 523 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 538 through 552 removed outlier: 3.957A pdb=" N PHEAP1 549 " --> pdb=" O TYRAP1 545 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 561 through 567 removed outlier: 3.584A pdb=" N ALAAP1 565 " --> pdb=" O GLYAP1 561 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEUAP1 566 " --> pdb=" O GLUAP1 562 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 631 through 645 removed outlier: 3.822A pdb=" N LEUAP1 635 " --> pdb=" O HISAP1 631 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SERAP1 640 " --> pdb=" O METAP1 636 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 655 through 667 removed outlier: 5.221A pdb=" N THRAP1 661 " --> pdb=" O THRAP1 657 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VALAP1 662 " --> pdb=" O GLYAP1 658 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 815 through 822 removed outlier: 3.968A pdb=" N THRAP1 819 " --> pdb=" O SERAP1 815 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILEAP1 820 " --> pdb=" O LEUAP1 816 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 836 through 844 removed outlier: 3.651A pdb=" N SERAP1 841 " --> pdb=" O ASPAP1 837 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASPAP1 844 " --> pdb=" O GLUAP1 840 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 909 through 916 removed outlier: 4.297A pdb=" N SERAP1 913 " --> pdb=" O THRAP1 909 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 926 through 939 removed outlier: 3.842A pdb=" N GLYAP1 930 " --> pdb=" O ASPAP1 926 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASPAP1 932 " --> pdb=" O TRPAP1 928 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEUAP1 938 " --> pdb=" O ALAAP1 934 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 954 through 965 removed outlier: 4.560A pdb=" N HISAP1 958 " --> pdb=" O ASNAP1 954 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 975 through 987 removed outlier: 4.065A pdb=" N LEUAP1 980 " --> pdb=" O HISAP1 976 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEUAP1 984 " --> pdb=" O LEUAP1 980 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 987 through 992 removed outlier: 3.796A pdb=" N PHEAP1 992 " --> pdb=" O PHEAP1 988 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 997 through 1005 Processing helix chain 'AP1' and resid 1061 through 1072 Processing helix chain 'AP1' and resid 1088 through 1100 removed outlier: 3.831A pdb=" N ILEAP11093 " --> pdb=" O LYSAP11089 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASPAP11098 " --> pdb=" O LYSAP11094 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEAP11099 " --> pdb=" O TYRAP11095 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1136 through 1141 Processing helix chain 'AP1' and resid 1160 through 1168 removed outlier: 3.680A pdb=" N ASNAP11164 " --> pdb=" O LEUAP11160 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEUAP11166 " --> pdb=" O ALAAP11162 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1224 through 1233 removed outlier: 4.237A pdb=" N ILEAP11230 " --> pdb=" O GLUAP11226 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1236 through 1241 removed outlier: 3.723A pdb=" N SERAP11240 " --> pdb=" O GLNAP11236 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1243 through 1247 Processing helix chain 'AP1' and resid 1261 through 1277 Processing helix chain 'AP1' and resid 1284 through 1298 removed outlier: 3.905A pdb=" N GLUAP11298 " --> pdb=" O METAP11294 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1305 through 1318 Processing helix chain 'AP1' and resid 1345 through 1360 removed outlier: 4.253A pdb=" N ARGAP11349 " --> pdb=" O LYSAP11345 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1375 through 1385 Processing helix chain 'AP1' and resid 1478 through 1485 Processing helix chain 'AP1' and resid 1498 through 1505 Processing helix chain 'AP1' and resid 1506 through 1509 removed outlier: 3.882A pdb=" N LEUAP11509 " --> pdb=" O ASNAP11506 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 1506 through 1509' Processing helix chain 'AP1' and resid 1544 through 1548 Processing helix chain 'AP1' and resid 1551 through 1556 removed outlier: 3.977A pdb=" N ASNAP11556 " --> pdb=" O ALAAP11553 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1571 through 1579 removed outlier: 3.543A pdb=" N ILEAP11575 " --> pdb=" O ASPAP11571 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VALAP11576 " --> pdb=" O VALAP11572 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1584 through 1599 Proline residue: AP11590 - end of helix Processing helix chain 'AP1' and resid 1607 through 1623 Processing helix chain 'AP1' and resid 1631 through 1641 removed outlier: 3.619A pdb=" N ALAAP11637 " --> pdb=" O ASNAP11633 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEUAP11638 " --> pdb=" O LYSAP11634 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILEAP11639 " --> pdb=" O SERAP11635 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLNAP11640 " --> pdb=" O THRAP11636 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1642 through 1646 removed outlier: 4.213A pdb=" N VALAP11645 " --> pdb=" O ALAAP11642 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHEAP11646 " --> pdb=" O SERAP11643 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 1642 through 1646' Processing helix chain 'AP1' and resid 1652 through 1668 Processing helix chain 'AP1' and resid 1725 through 1735 removed outlier: 3.613A pdb=" N LEUAP11730 " --> pdb=" O THRAP11726 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALAP11731 " --> pdb=" O ALAAP11727 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1752 through 1764 Processing helix chain 'AP1' and resid 1778 through 1782 Processing helix chain 'AP1' and resid 1800 through 1806 Processing helix chain 'AP1' and resid 1823 through 1831 removed outlier: 3.782A pdb=" N GLYAP11827 " --> pdb=" O SERAP11823 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1872 through 1877 Processing helix chain 'AP1' and resid 1888 through 1900 Processing helix chain 'AP1' and resid 1906 through 1925 removed outlier: 3.511A pdb=" N LEUAP11918 " --> pdb=" O LEUAP11914 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLNAP11921 " --> pdb=" O THRAP11917 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALAP11922 " --> pdb=" O LEUAP11918 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 1939 through 1950 Processing helix chain 'AP1' and resid 1975 through 1987 removed outlier: 3.886A pdb=" N ASNAP11979 " --> pdb=" O ILEAP11975 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYSAP11980 " --> pdb=" O SERAP11976 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLNAP11982 " --> pdb=" O LYSAP11978 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2033 through 2047 Processing helix chain 'AP1' and resid 2060 through 2071 removed outlier: 3.960A pdb=" N ILEAP12064 " --> pdb=" O