Starting phenix.real_space_refine on Fri Mar 15 16:48:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cu3_30470/03_2024/7cu3_30470_updated.pdb" } resolution = 2.65 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= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 96 5.16 5 C 8092 2.51 5 N 1913 2.21 5 O 2100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ARG 297": "NH1" <-> "NH2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 542": "NH1" <-> "NH2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ARG 764": "NH1" <-> "NH2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A GLU 906": "OE1" <-> "OE2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A ARG 1094": "NH1" <-> "NH2" Residue "A ARG 1193": "NH1" <-> "NH2" Residue "A ARG 1200": "NH1" <-> "NH2" Residue "A ARG 1275": "NH1" <-> "NH2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A ARG 1481": "NH1" <-> "NH2" Residue "A ARG 1545": "NH1" <-> "NH2" Residue "A ARG 1556": "NH1" <-> "NH2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12209 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10353 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1277, 10325 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1231} Chain breaks: 5 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 91 Conformer: "B" Number of residues, atoms: 1277, 10325 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 1231} Chain breaks: 5 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 91 bond proxies already assigned to first conformer: 10563 Chain: "B" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1379 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 477 Unusual residues: {'6OU': 12, 'CLR': 2, 'NAG': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'6OU:plan-1': 5, '6OU:plan-2': 2, '6OU:plan-3': 2} Unresolved non-hydrogen planarities: 33 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATHR A1387 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A1387 " occ=0.50 residue: pdb=" N AGLY A1388 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1388 " occ=0.50 residue: pdb=" N AGLU A1389 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A1389 " occ=0.50 residue: pdb=" N AASP A1390 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A1390 " occ=0.50 Time building chain proxies: 11.85, per 1000 atoms: 0.97 Number of scatterers: 12209 At special positions: 0 Unit cell: (157.795, 117.04, 114.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 8 15.00 O 2100 8.00 N 1913 7.00 C 8092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.04 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.04 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 270 " distance=1.99 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 273 " distance=2.02 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 350 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 385 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 370 " 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 Links applied NAG-ASN " NAG A2001 " - " ASN A 210 " " NAG A2002 " - " ASN A1064 " " NAG A2003 " - " ASN A 216 " Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 3.8 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2776 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 2 sheets defined 64.3% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.711A pdb=" N SER A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 65 through 90 removed outlier: 4.127A pdb=" N TYR A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 138 through 157 Proline residue: A 145 - end of helix removed outlier: 3.712A pdb=" N ARG A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ILE A 156 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 199 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.501A pdb=" N SER A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 312 through 335 removed outlier: 3.853A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 384 through 402 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.485A pdb=" N SER A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 465 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.779A pdb=" N