Starting phenix.real_space_refine on Sun Aug 4 19:43:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_19433.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_19433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_19433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_19433.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rq4_19433/08_2024/8rq4_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 Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 774": "OD1" <-> "OD2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1425": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.72, per 1000 atoms: 0.78 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 3.0 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: 1.55 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: 4.60 Time building geometry restraints manager: 5.36 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: 98.93 - 106.01: 196 106.01 - 113.10: 6448 113.10 - 120.18: 4208 120.18 - 127.26: 4560 127.26 - 134.35: 126 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: 10.980 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: 0.000 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.170 ------------------------------------------------------------------------------- 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 11449 Z= 0.424 Angle : 0.716 18.322 15538 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.201 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: 0.2603 time to fit residues: 65.9314 Evaluate side-chains 121 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11449 Z= 0.177 Angle : 0.564 10.278 15538 Z= 0.285 Chirality : 0.041 0.187 1816 Planarity : 0.004 0.044 1916 Dihedral : 7.380 85.598 1626 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.98 % Allowed : 33.92 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.014 0.001 TYR A 561 ARG 0.006 0.000 ARG A1372 *********************** 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 fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7674 (m-10) cc_final: 0.7368 (m-90) REVERT: A 140 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7830 (mp) REVERT: A 165 TYR cc_start: 0.6846 (m-80) cc_final: 0.6491 (m-10) REVERT: A 476 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 712 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7899 (mtpp) REVERT: A 747 MET cc_start: 0.7491 (mpp) cc_final: 0.7056 (mpp) REVERT: A 779 ILE cc_start: 0.7990 (mm) cc_final: 0.7648 (mt) outliers start: 37 outliers final: 15 residues processed: 155 average time/residue: 0.2107 time to fit residues: 48.8080 Evaluate side-chains 134 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 476 LEU 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 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 126 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11449 Z= 0.171 Angle : 0.535 9.460 15538 Z= 0.266 Chirality : 0.040 0.179 1816 Planarity : 0.003 0.038 1916 Dihedral : 7.094 87.314 1621 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.55 % Allowed : 33.60 % 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: 1.91 (0.23), residues: 1396 helix: 2.35 (0.17), residues: 935 sheet: -0.89 (0.63), residues: 74 loop : -1.07 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.016 0.001 PHE A 535 TYR 0.011 0.001 TYR A1137 ARG 0.005 0.000 ARG A1372 *********************** 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 170 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 126 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7752 (m-10) cc_final: 0.7542 (m-10) REVERT: A 140 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (mp) REVERT: A 161 MET cc_start: 0.6569 (mpp) cc_final: 0.6094 (pmm) REVERT: A 165 TYR cc_start: 0.6829 (m-80) cc_final: 0.6516 (m-10) REVERT: A 712 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7946 (mtpp) REVERT: A 747 MET cc_start: 0.7552 (mpp) cc_final: 0.7291 (mpp) REVERT: A 779 ILE cc_start: 0.7980 (mm) cc_final: 0.7666 (mt) REVERT: A 859 MET cc_start: 0.1027 (OUTLIER) cc_final: 0.0558 (pmm) REVERT: A 1058 THR cc_start: 0.7684 (m) cc_final: 0.7472 (m) REVERT: A 1079 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7515 (mpt180) outliers start: 44 outliers final: 23 residues processed: 163 average time/residue: 0.2017 time to fit residues: 50.0865 Evaluate side-chains 143 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 106 TYR Chi-restraints excluded: chain A residue 111 LEU 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 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 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 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 1079 ARG 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 125 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ** A1367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11449 Z= 0.411 Angle : 0.648 8.535 15538 Z= 0.327 Chirality : 0.044 0.159 1816 Planarity : 0.004 0.038 1916 Dihedral : 7.451 85.167 1621 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.96 % Allowed : 31.75 % Favored : 62.29 % 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: 