LYSAP12060 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SERAP12069 " --> pdb=" O ARGAP12065 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILEAP12070 " --> pdb=" O PHEAP12066 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2084 through 2089 removed outlier: 4.159A pdb=" N ILEAP12089 " --> pdb=" O ASPAP12085 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2098 through 2123 removed outlier: 4.111A pdb=" N TYRAP12104 " --> pdb=" O ARGAP12100 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILEAP12105 " --> pdb=" O GLNAP12101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLUAP12115 " --> pdb=" O ASNAP12111 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2126 through 2143 removed outlier: 4.327A pdb=" N GLUAP12132 " --> pdb=" O THRAP12128 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASNAP12143 " --> pdb=" O TYRAP12139 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2149 through 2160 Processing helix chain 'AP1' and resid 2166 through 2184 removed outlier: 3.509A pdb=" N LEUAP12170 " --> pdb=" O GLYAP12166 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N METAP12173 " --> pdb=" O LEUAP12169 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLUAP12178 " --> pdb=" O SERAP12174 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2185 through 2189 removed outlier: 3.935A pdb=" N SERAP12189 " --> pdb=" O LYSAP12186 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2197 through 2206 removed outlier: 3.743A pdb=" N LYSAP12201 " --> pdb=" O GLYAP12197 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2221 through 2228 removed outlier: 3.723A pdb=" N SERAP12227 " --> pdb=" O ARGAP12224 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2270 through 2274 removed outlier: 3.777A pdb=" N ARGAP12274 " --> pdb=" O ARGAP12271 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2284 through 2288 removed outlier: 3.856A pdb=" N SERAP12287 " --> pdb=" O GLUAP12284 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2290 through 2296 Processing helix chain 'AP1' and resid 2327 through 2331 removed outlier: 3.564A pdb=" N HISAP12330 " --> pdb=" O PROAP12327 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2337 through 2352 removed outlier: 3.514A pdb=" N ILEAP12341 " --> pdb=" O SERAP12337 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHEAP12342 " --> pdb=" O ARGAP12338 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SERAP12352 " --> pdb=" O ILEAP12348 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2371 through 2383 removed outlier: 4.539A pdb=" N LYSAP12375 " --> pdb=" O GLYAP12371 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2390 through 2405 Processing helix chain 'AP1' and resid 2407 through 2415 Processing helix chain 'AP1' and resid 2415 through 2426 removed outlier: 3.700A pdb=" N LEUAP12426 " --> pdb=" O PHEAP12422 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2446 through 2451 Processing helix chain 'AP1' and resid 2454 through 2459 Processing helix chain 'AP1' and resid 2460 through 2488 removed outlier: 3.801A pdb=" N LEUAP12466 " --> pdb=" O SERAP12462 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUAP12473 " --> pdb=" O LEUAP12469 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASNAP12477 " --> pdb=" O LEUAP12473 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALAAP12478 " --> pdb=" O ASNAP12474 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEUAP12481 " --> pdb=" O ASNAP12477 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILEAP12482 " --> pdb=" O ALAAP12478 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2495 through 2505 Processing helix chain 'AP1' and resid 2522 through 2534 removed outlier: 3.636A pdb=" N THRAP12526 " --> pdb=" O TYRAP12522 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2542 through 2560 removed outlier: 3.552A pdb=" N TYRAP12546 " --> pdb=" O ASNAP12542 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEUAP12550 " --> pdb=" O TYRAP12546 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEUAP12551 " --> pdb=" O TYRAP12547 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2566 through 2571 removed outlier: 3.600A pdb=" N VALAP12571 " --> pdb=" O ARGAP12568 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2572 through 2586 removed outlier: 3.746A pdb=" N ILEAP12576 " --> pdb=" O TYRAP12572 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASPAP12577 " --> pdb=" O LYSAP12573 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2596 through 2606 removed outlier: 3.716A pdb=" N PHEAP12601 " --> pdb=" O ILEAP12597 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THRAP12602 " --> pdb=" O ASNAP12598 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VALAP12604 " --> pdb=" O GLUAP12600 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2613 through 2618 Processing helix chain 'AP1' and resid 2627 through 2649 removed outlier: 4.033A pdb=" N LYSAP12646 " --> pdb=" O GLUAP12642 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VALAP12647 " --> pdb=" O LYSAP12643 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2650 through 2651 No H-bonds generated for 'chain 'AP1' and resid 2650 through 2651' Processing helix chain 'AP1' and resid 2652 through 2656 Processing helix chain 'AP1' and resid 2657 through 2676 removed outlier: 4.065A pdb=" N ARGAP12667 " --> pdb=" O METAP12663 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEUAP12674 " --> pdb=" O ASNAP12670 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2678 through 2701 removed outlier: 4.358A pdb=" N ASNAP12682 " --> pdb=" O LEUAP12678 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEUAP12683 " --> pdb=" O SERAP12679 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2710 through 2722 Processing helix chain 'AP1' and resid 2726 through 2734 Processing helix chain 'AP1' and resid 2740 through 2745 removed outlier: 4.041A pdb=" N LEUAP12744 " --> pdb=" O ALAAP12740 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2757 through 2762 removed outlier: 3.603A pdb=" N LEUAP12761 " --> pdb=" O ILEAP12757 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRPAP12762 " --> pdb=" O PHEAP12758 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 2757 through 2762' Processing helix chain 'AP1' and resid 2779 through 2791 removed outlier: 4.000A pdb=" N VALAP12786 " --> pdb=" O LEUAP12782 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2796 through 2800 Processing helix chain 'AP1' and resid 2802 through 2817 removed outlier: 3.708A pdb=" N ASPAP12806 " --> pdb=" O GLNAP12802 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYSAP12816 " --> pdb=" O SERAP12812 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2817 through 2822 removed outlier: 3.600A pdb=" N LEUAP12821 " --> pdb=" O CYSAP12817 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUAP12822 " --> pdb=" O SERAP12818 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 