VAL A 479 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 482 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 500 Processing helix chain 'A' and resid 506 through 528 Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 556 through 567 Processing helix chain 'A' and resid 572 through 602 removed outlier: 4.672A pdb=" N LEU A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.985A pdb=" N PHE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 940 removed outlier: 4.634A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 971 Processing helix chain 'A' and resid 981 through 999 removed outlier: 3.926A pdb=" N LEU A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix removed outlier: 4.879A pdb=" N ILE A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 997 " --> pdb=" O PRO A 993 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1039 removed outlier: 4.206A pdb=" N GLY A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LYS A1015 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1112 Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.653A pdb=" N TYR A1135 " --> pdb=" O HIS A1132 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A1143 " --> pdb=" O VAL A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1163 removed outlier: 3.758A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 Processing helix chain 'A' and resid 1198 through 1207 removed outlier: 4.311A pdb=" N MET A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1227 removed outlier: 4.186A pdb=" N LEU A1227 " --> pdb=" O GLN A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1262 Processing helix chain 'A' and resid 1265 through 1268 No H-bonds generated for 'chain 'A' and resid 1265 through 1268' Processing helix chain 'A' and resid 1272 through 1293 Processing helix chain 'A' and resid 1297 through 1317 removed outlier: 4.341A pdb=" N CYS A1315 " --> pdb=" O PHE A1311 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY A1316 " --> pdb=" O PHE A1312 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1334 Processing helix chain 'A' and resid 1336 through 1357 Processing helix chain 'A' and resid 1375 through 1386 removed outlier: 3.744A pdb=" N VAL A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1397 Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1420 through 1436 Processing helix chain 'A' and resid 1439 through 1453 Processing helix chain 'A' and resid 1464 through 1477 Processing helix chain 'A' and resid 1488 through 1496 Processing helix chain 'A' and resid 1509 through 1523 removed outlier: 4.913A pdb=" N HIS A1523 " --> pdb=" O MET A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1541 Processing helix chain 'A' and resid 1544 through 1547 No H-bonds generated for 'chain 'A' and resid 1544 through 1547' Processing helix chain 'A' and resid 1550 through 1577 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 268 through 297 Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.528A pdb=" N ASP B 302 " --> pdb=" O LEU B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 310 through 325 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.858A pdb=" N ARG B 349 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 206 through 209 Processing sheet with id= B, first strand: chain 'A' and resid 1060 through 1064 665 hydrogen bonds defined for protein. 1875 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: 3.48 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1824 1.30 - 1.43: 3428 1.43 - 1.56: 6967 1.56 - 1.68: 135 1.68 - 1.81: 149 Bond restraints: 12503 Sorted by residual: bond pdb=" C16 6OU A2010 " pdb=" O17 6OU A2010 " ideal model delta sigma weight residual 1.207 1.412 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C07 6OU A2010 " pdb=" C08 6OU A2010 " ideal model delta sigma weight residual 1.524 1.336 0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C16 6OU A2010 " pdb=" O18 6OU A2010 " ideal model delta sigma weight residual 1.327 1.176 0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" C16 6OU A2006 " pdb=" O18 6OU A2006 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C16 6OU A2013 " pdb=" O18 6OU A2013 " ideal model delta sigma weight