Starting phenix.real_space_refine (version: dev) on Fri Feb 24 01:46:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m68_23690/02_2023/7m68_23690_trim_updated.pdb" } resolution = 4.04 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 ------------------------------------------------------------------------------- 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= -0.001 sd= 0.907 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21806 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 21806 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 37, 'TRANS': 1352} Chain breaks: 4 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 129 Time building chain proxies: 10.53, per 1000 atoms: 0.48 Number of scatterers: 21806 At special positions: 0 Unit cell: (131.968, 117.534, 103.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 3 15.00 O 1981 8.00 N 1833 7.00 C 7024 6.00 H 10919 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 946 " - pdb=" SG CYS A1017 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.99 Conformation dependent library (CDL) restraints added in 1.8 seconds 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 6 sheets defined 64.6% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.671A pdb=" N GLY A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 Processing helix chain 'A' and resid 94 through 97 removed outlier: 3.627A pdb=" N GLU A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 101 through 123 removed outlier: 4.332A pdb=" N LEU A 120 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 123 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 159 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.852A pdb=" N ILE A 171 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 183 " --> pdb=" O CYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.716A pdb=" N HIS A 201 " --> pdb=" O GLN A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.642A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.678A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 327 removed outlier: 3.778A pdb=" N LEU A 275 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A 281 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 282 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 284 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 285 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 286 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE A 302 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 304 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.501A pdb=" N ILE A 310 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 316 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 390 removed outlier: 3.735A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 402 through 419 removed outlier: 4.358A pdb=" N VAL A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 443 removed outlier: 4.176A pdb=" N GLY A 429 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 3.569A pdb=" N ILE A 435 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 492 Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 494 through 500 Processing helix chain 'A' and resid 503 through 537 removed outlier: 3.713A pdb=" N ASN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 554 removed outlier: 4.193A pdb=" N ALA A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 603 removed outlier: 4.497A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix Proline residue: A 582 - end of helix removed outlier: 4.191A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 719 through 728 Processing helix chain 'A' and resid 732 through 738 removed outlier: 4.291A pdb=" N LEU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 785 through 795 removed outlier: 3.504A pdb=" N HIS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 837 through 842 removed outlier: 3.512A pdb=" N LYS A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 849 No H-bonds generated for 'chain 'A' and resid 846 through 849' Processing helix chain 'A' and resid 918 through 929 removed outlier: 3.742A pdb=" N GLU A 921 " --> pdb=" O GLY A 918 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 923 " --> pdb=" O ASP A 920 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 925 " --> pdb=" O ASN A 922 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 929 " --> pdb=" O ARG A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 948 through 981 Processing helix chain 'A' and resid 988 through 1034 removed outlier: 3.683A pdb=" N LEU A1013 " --> pdb=" O GLN A1009 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1043 Processing helix chain 'A' and resid 1046 through 1088 removed outlier: 3.984A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A1058 " --> pdb=" O SER A1054 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1137 removed outlier: 4.169A pdb=" N ILE A1093 " --> pdb=" O TRP A1090 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A1094 " --> pdb=" O GLN A1091 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A1097 " --> pdb=" O PHE A1094 " (cutoff:3.500A) Proline residue: A1098 - end of helix removed outlier: 4.732A pdb=" N ARG A1115 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A1125 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A1126 " --> pdb=" O ILE A1123 " (cutoff:3.500A) Proline residue: A1127 - end of helix removed outlier: 3.637A pdb=" N THR A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1148 through 1201 Proline residue: A1168 - end of helix Processing helix chain 'A' and resid 1206 through 1247 removed outlier: 4.076A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A1219 " --> pdb=" O TYR A1215 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1228 " --> pdb=" O ASN A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1320 removed outlier: 3.912A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1363 through 1367 Processing helix chain 'A' and resid 1376 through 1385 Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1412 through 1425 Processing helix chain 'A' and resid 1443 through 1454 Processing helix chain 'A' and resid 1468 through 1473 Processing sheet with id= A, first strand: chain 'A' and resid 613 through 615 removed outlier: 3.794A pdb=" N ILE A 626 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 659 through 662 removed outlier: 6.578A pdb=" N SER A 822 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 662 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA A 824 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 833 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 827 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ILE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.422A pdb=" N THR A 773 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N VAL A 696 " --> pdb=" O THR A 773 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 775 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1293 through 1296 Processing sheet with id= E, first strand: chain 'A' and resid 1476 through 1479 removed outlier: 3.525A pdb=" N GLY A1303 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 645 through 649 removed outlier: 5.480A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 682 " --> pdb=" O LEU A 635 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1575 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: 9.23 Time building geometry restraints manager: 18.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10904 1.04 - 1.25: 1570 1.25 - 1.45: 3231 1.45 - 1.66: 6242 1.66 - 1.87: 75 Bond restraints: 22022 Sorted by residual: bond pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O1P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.525 1.611 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O2P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.528 1.479 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" CB CYS A1017 " pdb=" SG CYS A1017 " ideal model delta sigma weight residual 1.808 1.866 -0.058 3.30e-02 9.18e+02 3.14e+00 ... (remaining 22017 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.78: 691 106.78 - 113.60: 25762 113.60 - 120.42: 7431 120.42 - 127.24: 5807 127.24 - 134.05: 113 Bond angle restraints: 39804 Sorted by residual: angle pdb=" CB TPO A 911 " pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 119.31 109.18 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " pdb=" O1P TPO A 911 " ideal model delta sigma weight residual 100.43 109.65 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" C LEU A 559 " pdb=" N THR A 560 " pdb=" CA THR A 560 " ideal model delta sigma weight residual 122.61 127.34 -4.73 1.56e+00 4.11e-01 9.19e+00 angle pdb=" CA ARG A 638 " pdb=" CB ARG A 638 " pdb=" CG ARG A 638 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " pdb=" CG LEU A 135 " ideal model delta sigma weight residual 116.30 126.50 -10.20 3.50e+00 8.16e-02 8.49e+00 ... (remaining 39799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 7936 17.08 - 34.16: 755 34.16 - 51.24: 126 51.24 - 68.32: 28 68.32 - 85.40: 12 Dihedral angle restraints: 8857 sinusoidal: 4055 harmonic: 4802 Sorted by residual: dihedral pdb=" CA SER A 846 " pdb=" C SER A 846 " pdb=" N PRO A 847 " pdb=" CA PRO A 847 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE A1352 " pdb=" C ILE A1352 " pdb=" N PRO A1353 " pdb=" CA PRO A1353 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA CYS A 546 " pdb=" C CYS A 546 " pdb=" N THR A 547 " pdb=" CA THR A 547 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1240 0.036 - 0.072: 368 0.072 - 0.109: 123 0.109 - 0.145: 36 0.145 - 0.181: 5 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA VAL A 624 " pdb=" N VAL A 624 " pdb=" C VAL A 624 " pdb=" CB VAL A 624 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ILE A 626 " pdb=" N ILE A 626 " pdb=" C ILE A 626 " pdb=" CB ILE A 626 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE A1352 " pdb=" N ILE A1352 " pdb=" C ILE A1352 " pdb=" CB ILE A1352 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1769 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 576 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 577 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 577 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 577 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 304 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 305 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1126 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A1127 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " -0.030 5.00e-02 4.00e+02 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 4636 2.31 - 2.89: 48721 2.89 - 3.46: 54443 3.46 - 4.03: 69363 4.03 - 4.60: 105994 Nonbonded interactions: 283157 Sorted by model distance: nonbonded pdb=" O LEU A 802 " pdb=" HZ3 LYS A 807 " model vdw 1.743 1.850 nonbonded pdb=" O GLY A 797 " pdb=" H GLY A 800 " model vdw 1.763 1.850 nonbonded pdb=" O VAL A1447 " pdb=" HG1 THR A1451 " model vdw 1.768 1.850 nonbonded pdb=" O ALA A 278 " pdb=" HG1 THR A 282 " model vdw 1.779 1.850 nonbonded pdb=" O ILE A1097 " pdb=" HG SER A1100 " model vdw 1.780 1.850 ... (remaining 283152 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 46 5.16 5 C 7024 2.51 5 N 1833 2.21 5 O 1981 1.98 5 H 10919 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.58 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 7.700 Check model and map are aligned: 0.330 Process input model: 67.900 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 0.106 11103 Z= 0.317 Angle : 0.749 10.200 15067 Z= 0.398 Chirality : 0.042 0.181 1772 Planarity : 0.005 0.073 1879 Dihedral : 13.487 85.370 3985 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1371 helix: 1.01 (0.16), residues: 925 sheet: -0.93 (0.61), residues: 54 loop : -2.53 (0.29), residues: 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 366 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 372 average time/residue: 0.4996 time to fit residues: 271.0527 Evaluate side-chains 235 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3058 time to fit residues: 4.