2817 through 2822' Processing helix chain 'AP1' and resid 2824 through 2845 removed outlier: 3.872A pdb=" N LYSAP12830 " --> pdb=" O METAP12826 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYSAP12839 " --> pdb=" O SERAP12835 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VALAP12840 " --> pdb=" O TRPAP12836 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILEAP12841 " --> pdb=" O LEUAP12837 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2853 through 2865 removed outlier: 4.492A pdb=" N GLUAP12862 " --> pdb=" O CYSAP12858 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLUAP12863 " --> pdb=" O SERAP12859 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2866 through 2876 removed outlier: 3.870A pdb=" N ARGAP12870 " --> pdb=" O ALAAP12866 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THRAP12872 " --> pdb=" O GLUAP12868 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2877 through 2886 removed outlier: 3.709A pdb=" N SERAP12886 " --> pdb=" O ASPAP12882 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2890 through 2905 removed outlier: 3.797A pdb=" N LEUAP12904 " --> pdb=" O PHEAP12900 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEUAP12905 " --> pdb=" O GLYAP12901 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2915 through 2946 removed outlier: 3.790A pdb=" N HISAP12919 " --> pdb=" O ASPAP12915 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASPAP12920 " --> pdb=" O PROAP12916 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUAP12923 " --> pdb=" O HISAP12919 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYRAP12924 " --> pdb=" O ASPAP12920 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASPAP12925 " --> pdb=" O TYRAP12921 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VALAP12944 " --> pdb=" O SERAP12940 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2954 through 2960 removed outlier: 3.979A pdb=" N LYSAP12958 " --> pdb=" O ILEAP12954 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEUAP12959 " --> pdb=" O PHEAP12955 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILEAP12960 " --> pdb=" O THRAP12956 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 2954 through 2960' Processing helix chain 'AP1' and resid 2970 through 2974 removed outlier: 3.516A pdb=" N ARGAP12973 " --> pdb=" O GLNAP12970 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2981 through 2996 removed outlier: 3.817A pdb=" N PHEAP12985 " --> pdb=" O ILEAP12981 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 2997 through 3010 removed outlier: 3.899A pdb=" N GLUAP13003 " --> pdb=" O ARGAP12999 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUAP13004 " --> pdb=" O GLNAP13000 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3014 through 3036 removed outlier: 4.133A pdb=" N ARGAP13018 " --> pdb=" O GLNAP13014 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLUAP13020 " --> pdb=" O ASPAP13016 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3043 through 3066 removed outlier: 3.665A pdb=" N TYRAP13050 " --> pdb=" O ILEAP13046 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEAP13051 " --> pdb=" O LEUAP13047 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SERAP13053 " --> pdb=" O GLYAP13049 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHEAP13058 " --> pdb=" O ILEAP13054 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3067 through 3069 No H-bonds generated for 'chain 'AP1' and resid 3067 through 3069' Processing helix chain 'AP1' and resid 3082 through 3087 removed outlier: 3.702A pdb=" N CYSAP13087 " --> pdb=" O ILEAP13083 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3087 through 3104 removed outlier: 3.765A pdb=" N HISAP13096 " --> pdb=" O LEUAP13092 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLUAP13097 " --> pdb=" O SERAP13093 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARGAP13100 " --> pdb=" O HISAP13096 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHEAP13101 " --> pdb=" O GLUAP13097 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHEAP13102 " --> pdb=" O LEUAP13098 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSAP13103 " --> pdb=" O SERAP13099 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3112 through 3117 removed outlier: 3.884A pdb=" N METAP13117 " --> pdb=" O GLUAP13113 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3117 through 3126 removed outlier: 3.966A pdb=" N THRAP13121 " --> pdb=" O METAP13117 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUAP13122 " --> pdb=" O TYRAP13118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHEAP13123 " --> pdb=" O PHEAP13119 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3129 through 3131 No H-bonds generated for 'chain 'AP1' and resid 3129 through 3131' Processing helix chain 'AP1' and resid 3132 through 3155 removed outlier: 3.662A pdb=" N LEUAP13140 " --> pdb=" O PHEAP13136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARGAP13150 " --> pdb=" O ARGAP13146 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHEAP13152 " --> pdb=" O SERAP13148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARGAP13153 " --> pdb=" O VALAP13149 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUAP13155 " --> pdb=" O ARGAP13151 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3175 through 3180 Processing helix chain 'AP1' and resid 3203 through 3210 Processing helix chain 'AP1' and resid 3211 through 3218 removed outlier: 4.292A pdb=" N PHEAP13218 " --> pdb=" O TYRAP13214 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3225 through 3243 removed outlier: 4.156A pdb=" N GLUAP13229 " --> pdb=" O ASNAP13225 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYSAP13231 " --> pdb=" O SERAP13227 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SERAP13232 " --> pdb=" O SERAP13228 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THRAP13238 " --> pdb=" O ALAAP13234 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILEAP13239 " --> pdb=" O ILEAP13235 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3256 through 3272 removed outlier: 3.537A pdb=" N VALAP13260 " --> pdb=" O SERAP13256 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASNAP13262 " --> pdb=" O SERAP13258 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHEAP13271 " --> pdb=" O GLUAP13267 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYSAP13272 " --> pdb=" O THRAP13268 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3287 through 3309 removed outlier: 3.549A pdb=" N PHEAP13291 " --> pdb=" O SERAP13287 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYSAP13293 " --> pdb=" O PROAP13289 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VALAP13301 " --> pdb=" O ILEAP13297 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3315 through 3330 Processing helix chain 'AP1' and resid 3336 through 3358 removed outlier: 3.946A pdb=" N GLNAP13340 " --> pdb=" O PROAP13336 