residual 1.327 1.422 -0.095 2.00e-02 2.50e+03 2.28e+01 ... (remaining 12498 not shown) Histogram of bond angle deviations from ideal: 99.44 - 106.36: 307 106.36 - 113.28: 6947 113.28 - 120.20: 4694 120.20 - 127.12: 4810 127.12 - 134.04: 130 Bond angle restraints: 16888 Sorted by residual: angle pdb=" O22 6OU A2006 " pdb=" P23 6OU A2006 " pdb=" O26 6OU A2006 " ideal model delta sigma weight residual 93.95 110.58 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" O22 6OU A2015 " pdb=" P23 6OU A2015 " pdb=" O26 6OU A2015 " ideal model delta sigma weight residual 93.95 110.13 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O22 6OU A2014 " pdb=" P23 6OU A2014 " pdb=" O26 6OU A2014 " ideal model delta sigma weight residual 93.95 109.37 -15.42 3.00e+00 1.11e-01 2.64e+01 angle pdb=" O22 6OU A2013 " pdb=" P23 6OU A2013 " pdb=" O26 6OU A2013 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU A2007 " pdb=" P23 6OU A2007 " pdb=" O26 6OU A2007 " ideal model delta sigma weight residual 93.95 109.05 -15.10 3.00e+00 1.11e-01 2.53e+01 ... (remaining 16883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 7287 35.29 - 70.58: 259 70.58 - 105.87: 41 105.87 - 141.16: 13 141.16 - 176.45: 9 Dihedral angle restraints: 7609 sinusoidal: 3330 harmonic: 4279 Sorted by residual: dihedral pdb=" CB CYS B 200 " pdb=" SG CYS B 200 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual 93.00 153.59 -60.59 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CA BGLU A1389 " pdb=" C BGLU A1389 " pdb=" N BASP A1390 " pdb=" CA BASP A1390 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C15 6OU A2005 " pdb=" C16 6OU A2005 " pdb=" O18 6OU A2005 " pdb=" C19 6OU A2005 " ideal model delta sinusoidal sigma weight residual 175.68 -0.77 176.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1544 0.057 - 0.114: 323 0.114 - 0.170: 28 0.170 - 0.227: 10 0.227 - 0.284: 1 Chirality restraints: 1906 Sorted by residual: chirality pdb=" CA HIS A 471 " pdb=" N HIS A 471 " pdb=" C HIS A 471 " pdb=" CB HIS A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C13 CLR A2017 " pdb=" C12 CLR A2017 " pdb=" C14 CLR A2017 " pdb=" C17 CLR A2017 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN A 210 " pdb=" N ASN A 210 " pdb=" C ASN A 210 " pdb=" CB ASN A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1903 not shown) Planarity restraints: 2051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.035 2.00e-02 2.50e+03 2.94e-02 1.08e+01 pdb=" C7 NAG A2001 " -0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " -0.010 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.046 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1136 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ILE A1136 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE A1136 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A1137 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 586 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C ALA A 586 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA A 586 " 0.013 2.00e-02 2.50e+03 pdb=" N THR A 587 " 0.012 2.00e-02 2.50e+03 ... (remaining 2048 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1111 2.74 - 3.28: 12241 3.28 - 3.82: 21125 3.82 - 4.36: 25813 4.36 - 4.90: 42702 Nonbonded interactions: 102992 Sorted by model distance: nonbonded pdb=" O THR A 947 " pdb=" OG1 THR A 947 " model vdw 2.196 2.440 nonbonded pdb=" N ASP A 250 " pdb=" OD1 ASP A 250 " model vdw 2.212 2.520 nonbonded pdb=" O ASN A 404 " pdb=" NH2 ARG A 413 " model vdw 2.239 2.520 nonbonded pdb=" OG1 THR A1207 " pdb=" OE1 GLN A1208 " model vdw 2.261 2.440 nonbonded pdb=" O THR A1529 " pdb=" OG1 THR A1529 " model vdw 2.294 2.440 ... (remaining 102987 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=0.50 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.750 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 42.830 Find NCS groups from input model: 0.320 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.009 0.205 12503 Z= 0.574 Angle : 0.992 16.633 16888 Z= 0.445 Chirality : 0.047 0.284 1906 Planarity : 0.005 0.046 2048 Dihedral : 19.751 176.455 4800 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.43 % Allowed : 6.87 