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 424 ASN A 790 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 11103 Z= 0.151 Angle : 0.519 5.694 15067 Z= 0.294 Chirality : 0.037 0.149 1772 Planarity : 0.005 0.046 1879 Dihedral : 5.157 83.780 1498 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.23), residues: 1371 helix: 1.20 (0.17), residues: 919 sheet: -0.65 (0.61), residues: 55 loop : -2.21 (0.29), residues: 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 288 average time/residue: 0.4555 time to fit residues: 194.6384 Evaluate side-chains 221 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 1.681 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2454 time to fit residues: 3.2817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 928 HIS A1055 ASN ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN ** A1269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 11103 Z= 0.292 Angle : 0.597 7.672 15067 Z= 0.340 Chirality : 0.039 0.176 1772 Planarity : 0.005 0.040 1879 Dihedral : 5.113 77.401 1498 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1371 helix: 0.56 (0.17), residues: 915 sheet: -0.71 (0.58), residues: 65 loop : -2.32 (0.30), residues: 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4243 time to fit residues: 167.2654 Evaluate side-chains 203 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 84 optimal weight: 0.4980 chunk 126 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11103 Z= 0.223 Angle : 0.523 4.760 15067 Z= 0.297 Chirality : 0.037 0.152 1772 Planarity : 0.004 0.037 1879 Dihedral : 5.011 75.044 1498 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1371 helix: 0.46 (0.17), residues: 912 sheet: -1.02 (0.62), residues: 52 loop : -2.26 (0.29), residues: 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.4154 time to fit residues: 162.3842 Evaluate side-chains 206 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.925 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN A 364 HIS ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 11103 Z= 0.237 Angle : 0.536 6.029 15067 Z= 0.304 Chirality : 0.037 0.155 1772 Planarity : 0.004 0.036 1879 Dihedral : 4.967 72.479 1498 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1371 helix: 0.34 (0.17), residues: 919 sheet: -0.79 (0.59), residues: 65 loop : -2.42 (0.30), residues: 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.4033 time to fit residues: 157.3580 Evaluate side-chains 202 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 11103 Z= 0.151 Angle : 0.500 5.676 15067 Z= 0.277 Chirality : 0.036 0.153 1772 Planarity : 0.004 0.036 1879 Dihedral : 4.791 72.080 1498 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.23), residues: 1371 helix: 0.55 (0.17), residues: 920 sheet: -0.80 (0.59), residues: 65 loop : -2.43 (0.29), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.4051 time to fit residues: 161.6004 Evaluate side-chains 210 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 11103 Z= 0.259 Angle : 0.564 6.755 15067 Z= 0.319 Chirality : 0.038 0.161 1772 Planarity : 0.004 0.038 1879 Dihedral : 4.932 69.129 1498 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1371 helix: 0.30 (0.17), residues: 916 sheet: -0.71 (0.60), residues: 65 loop : -2.49 (0.29), residues: 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.4001 time to fit residues: 152.8376 Evaluate side-chains 204 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 11103 Z= 0.136 Angle : 0.486 5.792 15067 Z= 0.268 Chirality : 0.036 0.146 1772 Planarity : 0.004 0.035 1879 Dihedral : 4.705 69.141 1498 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1371 helix: 0.64 (0.17), residues: 910 sheet: -0.76 (0.60), residues: 65 loop : -2.39 (0.29), residues: 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.4170 time to fit residues: 168.3079 Evaluate side-chains 212 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11103 Z= 0.277 Angle : 0.582 7.495 15067 Z= 0.328 Chirality : 0.038 0.155 1772 Planarity : 0.004 0.070 1879 Dihedral : 4.910 66.886 1498 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1371 helix: 0.38 (0.17), residues: 908 sheet: -0.79 (0.59), residues: 65 loop : -2.38 (0.29), residues: 398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.3939 time to fit residues: 153.0853 Evaluate side-chains 205 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 HIS ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN A1020 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11103 Z= 0.340 Angle : 0.637 8.991 15067 Z= 0.362 Chirality : 0.040 0.186 1772 Planarity : 0.005 0.057 1879 Dihedral : 5.212 64.173 1498 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1371 helix: -0.12 (0.17), residues: 898 sheet: -1.03 (0.59), residues: 65 loop : -2.44 (0.29), residues: 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.4181 time to fit residues: 155.0580 Evaluate side-chains 199 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 HIS ** A1055 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.114159 restraints weight = 78594.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.119037 restraints weight = 32439.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.121959 restraints weight = 17587.561| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3985 r_free = 0.3985 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 11103 Z= 0.156 Angle : 0.514 5.794 15067 Z= 0.286 Chirality : 0.036 0.150 1772 Planarity : 0.004 0.034 1879 Dihedral : 4.897 64.536 1498 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.23), residues: 1371 helix: 0.34 (0.17), residues: 902 sheet: -0.94 (0.59), residues: 65 loop : -2.28 (0.30), residues: 404 =============================================================================== Job complete usr+sys time: 4409.42 seconds wall clock time: 78 minutes 32.35 seconds (4712.35 seconds total)