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3364 through 3389 removed outlier: 3.859A pdb=" N LYSAP13380 " --> pdb=" O VALAP13376 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEUAP13381 " --> pdb=" O SERAP13377 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THRAP13385 " --> pdb=" O LEUAP13381 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRPAP13386 " --> pdb=" O GLUAP13382 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3392 through 3397 removed outlier: 3.622A pdb=" N LYSAP13396 " --> pdb=" O SERAP13392 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THRAP13397 " --> pdb=" O GLUAP13393 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 3392 through 3397' Processing helix chain 'AP1' and resid 3398 through 3400 No H-bonds generated for 'chain 'AP1' and resid 3398 through 3400' Processing helix chain 'AP1' and resid 3401 through 3413 removed outlier: 3.950A pdb=" N PHEAP13406 " --> pdb=" O GLYAP13402 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYRAP13407 " --> pdb=" O LYSAP13403 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3428 through 3441 removed outlier: 3.599A pdb=" N LEUAP13437 " --> pdb=" O SERAP13433 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHEAP13438 " --> pdb=" O SERAP13434 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHEAP13439 " --> pdb=" O LEUAP13435 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3443 through 3446 Processing helix chain 'AP1' and resid 3447 through 3465 removed outlier: 4.086A pdb=" N ALAAP13456 " --> pdb=" O ASPAP13452 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHEAP13457 " --> pdb=" O LEUAP13453 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLNAP13462 " --> pdb=" O TYRAP13458 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUAP13463 " --> pdb=" O LYSAP13459 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3471 through 3483 removed outlier: 3.567A pdb=" N LEUAP13475 " --> pdb=" O ILEAP13471 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3485 through 3512 removed outlier: 3.538A pdb=" N ARGAP13492 " --> pdb=" O LEUAP13488 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILEAP13493 " --> pdb=" O ILEAP13489 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYSAP13498 " --> pdb=" O THRAP13494 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SERAP13499 " --> pdb=" O ASNAP13495 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEUAP13500 " --> pdb=" O GLYAP13496 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3517 through 3544 removed outlier: 3.589A pdb=" N LEUAP13521 " --> pdb=" O ASNAP13517 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYSAP13522 " --> pdb=" O VALAP13518 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLNAP13523 " --> pdb=" O ASPAP13519 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERAP13528 " --> pdb=" O SERAP13524 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASNAP13530 " --> pdb=" O ARGAP13526 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYSAP13534 " --> pdb=" O ASNAP13530 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILEAP13535 " --> pdb=" O ASNAP13531 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3547 through 3554 removed outlier: 3.909A pdb=" N ILEAP13551 " --> pdb=" O ALAAP13547 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3581 through 3587 removed outlier: 4.224A pdb=" N METAP13587 " --> pdb=" O THRAP13584 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3601 through 3617 removed outlier: 3.635A pdb=" N SERAP13606 " --> pdb=" O ASPAP13602 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3623 through 3640 Processing helix chain 'AP1' and resid 3653 through 3674 removed outlier: 3.782A pdb=" N LEUAP13668 " --> pdb=" O LEUAP13664 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILEAP13674 " --> pdb=" O GLUAP13670 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3690 through 3696 Processing helix chain 'AP1' and resid 3710 through 3727 removed outlier: 4.303A pdb=" N ILEAP13716 " --> pdb=" O PHEAP13712 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEUAP13717 " --> pdb=" O PHEAP13713 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASPAP13718 " --> pdb=" O PHEAP13714 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEUAP13719 " --> pdb=" O LYSAP13715 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUAP13720 " --> pdb=" O ILEAP13716 " (cutoff:3.500A) Proline residue: AP13721 - end of helix Processing helix chain 'AP1' and resid 3737 through 3756 removed outlier: 4.102A pdb=" N GLNAP13747 " --> pdb=" O METAP13743 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SERAP13748 " --> pdb=" O ALAAP13744 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VALAP13756 " --> pdb=" O SERAP13752 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3756 through 3781 removed outlier: 4.129A pdb=" N LYSAP13769 " --> pdb=" O ASNAP13765 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3792 through 3805 removed outlier: 4.153A pdb=" N ASPAP13797 " --> pdb=" O LYSAP13793 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYSAP13804 " --> pdb=" O ARGAP13800 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRPAP13805 " --> pdb=" O LEUAP13801 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3805 through 3824 removed outlier: 4.115A pdb=" N ASPAP13811 " --> pdb=" O PROAP13807 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYRAP13823 " --> pdb=" O VALAP13819 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3830 through 3850 removed outlier: 3.544A pdb=" N LEUAP13834 " --> pdb=" O GLNAP13830 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASPAP13835 " --> pdb=" O LYSAP13831 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALAAP13836 " --> pdb=" O ILEAP13832 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEUAP13840 " --> pdb=" O ALAAP13836 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SERAP13841 " --> pdb=" O LYSAP13837 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SERAP13842 " --> pdb=" O SERAP13838 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHEAP13843 " --> pdb=" O THRAP13839 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N HISAP13846 " --> pdb=" O SERAP13842 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3855 through 3880 removed outlier: 4.251A pdb=" N GLUAP13859 " --> pdb=" O SERAP13855 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYSAP13873 " --> pdb=" O ASNAP13869 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3884 through 3897 removed outlier: 4.006A pdb=" N ILEAP13890 " --> pdb=" O VALAP13886 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3914 through 3936 removed outlier: 3.502A pdb=" N THRAP13922 " --> pdb=" O ALAAP13918 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SERAP13925 " --> pdb=" O ARGAP13921 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILEAP13927 " --> pdb=" O PHEAP13923 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEUAP13928 " --> pdb=" O THRAP13924 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SERAP13929 " --> pdb=" O SERAP13925 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3948 through 3964 removed outlier: 4.602A pdb=" N LYSAP13954 " --> pdb=" O SERAP13950 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUAP13963 " --> pdb=" O ASNAP13959 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARGAP13964 " --> pdb=" O VALAP13960 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3964 through 3982 removed outlier: 3.885A pdb=" N LYSAP13970 " --> pdb=" O SERAP13966 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUAP13978 " --> pdb=" O THRAP13974 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEUAP13979 " --> pdb=" O ALAAP13975 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYSAP13980 " --> pdb=" O LEUAP13976 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 3991 through 3997 Processing helix chain 'AP1' and resid 3998 through 4000 No H-bonds generated for 'chain 'AP1' and resid 3998 through 4000' Processing helix chain 'AP1' and resid 4002 through 4040 removed outlier: 3.581A pdb=" N THRAP14011 " --> pdb=" O TYRAP14007 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VALAP14013 " --> pdb=" O ALAAP14009 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEUAP14014 " --> pdb=" O METAP14010 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEAP14019 " --> pdb=" O GLUAP14015 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THRAP14024 " --> pdb=" O TYRAP14020 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 4625 through 4640 Processing helix chain 'AP1' and resid 4640 through 4656 removed outlier: 3.700A pdb=" N ILEAP14654 " --> pdb=" O GLNAP14650 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLUAP14656 " --> pdb=" O ARGAP14652 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 4719 through 4737 removed outlier: 4.406A pdb=" N LEUAP14723 " --> pdb=" O LYSAP14719 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLNAP14737 " --> pdb=" O LYSAP14733 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 4763 through 4773 Processing helix chain 'AP1' and resid 4782 through 4800 Processing helix chain 'AP1' and resid 4820 through 4832 removed outlier: 3.659A pdb=" N LYSAP14825 " --> pdb=" O GLUAP14821 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 4861 through 4864 Processing helix chain 'AP1' and resid 4890 through 4907 Processing helix chain 'xP1' and resid 60 through 69 Processing sheet with id=AA1, first strand: chain 'AP1' and resid 264 through 265 Processing sheet with id=AA2, first strand: chain 'AP1' and resid 312 through 315 removed outlier: 6.390A pdb=" N METAP1 312 " --> pdb=" O ILEAP1 456 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEUAP1 458 " --> pdb=" O METAP1 312 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILEAP1 314 " --> pdb=" O LEUAP1 458 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'AP1' and resid 340 through 341 removed outlier: 7.221A pdb=" N ILEAP1 341 " --> pdb=" O GLUAP1 385 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VALAP1 382 " --> pdb=" O ILEAP1 425 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THRAP1 427 " --> pdb=" O VALAP1 382 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILEAP1 384 " --> pdb=" O THRAP1 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'AP1' and resid 675 through 677 removed outlier: 6.609A pdb=" N VALAP1 676 " --> pdb=" O ASPAP1 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'AP1' and resid 1081 through 1082 removed outlier: 6.217A pdb=" N ILEAP11081 " --> pdb=" O GLNAP11194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'AP1' and resid 1173 through 1175 Processing sheet with id=AA7, first strand: chain 'AP1' and resid 1536 through 1538 removed outlier: 3.858A pdb=" N ALAAP11537 " --> pdb=" O VALAP11364 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILEAP11561 " --> pdb=" O LEUAP11365 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AP1' and resid 1393 through 1394 removed outlier: 6.146A pdb=" N ASNAP11393 " --> pdb=" O ASPAP11492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'AP1' and resid 1811 through 1812 Processing sheet with id=AB1, first strand: chain 'AP1' and resid 2005 through 2008 Processing sheet with id=AB2, first strand: chain 'AP1' and resid 2261 through 2262 removed outlier: 8.089A pdb=" N METAP12262 " --> pdb=" O LEUAP12050 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEUAP12052 " --> pdb=" O METAP12262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'AP1' and resid 2075 through 2080 removed outlier: 3.681A pdb=" N ILEAP12210 " --> pdb=" O ASPAP12076 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHEAP12078 " --> pdb=" O ILEAP12210 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N METAP12080 " --> pdb=" O ASPAP12212 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALAAP12214 " --> pdb=" O METAP12080 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'AP1' and resid 2090 through 2094 removed outlier: 4.950A pdb=" N GLYAP12092 " --> pdb=" O PHEAP12195 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHEAP12195 " --> pdb=" O GLYAP12092 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'AP1' and resid 4742 through 4743 removed outlier: 5.818A pdb=" N TYRAP14703 " --> pdb=" O GLYAP14742 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VALAP14746 " --> pdb=" O ILEAP14705 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILEAP14707 " --> pdb=" O VALAP14746 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHEAP14748 " --> pdb=" O ILEAP14707 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEUAP14709 " --> pdb=" O PHEAP14748 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYSAP14747 " --> pdb=" O GLUAP14754 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLUAP14754 " --> pdb=" O LYSAP14747 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AP1' and resid 4742 through 4743 removed outlier: 5.818A pdb=" N TYRAP14703 " --> pdb=" O GLYAP14742 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLNAP14704 " --> pdb=" O LEUAP14808 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILEAP14810 " --> pdb=" O GLNAP14704 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N METAP14706 " --> pdb=" O ILEAP14810 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ILEAP14812 " --> pdb=" O METAP14706 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALAAP14708 " --> pdb=" O ILEAP14812 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLNAP14807 " --> pdb=" O METAP14836 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VALAP14838 " --> pdb=" O GLNAP14807 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLUAP14809 " --> pdb=" O VALAP14838 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VALAP14840 " --> pdb=" O GLUAP14809 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VALAP14811 " --> pdb=" O VALAP14840 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'AP1' and resid 4855 through 4860 removed outlier: 9.094A pdb=" N GLNAP14856 " --> pdb=" O LEUAP14869 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LEUAP14869 " --> pdb=" O GLNAP14856 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N ASNAP14858 " --> pdb=" O PROAP14867 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILEAP14860 " --> pdb=" O GLYAP14865 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'xP1' and resid 34 through 36 1328 hydrogen bonds defined for protein. 