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.75 (0.20), residues: 1438 helix: -0.41 (0.15), residues: 963 sheet: 0.20 (1.62), residues: 12 loop : -2.72 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1085 HIS 0.004 0.001 HIS A1132 PHE 0.015 0.002 PHE A 184 TYR 0.020 0.002 TYR A1426 ARG 0.004 0.001 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 1.504 Fit side-chains REVERT: A 59 MET cc_start: 0.7500 (mmm) cc_final: 0.7297 (tpt) REVERT: A 108 CYS cc_start: 0.7075 (m) cc_final: 0.6775 (m) REVERT: A 235 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: A 380 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7573 (ppp) REVERT: A 409 GLU cc_start: 0.6592 (pt0) cc_final: 0.6189 (tt0) REVERT: A 415 TYR cc_start: 0.7815 (m-80) cc_final: 0.7358 (m-10) REVERT: A 432 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 757 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8470 (mm110) REVERT: A 851 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8068 (ttm170) REVERT: A 903 MET cc_start: 0.8693 (mtp) cc_final: 0.8399 (mtm) REVERT: A 1003 MET cc_start: 0.8938 (mmm) cc_final: 0.8588 (mmm) REVERT: A 1009 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 1029 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7956 (tt) REVERT: A 1200 ARG cc_start: 0.7017 (mtm180) cc_final: 0.6777 (mtt180) REVERT: A 1270 GLN cc_start: 0.8002 (mt0) cc_final: 0.7696 (mm-40) REVERT: A 1318 HIS cc_start: 0.8042 (t-170) cc_final: 0.7832 (t-90) REVERT: A 1476 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6741 (ptp) REVERT: A 1491 LYS cc_start: 0.7346 (ptmm) cc_final: 0.6558 (ttpp) REVERT: A 1492 PHE cc_start: 0.7335 (m-80) cc_final: 0.6849 (m-80) REVERT: A 1509 LYS cc_start: 0.7912 (ttpm) cc_final: 0.7538 (mppt) REVERT: B 279 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: B 356 ASP cc_start: 0.8341 (t0) cc_final: 0.8108 (t0) outliers start: 44 outliers final: 15 residues processed: 241 average time/residue: 1.1098 time to fit residues: 292.8774 Evaluate side-chains 185 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 371 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 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 135 GLN A 334 GLN A 759 HIS A 934 ASN A1296 ASN A1449 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12503 Z= 0.153 Angle : 0.515 11.159 16888 Z= 0.262 Chirality : 0.038 0.267 1906 Planarity : 0.004 0.046 2048 Dihedral : 19.783 158.265 2137 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.12 % Allowed : 12.10 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1438 helix: 1.08 (0.16), residues: 945 sheet: -1.01 (1.68), residues: 10 loop : -2.15 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.003 0.001 HIS A1132 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A1426 ARG 0.003 0.000 ARG A1521 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 189 time to evaluate : 1.338 Fit side-chains REVERT: A 59 MET cc_start: 0.7459 (mmm) cc_final: 0.7248 (tpt) REVERT: A 72 PHE cc_start: 0.8050 (t80) cc_final: 0.7773 (t80) REVERT: A 108 CYS cc_start: 0.7051 (m) cc_final: 0.6726 (m) REVERT: A 235 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: A 380 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7386 (ppp) REVERT: A 409 GLU cc_start: 0.6589 (pt0) cc_final: 0.6182 (tt0) REVERT: A 571 TRP cc_start: 0.8089 (m100) cc_final: 0.7868 (m100) REVERT: A 757 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8407 (mm110) REVERT: A 880 ASP cc_start: 0.7622 (m-30) cc_final: 0.6980 (t0) REVERT: A 903 MET cc_start: 0.8719 (mtp) cc_final: 0.8379 (ttm) REVERT: A 1003 MET cc_start: 0.8898 (mmm) cc_final: 0.8614 (mmm) REVERT: A 1005 LYS cc_start: 0.8650 (tttm) cc_final: 0.8405 (tttt) REVERT: A 1009 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 1029 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 1244 MET cc_start: 0.7192 (mmp) cc_final: 0.6935 (mtp) REVERT: A 1270 GLN cc_start: 0.7814 (mt0) cc_final: 0.7546 (mm-40) REVERT: A 1302 MET cc_start: 0.7662 (ttm) cc_final: 0.7423 (ttt) REVERT: A 1318 HIS cc_start: 0.8021 (t-170) cc_final: 0.7815 (t-90) REVERT: A 1334 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (mttp) REVERT: A 1476 MET cc_start: 