Starting phenix.real_space_refine on Tue Jul 29 10:49:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.map" model { file = "/net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rq4_19433/07_2025/8rq4_19433.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7282 2.51 5 N 1868 2.21 5 O 2009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11210 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 11137 Classifications: {'peptide': 1402} Link IDs: {'PTRANS': 42, 'TRANS': 1359} Chain breaks: 2 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 73 Unusual residues: {'RTO': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.52, per 1000 atoms: 0.76 Number of scatterers: 11210 At special positions: 0 Unit cell: (103.35, 133.9, 144.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2009 8.00 N 1868 7.00 C 7282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 25 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.4 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 69.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 4.282A pdb=" N LEU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.690A pdb=" N LEU A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.509A pdb=" N SER A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 96 through 120 removed outlier: 4.020A pdb=" N TYR A 100 " --> pdb=" O PRO A 96 " (cutoff:3.500A) Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 128 through 155 removed outlier: 4.358A pdb=" N PHE A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 183 removed outlier: 3.621A pdb=" N PHE A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 218 removed outlier: 3.725A pdb=" N HIS A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 265 removed outlier: 4.727A pdb=" N LYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 332 removed outlier: 5.908A pdb=" N VAL A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 353 through 401 removed outlier: 4.507A pdb=" N TYR A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 358 " --> pdb=" O TRP A 354 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.704A pdb=" N TYR A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 456 removed outlier: 4.086A pdb=" N SER A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TRP A 438 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 504 removed outlier: 4.085A pdb=" N ILE A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) Proline residue: A 471 - end of helix Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 513 through 565 removed outlier: 3.818A pdb=" N VAL A 521 " --> pdb=" O PHE A 517 " (cutoff:3.500A) Proline residue: A 550 - end of helix removed outlier: 4.331A pdb=" N ASP A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 591 removed outlier: 3.596A pdb=" N PHE A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Proline residue: A 588 - end of helix Processing helix chain 'A' and resid 591 through 614 removed outlier: 3.699A pdb=" N VAL A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 682 Processing helix chain 'A' and resid 710 through 717 Processing helix chain 'A' and resid 722 through 733 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 788 through 800 Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 840 through 848 removed outlier: 4.064A pdb=" N LYS A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 859 Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.907A pdb=" N TYR A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1006 removed outlier: 4.201A pdb=" N SER A1003 " --> pdb=" O TRP A 999 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A1004 " --> pdb=" O THR A1000 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A1005 " --> pdb=" O SER A1001 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1006 " --> pdb=" O ASP A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1061 removed outlier: 3.503A pdb=" N LEU A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1071 removed outlier: 3.837A pdb=" N PHE A1068 " --> pdb=" O PRO A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1113 removed outlier: 3.536A pdb=" N ILE A1076 " --> pdb=" O PRO A1072 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A1091 " --> pdb=" O VAL A1087 " (cutoff:3.500A) Proline residue: A1092 - end of helix Processing helix chain 'A' and resid 1118 through 1165 removed outlier: 3.949A pdb=" N ILE A1122 " --> pdb=" O VAL A1118 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1124 " --> pdb=" O ALA A1120 " (cutoff:3.500A) Proline residue: A1125 - end of helix removed outlier: 3.656A pdb=" N ILE A1128 " --> pdb=" O ILE A1124 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN A1143 " --> pdb=" O ALA A1139 