3864 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: 6.35 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 3701 1.28 - 1.35: 3628 1.35 - 1.42: 25 1.42 - 1.49: 3690 1.49 - 1.56: 7272 Bond restraints: 18316 Sorted by residual: bond pdb=" N HISAP1 276 " pdb=" CA HISAP1 276 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N VALAP1 275 " pdb=" CA VALAP1 275 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.06e+00 bond pdb=" N LEUAP1 261 " pdb=" CA LEUAP1 261 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.80e+00 bond pdb=" C SERAP1 239 " pdb=" N VALAP1 240 " ideal model delta sigma weight residual 1.329 1.362 -0.032 1.13e-02 7.83e+03 8.18e+00 bond pdb=" N VALAP1 264 " pdb=" CA VALAP1 264 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.98e+00 ... (remaining 18311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 24086 1.85 - 3.71: 1245 3.71 - 5.56: 130 5.56 - 7.41: 16 7.41 - 9.27: 9 Bond angle restraints: 25486 Sorted by residual: angle pdb=" N PROAP13567 " pdb=" CA PROAP13567 " pdb=" CB PROAP13567 " ideal model delta sigma weight residual 102.72 111.14 -8.42 1.06e+00 8.90e-01 6.31e+01 angle pdb=" N PROAP13594 " pdb=" CA PROAP13594 " pdb=" CB PROAP13594 " ideal model delta sigma weight residual 103.25 110.72 -7.47 1.05e+00 9.07e-01 5.06e+01 angle pdb=" CA ILEAP1 255 " pdb=" C ILEAP1 255 " pdb=" O ILEAP1 255 " ideal model delta sigma weight residual 120.39 114.64 5.75 1.05e+00 9.07e-01 3.00e+01 angle pdb=" N GLUAP1 463 " pdb=" CA GLUAP1 463 " pdb=" CB GLUAP1 463 " ideal model delta sigma weight residual 114.17 108.64 5.53 1.14e+00 7.69e-01 2.35e+01 angle pdb=" CA TYRAP1 252 " pdb=" C TYRAP1 252 " pdb=" O TYRAP1 252 " ideal model delta sigma weight residual 120.36 115.12 5.24 1.08e+00 8.57e-01 2.35e+01 ... (remaining 25481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.53: 10051 9.53 - 19.06: 631 19.06 - 28.60: 76 28.60 - 38.13: 16 38.13 - 47.66: 4 Dihedral angle restraints: 10778 sinusoidal: 0 harmonic: 10778 Sorted by residual: dihedral pdb=" CA ASNAP1 947 " pdb=" C ASNAP1 947 " pdb=" N THRAP1 948 " pdb=" CA THRAP1 948 " ideal model delta harmonic sigma weight residual 180.00 132.34 47.66 0 5.00e+00 4.00e-02 9.09e+01 dihedral pdb=" CA LEUAP14000 " pdb=" C LEUAP14000 " pdb=" N PROAP14001 " pdb=" CA PROAP14001 " ideal model delta harmonic sigma weight residual 180.00 140.11 39.89 0 5.00e+00 4.00e-02 6.36e+01 dihedral pdb=" CA THRAP1 948 " pdb=" C THRAP1 948 " pdb=" N ILEAP1 949 " pdb=" CA ILEAP1 949 " ideal model delta harmonic sigma weight residual -180.00 -140.67 -39.33 0 5.00e+00 4.00e-02 6.19e+01 ... (remaining 10775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2579 0.045 - 0.090: 769 0.090 - 0.134: 168 0.134 - 0.179: 40 0.179 - 0.224: 6 Chirality restraints: 3562 Sorted by residual: chirality pdb=" CA ILEAP1 255 " pdb=" N ILEAP1 255 " pdb=" C ILEAP1 255 " pdb=" CB ILEAP1 255 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VALAP1 264 " pdb=" N VALAP1 264 " pdb=" C VALAP1 264 " pdb=" CB VALAP1 264 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA HISAP1 276 " pdb=" N HISAP1 276 " pdb=" C HISAP1 276 " pdb=" CB HISAP1 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3559 not shown) Planarity restraints: 3654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUAP1 261 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C LEUAP1 261 " 0.048 2.00e-02 2.50e+03 pdb=" O LEUAP1 261 " -0.017 2.00e-02 2.50e+03 pdb=" N THRAP1 262 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUAP11509 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C LEUAP11509 " 0.048 2.00e-02 2.50e+03 pdb=" O LEUAP11509 " -0.018 2.00e-02 2.50e+03 pdb=" N GLUAP11510 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHEAP12594 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.37e+00 pdb=" C PHEAP12594 " 0.047 2.00e-02 2.50e+03 pdb=" O PHEAP12594 " -0.018 2.00e-02 2.50e+03 pdb=" N LEUAP12595 " -0.016 2.00e-02 2.50e+03 ... (remaining 3651 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 14711 3.12 - 3.72: 27489 3.72 - 4.31: 29654 4.31 - 4.90: 46065 Nonbonded interactions: 117938 Sorted by model distance: nonbonded pdb=" CA LYSAP1 263 " pdb=" CB LYSAP1 274 " model vdw 1.939 3.096 nonbonded pdb=" O LEUAP11779 " pdb=" N PHEAP11783 " model vdw 2.303 3.120 nonbonded pdb=" O GLYAP11401 " pdb=" N GLYAP11405 " model vdw 2.386 3.120 nonbonded pdb=" O LEUAP1 688 " pdb=" N VALAP1 812 " model vdw 2.390 3.120 nonbonded pdb=" O HISAP13789 " pdb=" N LYSAP13793 " model vdw 2.404 3.120 ... (remaining 117933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 0.394 18317 Z= 0.416 Angle : 0.950 9.267 25486 Z= 0.649 Chirality : 0.046 0.224 3562 Planarity : 0.003 0.028 3654 Dihedral : 8.011 47.658 3654 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.84 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 1.75 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.11), residues: 3608 helix: -2.44 (0.09), residues: 1989 sheet: -3.14 (0.29), residues: 199 loop : -3.40 (0.14), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.30 (18316) covalent geometry : angle 0.95008 / 0.65 (25486) hydrogen bonds : bond 0.21873 / 16.51 ( 1328) hydrogen bonds : angle 8.14434 / 6.20 ( 3864) Misc. bond : bond 0.39415 / 20.74 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.653 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0780 time to fit residues: 11.6183 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.069631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.056980 restraints weight = 156176.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056460 restraints weight = 125733.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056569 restraints weight = 109935.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056631 restraints weight = 100997.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056654 restraints weight = 98554.632| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18317 Z= 0.111 Angle : 0.455 8.321 25486 Z= 0.278 Chirality : 0.040 0.155 3562 Planarity : 0.002 0.019 3654 Dihedral : 4.688 32.791 3654 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3608 helix: 0.17 (0.11), residues: 2099 sheet: -2.74 (0.29), residues: 248 loop : -2.97 (0.16), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.11 (18316) covalent geometry : angle 0.45465 / 0.28 (25486) hydrogen bonds : bond 0.03143 / 2.35 ( 1328) hydrogen bonds : angle 3.85291 / 2.92 ( 3864) Misc. bond : bond 0.00678 / 0.36 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0800 time to fit residues: 11.9484 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 45 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 359 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 109 optimal weight: 40.0000 chunk 97 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.064734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051024 restraints weight = 154374.