0.6977 (ptp) cc_final: 0.6772 (ptp) REVERT: A 1492 PHE cc_start: 0.7422 (m-80) cc_final: 0.6912 (m-80) REVERT: A 1502 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6447 (tp30) REVERT: A 1509 LYS cc_start: 0.7830 (ttpm) cc_final: 0.7438 (mppt) REVERT: A 1510 LEU cc_start: 0.8266 (tp) cc_final: 0.7910 (tp) REVERT: B 279 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: B 281 ASP cc_start: 0.8238 (t70) cc_final: 0.7793 (t70) REVERT: B 356 ASP cc_start: 0.8335 (t0) cc_final: 0.8120 (t0) outliers start: 40 outliers final: 15 residues processed: 214 average time/residue: 1.0689 time to fit residues: 251.6812 Evaluate side-chains 190 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 934 ASN A1296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12503 Z= 0.148 Angle : 0.485 9.962 16888 Z= 0.247 Chirality : 0.037 0.207 1906 Planarity : 0.004 0.043 2048 Dihedral : 17.232 157.273 2117 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.12 % Allowed : 13.66 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1438 helix: 1.67 (0.17), residues: 950 sheet: -1.89 (1.11), residues: 20 loop : -1.86 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1287 HIS 0.002 0.001 HIS A 759 PHE 0.010 0.001 PHE A 184 TYR 0.014 0.001 TYR A1517 ARG 0.005 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 1.256 Fit side-chains REVERT: A 59 MET cc_start: 0.7460 (mmm) cc_final: 0.7243 (tpt) REVERT: A 72 PHE cc_start: 0.8071 (t80) cc_final: 0.7835 (t80) REVERT: A 79 MET cc_start: 0.7484 (tmm) cc_final: 0.6922 (ppp) REVERT: A 80 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: A 108 CYS cc_start: 0.6982 (m) cc_final: 0.6637 (m) REVERT: A 275 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 284 PHE cc_start: 0.7931 (m-80) cc_final: 0.7623 (m-10) REVERT: A 409 GLU cc_start: 0.6560 (pt0) cc_final: 0.6164 (tt0) REVERT: A 757 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8469 (mm110) REVERT: A 880 ASP cc_start: 0.7558 (m-30) cc_final: 0.6996 (t0) REVERT: A 903 MET cc_start: 0.8672 (mtp) cc_final: 0.8293 (ttm) REVERT: A 975 ASN cc_start: 0.8540 (m-40) cc_final: 0.8298 (m-40) REVERT: A 1003 MET cc_start: 0.8875 (mmm) cc_final: 0.8570 (mmm) REVERT: A 1009 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7410 (mt-10) REVERT: A 1232 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: A 1244 MET cc_start: 0.7372 (mmp) cc_final: 0.7111 (mtp) REVERT: A 1270 GLN cc_start: 0.7735 (mt0) cc_final: 0.7469 (mm-40) REVERT: A 1302 MET cc_start: 0.7631 (ttm) cc_final: 0.7335 (ttm) REVERT: A 1318 HIS cc_start: 0.8032 (t-170) cc_final: 0.7818 (t-90) REVERT: A 1334 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8540 (mttp) REVERT: A 1492 PHE cc_start: 0.7544 (m-80) cc_final: 0.7034 (m-80) REVERT: A 1502 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6291 (tp30) REVERT: A 1509 LYS cc_start: 0.7822 (ttpm) cc_final: 0.7535 (mppt) REVERT: A 1510 LEU cc_start: 0.8326 (tp) cc_final: 0.8096 (tp) REVERT: B 279 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: B 281 ASP cc_start: 0.8224 (t70) cc_final: 0.7791 (t70) outliers start: 40 outliers final: 18 residues processed: 205 average time/residue: 1.0087 time to fit residues: 228.5379 Evaluate side-chains 200 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1232 ASP Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 934 ASN A1296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12503 Z= 0.240 Angle : 0.530 10.332 16888 Z= 0.273 Chirality : 0.040 0.243 1906 Planarity : 0.004 0.044 2048 Dihedral : 16.953 167.263 2107 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.20 % Allowed : 14.75 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1438 helix: 1.66 (0.17), residues: 949 sheet: -0.82 (1.78), residues: 10 loop : -1.76 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1085 HIS 0.008 0.001 HIS A 91 PHE 0.013 0.001 PHE B 352 TYR 0.018 0.002 TYR A1426 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 174 time to evaluate : 1.219 Fit side-chains REVERT: A 37 TRP cc_start: 0.6405 (p-90) cc_final: 0.6162 (p-90) REVERT: A 59 MET cc_start: 0.7433 (mmm) cc_final: 0.7206 (tpt) REVERT: A 108 CYS cc_start: 0.7035 (m) cc_final: 0.6706 (m) REVERT: A 284 PHE cc_start: 0.8026 (m-80) cc_final: 0.7690 (m-10) REVERT: A 409 GLU cc_start: 0.6547 (pt0) cc_final: 0.6159 (tt0) REVERT: A 757 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8424 (mm110) REVERT: A 880 ASP cc_start: 0.7604 (m-30) cc_final: 0.7037 (t0) REVERT: A 903 MET cc_start: 0.8689 (mtp) cc_final: 0.8302 (ttm) REVERT: A 975 ASN cc_start: 0.8592 (m-40) cc_final: 0.8325 (m-40) REVERT: A 1003 MET cc_start: 0.8927 (mmm) cc_final: 0.8629 (mmm) REVERT: A 1009 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 1029 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8045 (tm) REVERT: A 1167 LEU cc_start: 0.8977 (mt) cc_final: 0.8701 (tp) REVERT: A 1244 MET cc_start: 0.7432 (mmp) cc_final: 0.7163 (mtp) REVERT: A 1270 GLN cc_start: 0.7840 (mt0) cc_final: 0.7596 (mm-40) REVERT: A 1318 HIS cc_start: 0.8062 (t-170) cc_final: 0.7824 (t-90) REVERT: A 1491 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6454 (ptmt) REVERT: A 1492 PHE cc_start: 0.7546 (m-80) cc_final: 0.6994 (m-80) REVERT: A 1502 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6376 (tp30) REVERT: A 1509 LYS cc_start: 0.7851 (ttpm) cc_final: 0.7563 (mppt) REVERT: A 1510 LEU cc_start: 0.8324 (tp) cc_final: 0.8082 (tp) REVERT: B 281 ASP cc_start: 0.8297 (t70) cc_final: 0.7835 (t70) outliers start: 41 outliers final: 22 residues processed: 203 average time/residue: 0.9082 time to fit residues: 205.4259 Evaluate side-chains 198 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1491 LYS Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 759 HIS A 934 ASN A1296 ASN A1524 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12503 Z= 0.253 Angle : 0.537 9.224 16888 Z= 0.277 Chirality : 0.040 0.231 1906 Planarity : 0.004 0.045 2048 Dihedral : 16.758 178.027 2107 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.12 % Allowed : 15.46 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1438 helix: 1.62 (0.17), residues: 951 sheet: -0.74 (1.80), residues: 10 loop : -1.71 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1085 HIS 0.007 0.001 HIS A 91 PHE 0.012 0.002 PHE B 352 TYR 0.018 0.002 TYR A1426 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 174 time to evaluate : 1.418 Fit side-chains REVERT: A 37 TRP cc_start: 0.6468 (p-90) cc_final: 0.6240 (p-90) REVERT: A 108 CYS cc_start: 0.6998 (m) cc_final: 0.6662 (m) REVERT: A 284 PHE cc_start: 0.8020 (m-80) cc_final: 0.7691 (m-10) REVERT: A 409 GLU cc_start: 0.6542 (pt0) cc_final: 0.6166 (tt0) REVERT: A 759 HIS cc_start: 0.6566 (m170) cc_final: 0.6364 (m170) REVERT: A 880 ASP cc_start: 0.7623 (m-30) cc_final: 0.7032 (t0) REVERT: A 903 MET cc_start: 0.8650 (mtp) cc_final: 0.8224 (ttm) REVERT: A 1009 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 1029 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8142 (tm) REVERT: A 1167 LEU cc_start: 0.8941 (mt) cc_final: 0.8664 (tp) REVERT: A 1244 MET cc_start: 0.7472 (mmp) cc_final: 0.7192 (mtp) REVERT: A 1270 GLN cc_start: 0.7924 (mt0) cc_final: 0.7704 (mm-40) REVERT: A 1318 HIS cc_start: 0.8089 (t-170) cc_final: 0.7874 (t-90) REVERT: A 1462 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 1491 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6439 (ptmt) REVERT: A 1492 PHE cc_start: 0.7551 (m-80) cc_final: 0.7006 (m-80) REVERT: A 1502 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6398 (tp30) REVERT: A 1509 LYS cc_start: 0.7959 (ttpm) cc_final: 0.7624 (mppt) REVERT: A 1510 LEU cc_start: 0.8305 (tp) cc_final: 0.8037 (tp) REVERT: B 281 ASP cc_start: 0.8244 (t70) cc_final: 0.7788 (t70) REVERT: B 340 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7857 (mttt) outliers start: 40 outliers final: 25 residues processed: 203 average time/residue: 0.9437 time to fit residues: 213.6359 Evaluate side-chains 200 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1491 LYS Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 934 ASN A1296 ASN A1524 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12503 Z= 0.228 Angle : 0.530 9.488 16888 Z= 0.272 Chirality : 0.039 0.217 1906 Planarity : 0.004 0.045 2048 Dihedral : 16.360 177.098 2104 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.36 % Allowed : 15.77 