1.44 (0.23), residues: 1396 helix: 1.95 (0.17), residues: 936 sheet: -0.84 (0.66), residues: 66 loop : -1.18 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 33 HIS 0.006 0.001 HIS A1053 PHE 0.018 0.002 PHE A 535 TYR 0.015 0.002 TYR A 561 ARG 0.006 0.000 ARG A1412 *********************** 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 198 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 124 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7912 (m-10) cc_final: 0.7625 (m-10) REVERT: A 127 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (m110) REVERT: A 161 MET cc_start: 0.6623 (mpp) cc_final: 0.5874 (pmm) REVERT: A 165 TYR cc_start: 0.7112 (m-80) cc_final: 0.6724 (m-10) REVERT: A 712 LYS cc_start: 0.8433 (mtpt) cc_final: 0.7948 (mtpp) REVERT: A 747 MET cc_start: 0.7572 (mpp) cc_final: 0.7277 (mpp) REVERT: A 779 ILE cc_start: 0.8106 (mm) cc_final: 0.7773 (mt) REVERT: A 859 MET cc_start: 0.1269 (OUTLIER) cc_final: 0.0939 (pmm) REVERT: A 1338 SER cc_start: 0.8564 (m) cc_final: 0.8331 (t) outliers start: 74 outliers final: 49 residues processed: 182 average time/residue: 0.2025 time to fit residues: 55.8865 Evaluate side-chains 166 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 442 ILE Chi-restraints excluded: chain A residue 459 ILE 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 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 1002 ASP Chi-restraints excluded: chain A residue 1003 SER 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 1212 ASN Chi-restraints excluded: chain A residue 1260 THR Chi-restraints excluded: chain A residue 1301 TYR Chi-restraints excluded: chain A residue 1313 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11449 Z= 0.184 Angle : 0.538 8.353 15538 Z= 0.269 Chirality : 0.040 0.167 1816 Planarity : 0.003 0.029 1916 Dihedral : 7.269 85.656 1621 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.11 % Allowed : 33.60 % Favored : 62.29 % 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: 2.23 (0.17), residues: 937 sheet: -0.88 (0.68), residues: 66 loop : -1.16 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.013 0.001 PHE A 576 TYR 0.014 0.001 TYR A 561 ARG 0.003 0.000 ARG A1412 *********************** 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 176 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 125 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8463 (m110) REVERT: A 161 MET cc_start: 0.6505 (mpp) cc_final: 0.5754 (pmm) REVERT: A 165 TYR cc_start: 0.6947 (m-80) cc_final: 0.6645 (m-10) REVERT: A 712 LYS cc_start: 0.8389 (mtpt) cc_final: 0.7916 (mtpp) REVERT: A 747 MET cc_start: 0.7498 (mpp) cc_final: 0.7227 (mpp) REVERT: A 779 ILE cc_start: 0.8078 (mm) cc_final: 0.7745 (mt) REVERT: A 859 MET cc_start: 0.1203 (OUTLIER) cc_final: 0.0796 (pmm) REVERT: A 1252 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8395 (t) REVERT: A 1338 SER cc_start: 0.8497 (m) cc_final: 0.8266 (t) outliers start: 51 outliers final: 39 residues processed: 165 average time/residue: 0.2167 time to fit residues: 53.1299 Evaluate side-chains 158 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 63 PHE 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 438 TRP Chi-restraints excluded: chain A residue 439 SER 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 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 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1003 SER 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 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 1413 SER 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 121 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 0.0570 chunk 130 optimal weight: 0.8980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11449 Z= 0.150 Angle : 0.533 10.367 15538 Z= 0.264 Chirality : 0.040 0.142 1816 Planarity : 0.003 0.029 1916 Dihedral : 7.140 87.638 1621 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.63 % Allowed : 33.76 % Favored : 62.61 % 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: 1.97 (0.23), residues: 1396 helix: 2.44 (0.17), residues: 932 sheet: -0.86 (0.70), residues: 66 loop : -1.14 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 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 A1412 *********************** 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 170 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7904 (m-10) cc_final: 0.7680 (m-90) REVERT: A 127 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8407 (m110) REVERT: A 161 MET cc_start: 0.6424 (mpp) cc_final: 0.5808 (pmm) REVERT: A 165 TYR cc_start: 0.6935 (m-80) cc_final: 0.6616 (m-10) REVERT: A 712 LYS cc_start: 0.8386 (mtpt) cc_final: 0.8057 (ptpp) REVERT: A 747 MET cc_start: 0.7482 (mpp) cc_final: 0.6749 (mpp) REVERT: A 779 ILE cc_start: 0.8055 (mm) cc_final: 0.7706 (mt) REVERT: A 859 MET cc_start: 0.1152 (OUTLIER) cc_final: 0.0767 (pmm) REVERT: A 1252 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8364 (t) REVERT: A 1338 SER cc_start: 0.8482 (m) cc_final: 0.8220 (t) REVERT: A 1439 GLN cc_start: 0.7929 (mp10) cc_final: 0.7590 (mm-40) outliers start: 