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050481 restraints weight = 132388.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050456 restraints weight = 122649.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050518 restraints weight = 115893.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.050657 restraints weight = 98409.322| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18317 Z= 0.148 Angle : 0.463 8.153 25486 Z= 0.287 Chirality : 0.040 0.174 3562 Planarity : 0.002 0.023 3654 Dihedral : 4.585 36.365 3654 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3608 helix: 1.26 (0.12), residues: 2141 sheet: -2.16 (0.32), residues: 230 loop : -2.77 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.15 (18316) covalent geometry : angle 0.46255 / 0.29 (25486) hydrogen bonds : bond 0.03382 / 2.53 ( 1328) hydrogen bonds : angle 3.69158 / 2.80 ( 3864) Misc. bond : bond 0.00799 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.721 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0790 time to fit residues: 11.7400 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 275 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 306 optimal weight: 0.0010 chunk 352 optimal weight: 20.0000 chunk 246 optimal weight: 0.5980 chunk 220 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.064481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.050789 restraints weight = 155744.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.050308 restraints weight = 135948.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.050373 restraints weight = 112448.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050625 restraints weight = 98465.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050655 restraints weight = 87312.623| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 18317 Z= 0.098 Angle : 0.389 7.565 25486 Z= 0.239 Chirality : 0.039 0.154 3562 Planarity : 0.001 0.020 3654 Dihedral : 3.889 27.180 3654 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3608 helix: 1.95 (0.12), residues: 2128 sheet: -1.93 (0.32), residues: 239 loop : -2.62 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00137 / 0.10 (18316) covalent geometry : angle 0.38887 / 0.24 (25486) hydrogen bonds : bond 0.02248 / 1.68 ( 1328) hydrogen bonds : angle 3.08276 / 2.34 ( 3864) Misc. bond : bond 0.00395 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.705 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0813 time to fit residues: 12.0355 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 103 optimal weight: 50.0000 chunk 317 optimal weight: 0.7980 chunk 174 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 131 optimal weight: 0.0670 chunk 206 optimal weight: 1.9990 chunk 18 optimal weight: 0.0030 chunk 200 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 overall best weight: 0.6730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.065003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051311 restraints weight = 155170.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.050782 restraints weight = 136221.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050986 restraints weight = 110373.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.051082 restraints weight = 96352.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051145 restraints weight = 86666.826| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 18317 Z= 0.059 Angle : 0.342 7.423 25486 Z= 0.207 Chirality : 0.039 0.143 3562 Planarity : 0.001 0.021 3654 Dihedral : 3.371 28.075 3654 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3608 helix: 2.38 (0.12), residues: 2141 sheet: -1.58 (0.33), residues: 243 loop : -2.52 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00084 / 0.06 (18316) covalent geometry : angle 0.34199 / 0.21 (25486) hydrogen bonds : bond 0.01840 / 1.36 ( 1328) hydrogen bonds : angle 2.63125 / 2.00 ( 3864) Misc. bond : bond 0.00290 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.776 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0782 time to fit residues: 11.6663 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 5 optimal weight: 7.9990 chunk 220 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 260 optimal weight: 0.0020 chunk 36 optimal weight: 9.9990 chunk 359 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 overall best weight: 3.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.062243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049413 restraints weight = 155058.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048553 restraints weight = 166217.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048675 restraints weight = 136625.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048745 restraints weight = 118605.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.048829 restraints weight = 110582.207| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.6125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18317 Z= 0.170 Angle : 0.455 7.021 25486 Z= 0.286 Chirality : 0.041 0.160 3562 Planarity : 0.002 0.021 3654 Dihedral : 4.371 27.158 3654 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3608 helix: 2.02 (0.12), residues: 2154 sheet: -1.64 (0.34), residues: 231 loop : -2.51 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.17 (18316) covalent geometry : angle 0.45464 / 0.29 (25486) hydrogen bonds : bond 0.03132 / 2.36 ( 1328) hydrogen bonds : angle 3.72328 / 2.82 ( 3864) Misc. bond : bond 0.00578 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.772 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0769 time to fit residues: 11.5566 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 343 optimal weight: 40.0000 chunk 268 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 chunk 338 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 334 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 214 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046271 restraints weight = 159485.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.045470 restraints weight = 176109.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045576 restraints weight = 147728.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045702 restraints weight = 122787.