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Proline residue: A1154 - end of helix removed outlier: 3.789A pdb=" N GLY A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1174 through 1225 removed outlier: 3.958A pdb=" N PHE A1178 " --> pdb=" O HIS A1174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1242 removed outlier: 3.554A pdb=" N VAL A1234 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A1240 " --> pdb=" O PHE A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 3.665A pdb=" N LEU A1248 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A1249 " --> pdb=" O THR A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1273 Processing helix chain 'A' and resid 1334 through 1344 removed outlier: 4.262A pdb=" N LEU A1339 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR A1340 " --> pdb=" O LYS A1336 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN A1341 " --> pdb=" O SER A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1372 Processing helix chain 'A' and resid 1387 through 1392 Processing helix chain 'A' and resid 1398 through 1409 Processing helix chain 'A' and resid 1411 through 1418 Processing helix chain 'A' and resid 1434 through 1450 removed outlier: 3.969A pdb=" N LYS A1450 " --> pdb=" O ALA A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1479 Processing helix chain 'A' and resid 1513 through 1520 removed outlier: 3.635A pdb=" N ASN A1520 " --> pdb=" O GLU A1516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 623 through 626 removed outlier: 5.727A pdb=" N ARG A 624 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 639 through 641 removed outlier: 7.173A pdb=" N SER A 639 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 697 through 700 removed outlier: 6.560A pdb=" N TYR A 778 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL A 814 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 780 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 663 " --> pdb=" O PHE A 813 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 830 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 666 " --> pdb=" O LEU A 830 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1318 through 1320 Processing sheet with id=AA5, first strand: chain 'A' and resid 1302 through 1304 Processing sheet with id=AA6, first strand: chain 'A' and resid 1326 through 1328 removed outlier: 6.591A pdb=" N GLY A1327 " --> pdb=" O MET A1501 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1374 through 1375 removed outlier: 4.153A pdb=" N THR A1374 " --> pdb=" O ILE A1453 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1455 " --> pdb=" O THR A1374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1385 through 1386 Processing sheet with id=AA9, first strand: chain 'A' and resid 1457 through 1458 Processing sheet with id=AB1, first strand: chain 'A' and resid 1503 through 1504 724 hydrogen bonds defined for protein. 2139 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1764 1.31 - 1.44: 3067 1.44 - 1.56: 6533 1.56 - 1.69: 3 1.69 - 1.81: 82 Bond restraints: 11449 Sorted by residual: bond pdb=" CAY Y01 A1700 " pdb=" OAW Y01 A1700 " ideal model delta sigma weight residual 1.332 1.432 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" CAP Y01 A1700 " pdb=" CAQ Y01 A1700 " ideal model delta sigma weight residual 1.541 1.639 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" N04 RTO A1701 " pdb=" S08 RTO A1701 " ideal model delta sigma weight residual 1.625 1.711 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" N04 RTO A1702 " pdb=" S08 RTO A1702 " ideal model delta sigma weight residual 1.625 1.708 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" CAS Y01 A1700 " pdb=" CBF Y01 A1700 " ideal model delta sigma weight residual 1.533 1.453 0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 11444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 15440 3.66 - 7.33: 90 7.33 - 10.99: 6 10.99 - 14.66: 0 14.66 - 18.32: 2 Bond angle restraints: 15538 Sorted by residual: angle pdb=" O09 RTO A1701 " pdb=" S08 RTO A1701 " pdb=" O10 RTO A1701 " ideal model delta sigma weight residual 119.19 100.87 18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" O09 RTO A1702 " pdb=" S08 RTO A1702 " pdb=" O10 RTO A1702 " ideal model delta sigma weight residual 119.19 100.94 18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C VAL A 32 " pdb=" N TRP A 33 " pdb=" CA TRP A 33 " ideal model delta sigma weight residual 121.14 114.43 6.71 1.75e+00 3.27e-01 1.47e+01 angle pdb=" CAM Y01 A1700 " pdb=" CAY Y01 A1700 " pdb=" OAW Y01 A1700 " ideal model delta sigma weight residual 111.19 120.45 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" CA LEU A1526 " pdb=" CB LEU A1526 " pdb=" CG LEU A1526 " ideal model delta sigma weight residual 116.30 126.65 -10.35 3.50e+00 8.16e-02 8.74e+00 ... (remaining 15533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5736 17.95 - 35.90: 846 35.90 - 53.86: 239 53.86 - 71.81: 39 71.81 - 89.76: 21 Dihedral angle restraints: 6881 sinusoidal: 2802 harmonic: 4079 Sorted by residual: dihedral pdb=" CA ASP A 774 " pdb=" CB ASP A 774 " pdb=" CG ASP A 774 " pdb=" OD1 ASP A 774 " ideal model delta sinusoidal sigma weight residual -30.00 -90.60 60.60 1 2.00e+01 2.50e-03 1.22e+01 dihedral pdb=" CA GLU A 454 " pdb=" C GLU A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta harmonic sigma weight residual -180.00 -162.74 -17.26 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP A 21 " pdb=" CB ASP A 21 " pdb=" CG ASP A 21 " pdb=" OD1 ASP A 21 " ideal model delta sinusoidal sigma weight residual -30.00 -89.64 59.64 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1674 0.080 - 0.160: 136 0.160 - 0.240: 4 0.240 - 0.320: 0 0.320 - 0.400: 2 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CBG Y01 A1700 " pdb=" CAQ Y01 A1700 " pdb=" CBD Y01 A1700 " pdb=" CBI Y01 A1700 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CBF Y01 A1700 " pdb=" CAS Y01 A1700 " pdb=" CBD Y01 A1700 " pdb=" CBH Y01 A1700 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CBI Y01 A1700 " pdb=" CAU Y01 A1700 " pdb=" CBE Y01 A1700 " pdb=" CBG Y01 A1700 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1813 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " -0.031 2.00e-02 2.50e+03 2.75e-02 1.89e+01 pdb=" CG TRP A 33 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1306 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO A1307 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A1307 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1307 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1138 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C VAL A1138 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL A1138 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A1139 " 0.013 2.00e-02 2.50e+03 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1660 2.75 - 3.29: 11458 3.29 - 3.82: 19320 3.82 - 4.36: 20666 4.36 - 4.90: 36919 Nonbonded interactions: 90023 Sorted by model distance: nonbonded pdb=" NE1 TRP A1181 " pdb=" OE1 GLN A1185 " model vdw 2.209 3.120 nonbonded pdb=" O VAL A 139 " pdb=" OH TYR A 171 " model vdw 2.245 3.040 nonbonded pdb=" O ASN A1319 " pdb=" OH TYR A1511 " model vdw 2.247 3.040 nonbonded pdb=" OH TYR A 64 " pdb=" ND1 HIS A 118 " model vdw 2.253 3.120 nonbonded pdb=" O PHE A1067 " pdb=" OG1 THR A1071 " model vdw 2.258 3.040 ... (remaining 90018 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.007 0.100 11450 Z= 0.280 Angle : 0.716 18.322 15540 Z= 0.337 Chirality : 0.046 0.400 1816 Planarity : 0.004 0.069 1916 Dihedral : 18.584 89.759 4238 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.64 % Allowed : 36.50 % Favored : 62.85 % 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: 1.28 (0.23), residues: 1396 helix: 1.78 (0.17), residues: 914 sheet: -0.44 (0.69), residues: 64 loop : -1.03 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP A 33 HIS 0.005 0.001 HIS A1367 PHE 0.017 0.001 PHE A1103 TYR 0.024 0.002 TYR A 726 ARG 0.003 0.000 ARG A1201 Details of bonding type rmsd hydrogen bonds : bond 0.12130 ( 724) hydrogen bonds : angle 5.02260 ( 2139) SS BOND : bond 0.00178 ( 1) SS BOND : angle 0.30511 ( 2) covalent geometry : bond 0.00660 (11449) covalent geometry : angle 0.71562 (15538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 597 SER cc_start: 0.7913 (m) cc_final: 0.7591 (p) REVERT: A 712 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8088 (mtpp) REVERT: A 747 MET cc_start: 0.7617 (mpp) cc_final: 0.7377 (mpp) REVERT: A 779 ILE cc_start: 0.8026 (mm) cc_final: 0.7758 (mt) REVERT: A 1495 MET cc_start: 0.6891 (pmm) cc_final: 0.6211 (tpp) outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.2401 time to fit residues: 61.3303 Evaluate side-chains 121 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.0870 chunk 109 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 661 GLN A 993 ASN A1185 GLN A1212 ASN A1240 ASN A1302 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.193570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148648 restraints weight = 13636.263| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.70 r_work: 0.3345 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11450 Z= 0.132 Angle : 0.564 10.255 15540 Z= 0.285 Chirality : 0.041 0.187 1816 Planarity : 0.004 0.044 1916 Dihedral : 7.379 85.593 1626 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.98 % Allowed : 34.00 % Favored : 63.01 % 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: 1.76 (0.23), residues: 1396 helix: 2.21 (0.17), residues: 933 sheet: -1.05 (0.61), residues: 76 loop : -1.00 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.022 0.001 PHE A 535 TYR 0.015 0.001 TYR A 561 ARG 0.006 0.000 ARG A1372 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 724) hydrogen bonds : angle 3.81207 ( 2139) SS BOND : bond 0.00063 ( 1) SS BOND : angle 1.47186 ( 2) covalent geometry : bond 0.00275 (11449) covalent geometry : angle 0.56386 (15538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8058 (m-10) cc_final: 0.7806 (m-90) REVERT: A 140 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8078 (mp) REVERT: A 165 TYR cc_start: 0.7280 (m-80) cc_final: 0.6871 (m-10) REVERT: A 210 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7345 (mtm-85) REVERT: A 643 ASP cc_start: 0.7129 (t0) cc_final: 0.6924 (t0) REVERT: A 712 LYS cc_start: 0.8472 (mtpt) cc_final: 0.7939 (mtpp) REVERT: A 747 MET cc_start: 0.7859 (mpp) cc_final: 0.7402 (mpp) REVERT: A 779 ILE cc_start: 0.7905 (mm) cc_final: 0.7605 (mt) REVERT: A 1372 ARG cc_start: 0.6396 (ttm-80) cc_final: 0.6011 (ptm160) outliers start: 37 outliers final: 15 residues processed: 155 average time/residue: 0.2153 time to fit residues: 49.5909 Evaluate side-chains 134 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1375 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 568 ASN A1240 ASN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.192164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148971 restraints weight = 13797.967| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.93 r_work: 0.3292 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11450 Z= 0.143 Angle : 0.547 8.613 15540 Z= 0.273 Chirality : 0.041 0.182 1816 Planarity : 0.004 0.044 1916 Dihedral : 7.125 86.824 1621 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.43 % Allowed : 33.20 % Favored : 62.37 % 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: 1.81 (0.23), residues: 1396 helix: 2.26 (0.17), residues: 936 sheet: -0.67 (0.68), residues: 64 loop : -1.13 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 33 HIS 0.005 0.001 HIS A1410 PHE 0.014 0.001 PHE A 535 TYR 0.011 0.001 TYR A1137 ARG 0.003 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 724) hydrogen bonds : angle 3.68881 ( 2139) SS BOND : bond 0.00488 ( 1) SS BOND : angle 1.28059 ( 2) covalent geometry : bond 0.00328 (11449) covalent geometry : angle 0.54717 (15538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8760 (OUTLIER) cc_final: 0.8501 (m110) REVERT: A 161 MET cc_start: 0.6962 (mpp) cc_final: 0.6453 (pmm) REVERT: A 165 TYR cc_start: 0.7377 (m-80) cc_final: 0.6923 (m-10) REVERT: A 210 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7515 (mtm-85) REVERT: A 643 ASP cc_start: 0.7246 (t0) cc_final: 0.6964 (t0) REVERT: A 712 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7986 (mtpp) REVERT: A 747 MET cc_start: 0.7916 (mpp) cc_final: 0.7600 (mpp) REVERT: A 779 ILE cc_start: 0.7954 (mm) cc_final: 0.7683 (mt) REVERT: A 859 MET cc_start: 0.0386 (OUTLIER) cc_final: 0.0061 (pmm) REVERT: A 1058 THR cc_start: 0.7991 (m) cc_final: 0.7785 (m) REVERT: A 1079 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7692 (mpt180) outliers start: 55 outliers final: 32 residues processed: 173 average time/residue: 0.2061 time to fit residues: 54.1678 Evaluate side-chains 154 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1134 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142968 restraints weight = 13685.658| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.99 r_work: 0.3242 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11450 Z= 0.201 Angle : 0.586 8.098 15540 Z= 0.295 Chirality : 0.043 0.157 1816 Planarity : 0.004 0.031 1916 Dihedral : 7.321 85.857 1621 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.72 % Allowed : 32.07 % Favored : 62.21 % 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: 1.70 (0.23), residues: 1396 helix: 2.17 (0.17), residues: 935 sheet: -0.80 (0.67), residues: 66 loop : -1.12 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 33 HIS 0.005 0.001 HIS A1053 PHE 0.015 0.001 PHE A 535 TYR 0.013 0.002 TYR A 510 ARG 0.006 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 724) hydrogen bonds : angle 3.80387 ( 2139) SS BOND : bond 0.00460 ( 1) SS BOND : angle 1.56950 ( 2) covalent geometry : bond 0.00489 (11449) covalent geometry : angle 0.58623 (15538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 125 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8563 (m110) REVERT: A 161 MET cc_start: 0.7019 (mpp) cc_final: 0.6219 (pmm) REVERT: A 165 TYR