45 outliers final: 32 residues processed: 163 average time/residue: 0.2053 time to fit residues: 50.2188 Evaluate side-chains 152 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 390 THR Chi-restraints excluded: chain A residue 419 LEU 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 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 828 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1079 ARG 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 1456 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 15 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11449 Z= 0.191 Angle : 0.541 9.653 15538 Z= 0.268 Chirality : 0.040 0.157 1816 Planarity : 0.003 0.029 1916 Dihedral : 7.161 88.106 1621 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.87 % Allowed : 33.36 % Favored : 62.77 % 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: 1.96 (0.23), residues: 1396 helix: 2.42 (0.17), residues: 934 sheet: -0.64 (0.71), residues: 64 loop : -1.17 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.013 0.001 PHE A1236 TYR 0.011 0.001 TYR A1137 ARG 0.004 0.000 ARG A1412 *********************** 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 166 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8433 (m110) REVERT: A 161 MET cc_start: 0.6446 (mpp) cc_final: 0.5854 (pmm) REVERT: A 165 TYR cc_start: 0.6961 (m-80) cc_final: 0.6635 (m-10) REVERT: A 712 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8043 (ptpp) REVERT: A 747 MET cc_start: 0.7493 (mpp) cc_final: 0.6748 (mpp) REVERT: A 779 ILE cc_start: 0.8083 (mm) cc_final: 0.7745 (mt) REVERT: A 859 MET cc_start: 0.1169 (OUTLIER) cc_final: 0.0798 (pmm) REVERT: A 1338 SER cc_start: 0.8485 (m) cc_final: 0.8219 (t) REVERT: A 1439 GLN cc_start: 0.7960 (mp10) cc_final: 0.7602 (mm-40) outliers start: 48 outliers final: 39 residues processed: 158 average time/residue: 0.2169 time to fit residues: 50.3842 Evaluate side-chains 157 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 390 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 439 SER 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 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 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 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 1413 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11449 Z= 0.241 Angle : 0.566 9.537 15538 Z= 0.282 Chirality : 0.041 0.141 1816 Planarity : 0.003 0.033 1916 Dihedral : 7.159 87.627 1621 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.51 % Allowed : 32.55 % Favored : 62.93 % 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: 1.85 (0.23), residues: 1396 helix: 2.31 (0.17), residues: 937 sheet: -0.67 (0.71), residues: 64 loop : -1.18 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP A 33 HIS 0.004 0.001 HIS A1410 PHE 0.013 0.001 PHE A1236 TYR 0.011 0.001 TYR A1137 ARG 0.004 0.000 ARG A1412 *********************** 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 177 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8102 (m-10) cc_final: 0.7107 (m-90) REVERT: A 127 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8460 (m110) REVERT: A 161 MET cc_start: 0.6427 (mpp) cc_final: 0.5846 (pmm) REVERT: A 165 TYR cc_start: 0.7025 (m-80) cc_final: 0.6731 (m-10) REVERT: A 712 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7957 (mtpp) REVERT: A 747 MET cc_start: 0.7506 (mpp) cc_final: 0.7222 (mpp) REVERT: A 779 ILE cc_start: 0.8125 (mm) cc_final: 0.7787 (mt) REVERT: A 859 MET cc_start: 0.1205 (OUTLIER) cc_final: 0.0837 (pmm) REVERT: A 1124 ILE cc_start: 0.8558 (mm) cc_final: 0.8356 (mt) REVERT: A 1143 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: A 1338 SER cc_start: 0.8555 (m) cc_final: 0.8245 (t) REVERT: A 1439 GLN cc_start: 0.8017 (mp10) cc_final: 0.7677 (mm-40) outliers start: 56 outliers final: 45 residues processed: 166 average time/residue: 0.2159 time to fit residues: 53.0862 Evaluate side-chains 165 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 206 SER Chi-restraints excluded: chain A residue 212 VAL 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 810 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 827 ILE Chi-restraints excluded: chain A residue 828 VAL 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 1042 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1079 ARG Chi-restraints excluded: chain A residue 1143 GLN 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 1332 THR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1413 SER Chi-restraints excluded: chain A residue 1422 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 117 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11449 Z= 0.312 Angle : 0.604 9.426 15538 Z= 0.300 Chirality : 0.042 0.163 1816 Planarity : 0.003 0.037 1916 Dihedral : 7.206 86.323 1621 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.51 % Allowed : 32.39 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.23), residues: 1396 helix: 2.15 (0.17), residues: 938 sheet: -0.83 (0.70), residues: 65 loop : -1.18 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 33 HIS 0.009 0.001 HIS A1410 PHE 0.014 0.001 