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045742 restraints weight = 108357.811| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18317 Z= 0.458 Angle : 0.815 10.255 25486 Z= 0.525 Chirality : 0.047 0.181 3562 Planarity : 0.005 0.028 3654 Dihedral : 7.043 44.472 3654 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.28 % Favored : 88.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3608 helix: 0.04 (0.11), residues: 2133 sheet: -2.19 (0.37), residues: 195 loop : -3.00 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.46 (18316) covalent geometry : angle 0.81501 / 0.53 (25486) hydrogen bonds : bond 0.06012 / 4.55 ( 1328) hydrogen bonds : angle 6.28776 / 4.73 ( 3864) Misc. bond : bond 0.01133 / 0.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.740 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0802 time to fit residues: 11.9942 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 10 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 122 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046738 restraints weight = 160237.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046173 restraints weight = 168355.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046163 restraints weight = 142081.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046301 restraints weight = 124482.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.046342 restraints weight = 110398.745| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.8088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18317 Z= 0.260 Angle : 0.576 7.148 25486 Z= 0.365 Chirality : 0.043 0.174 3562 Planarity : 0.003 0.022 3654 Dihedral : 5.597 34.333 3654 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.98 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3608 helix: 0.71 (0.12), residues: 2126 sheet: -2.22 (0.37), residues: 195 loop : -2.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.26 (18316) covalent geometry : angle 0.57639 / 0.37 (25486) hydrogen bonds : bond 0.04039 / 3.04 ( 1328) hydrogen bonds : angle 4.87653 / 3.69 ( 3864) Misc. bond : bond 0.00790 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.726 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0761 time to fit residues: 11.4066 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 223 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 304 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 271 optimal weight: 0.0270 chunk 182 optimal weight: 10.0000 chunk 308 optimal weight: 0.9990 chunk 265 optimal weight: 10.0000 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.060249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.047496 restraints weight = 159828.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046978 restraints weight = 161588.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047032 restraints weight = 137524.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047041 restraints weight = 139246.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047109 restraints weight = 113470.872| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 18317 Z= 0.117 Angle : 0.417 6.890 25486 Z= 0.258 Chirality : 0.040 0.174 3562 Planarity : 0.002 0.022 3654 Dihedral : 4.463 29.150 3654 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3608 helix: 1.77 (0.12), residues: 2158 sheet: -1.93 (0.39), residues: 185 loop : -2.71 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.12 (18316) covalent geometry : angle 0.41662 / 0.26 (25486) hydrogen bonds : bond 0.02700 / 2.01 ( 1328) hydrogen bonds : angle 3.66650 / 2.79 ( 3864) Misc. bond : bond 0.00476 / 0.25 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.700 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0785 time to fit residues: 11.6609 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 110 optimal weight: 20.0000 chunk 335 optimal weight: 0.9990 chunk 364 optimal weight: 30.0000 chunk 160 optimal weight: 7.9990 chunk 361 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 114 optimal weight: 0.4980 chunk 351 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.060152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047396 restraints weight = 159938.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046921 restraints weight = 154518.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046967 restraints weight = 126273.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.047137 restraints weight = 111300.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047168 restraints weight = 100245.722| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.8226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18317 Z= 0.119 Angle : 0.409 6.558 25486 Z= 0.255 Chirality : 0.040 0.166 3562 Planarity : 0.002 0.022 3654 Dihedral : 4.224 28.099 3654 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 3608 helix: 2.18 (0.12), residues: 2154 sheet: -1.86 (0.39), residues: 187 loop : -2.64 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.12 (18316) covalent geometry : angle 0.40922 / 0.25 (25486) hydrogen bonds : bond 0.02727 / 2.04 ( 1328) hydrogen bonds : angle 3.54824 / 2.71 ( 3864) Misc. bond : bond 0.00494 / 0.26 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7216 Ramachandran restraints generated. 3608 Oldfield, 0 Emsley, 3608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.745 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0764 time to fit residues: 11.4939 Evaluate side-chains 72 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 70 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 337 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 258 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 109 optimal weight: 50.0000 chunk 341 optimal weight: 20.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046721 restraints weight = 160357.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046209 restraints weight = 152549.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046247 restraints weight = 125202.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046320 restraints weight = 114236.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.046385 restraints weight = 104358.391| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18317 Z= 0.195 Angle : 0.482 6.650 25486 Z= 0.305 Chirality : 0.041 0.162 3562 Planarity : 0.002 0.024 3654 Dihedral : 4.750 33.393 3654 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3608 helix: 1.90 (0.12), residues: 2142 sheet: -2.01 (0.38), residues: 185 loop : -2.70 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYRAP1 65 PHE 0.000 0.000 PHEAP1 20 TRP 0.000 0.000 TRPAP1 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.19 (18316) covalent geometry : angle 0.48216 / 0.31 (25486) hydrogen bonds : bond 0.03422 / 2.57 ( 1328) hydrogen bonds : angle 4.15658 / 3.16 ( 3864) Misc. bond : bond 0.00650 / 0.34 ( 1) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2771.81 seconds wall clock time: 47 minutes 43.14 seconds (2863.14 seconds total)