cc_start: 0.7508 (m-80) cc_final: 0.7052 (m-10) REVERT: A 210 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7673 (mtm-85) REVERT: A 643 ASP cc_start: 0.7378 (t0) cc_final: 0.7122 (t0) REVERT: A 712 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7984 (mtpp) REVERT: A 747 MET cc_start: 0.7932 (mpp) cc_final: 0.7584 (mpp) REVERT: A 779 ILE cc_start: 0.8091 (mm) cc_final: 0.7765 (mt) REVERT: A 859 MET cc_start: 0.0507 (OUTLIER) cc_final: 0.0231 (pmm) REVERT: A 1328 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7893 (p) outliers start: 71 outliers final: 52 residues processed: 181 average time/residue: 0.2104 time to fit residues: 57.0248 Evaluate side-chains 174 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1018 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1086 THR Chi-restraints excluded: chain A residue 1138 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1328 VAL Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 115 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 568 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.191864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146409 restraints weight = 13530.236| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.87 r_work: 0.3306 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11450 Z= 0.123 Angle : 0.533 10.403 15540 Z= 0.265 Chirality : 0.040 0.149 1816 Planarity : 0.003 0.029 1916 Dihedral : 7.165 86.568 1621 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.35 % Allowed : 32.80 % Favored : 62.85 % 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: 1.89 (0.23), residues: 1396 helix: 2.34 (0.17), residues: 935 sheet: -0.77 (0.68), residues: 66 loop : -1.12 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.012 0.001 PHE A1236 TYR 0.012 0.001 TYR A1137 ARG 0.003 0.000 ARG A1142 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 724) hydrogen bonds : angle 3.62138 ( 2139) SS BOND : bond 0.00454 ( 1) SS BOND : angle 1.31247 ( 2) covalent geometry : bond 0.00273 (11449) covalent geometry : angle 0.53252 (15538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 126 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8347 (m-10) cc_final: 0.8058 (m-90) REVERT: A 127 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8508 (m110) REVERT: A 161 MET cc_start: 0.6840 (mpp) cc_final: 0.6034 (pmm) REVERT: A 165 TYR cc_start: 0.7387 (m-80) cc_final: 0.6942 (m-10) REVERT: A 210 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7612 (mtm-85) REVERT: A 643 ASP cc_start: 0.7412 (t0) cc_final: 0.7142 (t0) REVERT: A 712 LYS cc_start: 0.8458 (mtpt) cc_final: 0.7961 (mtpp) REVERT: A 747 MET cc_start: 0.7866 (mpp) cc_final: 0.7533 (mpp) REVERT: A 779 ILE cc_start: 0.7972 (mm) cc_final: 0.7664 (mt) REVERT: A 781 ASP cc_start: 0.6895 (t0) cc_final: 0.6598 (t70) REVERT: A 859 MET cc_start: 0.0422 (OUTLIER) cc_final: 0.0150 (pmm) REVERT: A 1252 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8472 (t) outliers start: 54 outliers final: 37 residues processed: 170 average time/residue: 0.2152 time to fit residues: 54.5174 Evaluate side-chains 157 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 438 TRP Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 568 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.191577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.146163 restraints weight = 13795.560| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.96 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11450 Z= 0.132 Angle : 0.550 10.228 15540 Z= 0.272 Chirality : 0.040 0.170 1816 Planarity : 0.003 0.029 1916 Dihedral : 7.157 87.091 1621 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.67 % Allowed : 32.47 % Favored : 62.85 % 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: 1.90 (0.23), residues: 1396 helix: 2.35 (0.17), residues: 935 sheet: -0.77 (0.69), residues: 66 loop : -1.13 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.012 0.001 PHE A1236 TYR 0.020 0.001 TYR A 561 ARG 0.004 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 724) hydrogen bonds : angle 3.59425 ( 2139) SS BOND : bond 0.00307 ( 1) SS BOND : angle 1.37817 ( 2) covalent geometry : bond 0.00304 (11449) covalent geometry : angle 0.55014 (15538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 121 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8291 (m110) REVERT: A 161 MET cc_start: 0.6380 (mpp) cc_final: 0.5924 (pmm) REVERT: A 712 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7805 (mtpp) REVERT: A 747 MET cc_start: 0.7444 (mpp) cc_final: 0.7213 (mpp) REVERT: A 779 ILE cc_start: 0.8171 (mm) cc_final: 0.7845 (mt) REVERT: A 859 MET cc_start: 0.1555 (OUTLIER) cc_final: 0.1133 (pmm) REVERT: A 1252 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8521 (t) outliers start: 58 outliers final: 41 residues processed: 168 average time/residue: 0.2043 time to fit residues: 51.5144 Evaluate side-chains 159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 133 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 82 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** 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 = 0.4135 r_free = 0.4135 target = 0.186819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141570 restraints weight = 13753.485| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.03 r_work: 0.3215 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11450 Z= 0.207 Angle : 0.615 9.679 15540 Z= 0.308 Chirality : 0.043 0.156 1816 Planarity : 0.004 0.032 1916 Dihedral : 7.332 85.372 1621 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.48 % Allowed : 31.27 % Favored : 63.26 % 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: 1.58 (0.23), residues: 1396 helix: 2.08 (0.17), residues: 935 sheet: -0.57 (0.70), residues: 64 loop : -1.25 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 33 HIS 0.005 0.001 HIS A1053 PHE 0.014 0.002 PHE A1103 TYR 0.025 0.002 TYR A 561 ARG 0.004 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 724) hydrogen bonds : angle 3.82863 ( 2139) SS BOND : bond 0.00456 ( 1) SS BOND : angle 1.45567 ( 2) covalent geometry : bond 0.00507 (11449) covalent geometry : angle 0.61439 (15538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 114 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8522 (m-10) cc_final: 0.7768 (m-90) REVERT: A 127 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8584 (m110) REVERT: A 161 MET cc_start: 0.6904 (mpp) cc_final: 0.6700 (pmm) REVERT: A 712 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7959 (mtpp) REVERT: A 747 MET cc_start: 0.7970 (mpp) cc_final: 0.7600 (mpp) REVERT: A 779 ILE cc_start: 0.8130 (mm) cc_final: 0.7827 (mt) REVERT: A 859 MET cc_start: 0.0659 (OUTLIER) cc_final: 0.0421 (pmm) REVERT: A 1124 ILE cc_start: 0.8725 (mm) cc_final: 0.8497 (mt) outliers start: 68 outliers final: 54 residues processed: 168 average time/residue: 0.2224 time to fit residues: 55.3402 Evaluate side-chains 170 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1309 LEU Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 702 GLN A1293 HIS ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.190643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142322 restraints weight = 13625.527| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.31 r_work: 0.3221 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11450 Z= 0.154 Angle : 0.574 9.659 15540 Z= 0.284 Chirality : 0.041 0.144 1816 Planarity : 0.003 0.052 1916 Dihedral : 7.197 85.261 1621 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.67 % Allowed : 31.99 % Favored : 63.34 % 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: 1.72 (0.23), residues: 1396 helix: 2.22 (0.17), residues: 932 sheet: -0.98 (0.69), residues: 67 loop : -1.17 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.012 0.001 PHE A1236 TYR 0.016 0.001 TYR A 561 ARG 0.004 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 724) hydrogen bonds : angle 3.71815 ( 2139) SS BOND : bond 0.00320 ( 1) SS BOND : angle 1.11184 ( 2) covalent geometry : bond 0.00368 (11449) covalent geometry : angle 0.57343 (15538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8534 (m-10) cc_final: 0.7765 (m-90) REVERT: A 127 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8563 (m110) REVERT: A 702 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7063 (mp10) REVERT: A 712 LYS cc_start: 0.8476 (mtpt) cc_final: 0.7964 (mtpp) REVERT: A 747 MET cc_start: 0.7933 (mpp) cc_final: 0.7563 (mpp) REVERT: A 779 ILE cc_start: 0.8145 (mm) cc_final: 0.7834 (mt) REVERT: A 859 MET cc_start: 0.0605 (OUTLIER) cc_final: 0.0368 (pmm) REVERT: A 1124 ILE cc_start: 0.8719 (mm) cc_final: 0.8497 (mt) outliers start: 58 outliers final: 47 residues processed: 157 average time/residue: 0.2629 time to fit residues: 61.9246 Evaluate side-chains 161 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 702 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.190055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146037 restraints weight = 13574.979| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.91 r_work: 0.3268 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11450 Z= 0.131 Angle : 0.563 9.543 15540 Z= 0.277 Chirality : 0.041 0.142 1816 Planarity : 0.003 0.032 1916 Dihedral : 7.107 85.920 1621 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.11 % Allowed : 32.39 % Favored : 63.50 % 