PHE A1236 TYR 0.011 0.001 TYR A1137 ARG 0.003 0.000 ARG A1412 *********************** 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 172 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 116 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8193 (m-10) cc_final: 0.7270 (m-90) REVERT: A 127 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8512 (m110) REVERT: A 161 MET cc_start: 0.6424 (mpp) cc_final: 0.5886 (pmm) REVERT: A 165 TYR cc_start: 0.7093 (m-80) cc_final: 0.6747 (m-10) REVERT: A 712 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7939 (mtpp) REVERT: A 747 MET cc_start: 0.7548 (mpp) cc_final: 0.7263 (mpp) REVERT: A 779 ILE cc_start: 0.8099 (mm) cc_final: 0.7767 (mt) REVERT: A 859 MET cc_start: 0.1251 (OUTLIER) cc_final: 0.0917 (pmm) REVERT: A 1338 SER cc_start: 0.8577 (m) cc_final: 0.8278 (t) REVERT: A 1411 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 1439 GLN cc_start: 0.8080 (mp10) cc_final: 0.7736 (mm-40) outliers start: 56 outliers final: 47 residues processed: 162 average time/residue: 0.2071 time to fit residues: 50.0664 Evaluate side-chains 165 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 353 VAL Chi-restraints excluded: chain A residue 390 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 490 ASN 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 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 828 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1003 SER 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 1091 LEU 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 1301 TYR 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 1411 LEU Chi-restraints excluded: chain A residue 1413 SER Chi-restraints excluded: chain A residue 1422 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 81 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11449 Z= 0.224 Angle : 0.581 11.488 15538 Z= 0.285 Chirality : 0.041 0.144 1816 Planarity : 0.003 0.031 1916 Dihedral : 7.095 86.448 1621 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.11 % Allowed : 32.31 % Favored : 63.58 % 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: 1.77 (0.23), residues: 1396 helix: 2.25 (0.17), residues: 934 sheet: -0.98 (0.69), residues: 67 loop : -1.13 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 33 HIS 0.003 0.001 HIS A1053 PHE 0.013 0.001 PHE A1236 TYR 0.011 0.001 TYR A1137 ARG 0.005 0.000 ARG A1404 ********************** 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 166 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 115 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8134 (m-10) cc_final: 0.7163 (m-90) REVERT: A 127 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8465 (m110) REVERT: A 161 MET cc_start: 0.6461 (mpp) cc_final: 0.5762 (pmm) REVERT: A 165 TYR cc_start: 0.7041 (m-80) cc_final: 0.6715 (m-10) REVERT: A 514 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: A 712 LYS cc_start: 0.8386 (mtpt) cc_final: 0.7956 (mtpp) REVERT: A 747 MET cc_start: 0.7496 (mpp) cc_final: 0.7212 (mpp) REVERT: A 779 ILE cc_start: 0.8086 (mm) cc_final: 0.7745 (mt) REVERT: A 859 MET cc_start: 0.1227 (OUTLIER) cc_final: 0.0894 (pmm) REVERT: A 1338 SER cc_start: 0.8541 (m) cc_final: 0.8240 (t) REVERT: A 1439 GLN cc_start: 0.8050 (mp10) cc_final: 0.7721 (mm-40) outliers start: 51 outliers final: 44 residues processed: 159 average time/residue: 0.2070 time to fit residues: 49.8420 Evaluate side-chains 160 residues out of total 1241 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 353 VAL Chi-restraints excluded: chain A residue 390 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 514 GLU 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 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 828 VAL 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 1042 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1091 LEU 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 1301 TYR 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 1413 SER Chi-restraints excluded: chain A residue 1422 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 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** 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 = 0.4165 r_free = 0.4165 target = 0.190113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144601 restraints weight = 13496.543| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.64 r_work: 0.3293 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11449 Z= 0.194 Angle : 0.575 12.548 15538 Z= 0.281 Chirality : 0.041 0.158 1816 Planarity : 0.003 0.031 1916 Dihedral : 6.986 87.231 1621 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.71 % Allowed : 32.80 % 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: 1.88 (0.23), residues: 1396 helix: 2.33 (0.17), residues: 934 sheet: -0.76 (0.71), residues: 65 loop : -1.13 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 33 HIS 0.005 0.001 HIS A1410 PHE 0.012 0.001 PHE A1236 TYR 0.012 0.001 TYR A1137 ARG 0.007 0.000 ARG A1412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3028.38 seconds wall clock time: 54 minutes 28.26 seconds (3268.26 seconds total)