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: 1.84 (0.23), residues: 1396 helix: 2.32 (0.17), residues: 932 sheet: -0.81 (0.70), residues: 65 loop : -1.17 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.011 0.001 PHE A1236 TYR 0.015 0.001 TYR A 561 ARG 0.004 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 724) hydrogen bonds : angle 3.64582 ( 2139) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.98093 ( 2) covalent geometry : bond 0.00300 (11449) covalent geometry : angle 0.56260 (15538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8470 (m-10) cc_final: 0.7665 (m-90) REVERT: A 127 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (m110) REVERT: A 702 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6914 (mp10) REVERT: A 712 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7965 (mtpp) REVERT: A 747 MET cc_start: 0.7892 (mpp) cc_final: 0.7524 (mpp) REVERT: A 779 ILE cc_start: 0.8064 (mm) cc_final: 0.7760 (mt) REVERT: A 859 MET cc_start: 0.0529 (OUTLIER) cc_final: 0.0301 (pmm) REVERT: A 1124 ILE cc_start: 0.8693 (mm) cc_final: 0.8482 (mt) REVERT: A 1411 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7409 (pp) REVERT: A 1439 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8102 (mm-40) outliers start: 51 outliers final: 41 residues processed: 154 average time/residue: 0.2462 time to fit residues: 56.5354 Evaluate side-chains 156 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 33 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 702 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.191262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146747 restraints weight = 13502.101| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.94 r_work: 0.3287 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11450 Z= 0.122 Angle : 0.563 9.536 15540 Z= 0.275 Chirality : 0.040 0.143 1816 Planarity : 0.003 0.032 1916 Dihedral : 7.026 86.738 1621 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.79 % Allowed : 32.47 % Favored : 63.74 % 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: 1.93 (0.23), residues: 1396 helix: 2.39 (0.17), residues: 932 sheet: -0.85 (0.70), residues: 65 loop : -1.12 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.012 0.001 PHE A1236 TYR 0.015 0.001 TYR A 561 ARG 0.003 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 724) hydrogen bonds : angle 3.59369 ( 2139) SS BOND : bond 0.00302 ( 1) SS BOND : angle 0.89499 ( 2) covalent geometry : bond 0.00272 (11449) covalent geometry : angle 0.56252 (15538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8457 (m-10) cc_final: 0.7659 (m-90) REVERT: A 702 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: A 712 LYS cc_start: 0.8456 (mtpt) cc_final: 0.7970 (mtpp) REVERT: A 747 MET cc_start: 0.7895 (mpp) cc_final: 0.7536 (mpp) REVERT: A 779 ILE cc_start: 0.8072 (mm) cc_final: 0.7775 (mt) REVERT: A 859 MET cc_start: 0.0571 (OUTLIER) cc_final: 0.0299 (pmm) REVERT: A 1439 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8084 (mm-40) outliers start: 47 outliers final: 39 residues processed: 151 average time/residue: 0.2128 time to fit residues: 48.2741 Evaluate side-chains 152 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 63 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 700 VAL Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1212 ASN Chi-restraints excluded: chain A residue 1236 PHE Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1422 LEU Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1525 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 702 GLN ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145571 restraints weight = 13532.190| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.98 r_work: 0.3262 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11450 Z= 0.147 Angle : 0.582 9.471 15540 Z= 0.284 Chirality : 0.041 0.167 1816 Planarity : 0.003 0.032 1916 Dihedral : 7.018 86.873 1621 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.03 % Allowed : 32.55 % Favored : 63.42 % 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: 1.86 (0.23), residues: 1396 helix: 2.32 (0.17), residues: 935 sheet: -0.81 (0.70), residues: 65 loop : -1.12 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 33 HIS 0.003 0.001 HIS A1053 PHE 0.013 0.001 PHE A 576 TYR 0.014 0.001 TYR A 561 ARG 0.003 0.000 ARG A1412 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 724) hydrogen bonds : angle 3.62859 ( 2139) SS BOND : bond 0.00290 ( 1) SS BOND : angle 0.88576 ( 2) covalent geometry : bond 0.00349 (11449) covalent geometry : angle 0.58181 (15538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.75 seconds wall clock time: 111 minutes 40.01 seconds (6700.01 seconds total)