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1438 helix: 1.68 (0.17), residues: 951 sheet: -0.75 (1.80), residues: 10 loop : -1.60 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1287 HIS 0.005 0.001 HIS A 91 PHE 0.011 0.001 PHE B 352 TYR 0.018 0.001 TYR A1426 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 172 time to evaluate : 1.256 Fit side-chains REVERT: A 37 TRP cc_start: 0.6465 (p-90) cc_final: 0.6244 (p-90) REVERT: A 80 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: A 108 CYS cc_start: 0.6997 (m) cc_final: 0.6678 (m) REVERT: A 284 PHE cc_start: 0.8006 (m-80) cc_final: 0.7636 (m-10) REVERT: A 409 GLU cc_start: 0.6476 (pt0) cc_final: 0.6111 (tt0) REVERT: A 844 HIS cc_start: 0.3790 (OUTLIER) cc_final: 0.3039 (p-80) REVERT: A 880 ASP cc_start: 0.7627 (m-30) cc_final: 0.7046 (t0) REVERT: A 903 MET cc_start: 0.8642 (mtp) cc_final: 0.8230 (ttm) REVERT: A 1003 MET cc_start: 0.8911 (mmm) cc_final: 0.8581 (mmm) REVERT: A 1009 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 1029 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8141 (tm) REVERT: A 1167 LEU cc_start: 0.8967 (mt) cc_final: 0.8732 (tp) REVERT: A 1244 MET cc_start: 0.7497 (mmp) cc_final: 0.7212 (mtp) REVERT: A 1318 HIS cc_start: 0.8096 (t-170) cc_final: 0.7881 (t-90) REVERT: A 1480 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5012 (mtmm) REVERT: A 1491 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6433 (ptmt) REVERT: A 1492 PHE cc_start: 0.7554 (m-80) cc_final: 0.7004 (m-80) REVERT: A 1502 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6354 (tp30) REVERT: A 1509 LYS cc_start: 0.7959 (ttpm) cc_final: 0.7624 (mppt) REVERT: A 1510 LEU cc_start: 0.8295 (tp) cc_final: 0.8023 (tp) REVERT: A 1520 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6825 (tp30) REVERT: B 281 ASP cc_start: 0.8236 (t70) cc_final: 0.7811 (t70) outliers start: 43 outliers final: 28 residues processed: 202 average time/residue: 0.9551 time to fit residues: 214.3346 Evaluate side-chains 205 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 844 HIS Chi-restraints excluded: chain A residue 947 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1056 ASP Chi-restraints excluded: chain A residue 1203 MET Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1424 LEU Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1480 LYS Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1491 LYS Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain A residue 1520 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 0.0030 chunk 85 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 757 GLN A 934 ASN A 975 ASN A1296 ASN A1524 ASN B 226 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12503 Z= 0.131 Angle : 0.469 8.058 16888 Z= 0.239 Chirality : 0.036 0.165 1906 Planarity : 0.004 0.043 2048 Dihedral : 15.141 174.057 2104 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.26 % Allowed : 17.10 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.38 (0.23), residues: 1438 helix: 2.03 (0.17), residues: 943 sheet: -0.79 (1.84), residues: 10 loop : -1.38 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1090 HIS 0.005 0.001 HIS A 91 PHE 0.008 0.001 PHE A1031 TYR 0.013 0.001 TYR A1426 ARG 0.003 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 1.294 Fit side-chains REVERT: A 37 TRP cc_start: 0.6387 (p-90) cc_final: 0.6147 (p-90) REVERT: A 59 MET cc_start: 0.7430 (mmm) cc_final: 0.7171 (tpt) REVERT: A 80 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: A 108 CYS cc_start: 0.6976 (m) cc_final: 0.6695 (m) REVERT: A 284 PHE cc_start: 0.7809 (m-80) cc_final: 0.7561 (m-10) REVERT: A 409 GLU cc_start: 0.6608 (pt0) cc_final: 0.6258 (tt0) REVERT: A 880 ASP cc_start: 0.7551 (m-30) cc_final: 0.7042 (t0) REVERT: A 903 MET cc_start: 0.8635 (mtp) cc_final: 0.8289 (ttm) REVERT: A 1003 MET cc_start: 0.8852 (mmm) cc_final: 0.8482 (mmm) REVERT: A 1029 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8072 (tm) REVERT: A 1318 HIS cc_start: 0.8171 (t-170) cc_final: 0.7948 (t-90) REVERT: A 1492 PHE cc_start: 0.7564 (m-80) cc_final: 0.7015 (m-80) REVERT: A 1502 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6192 (tp30) REVERT: A 1509 LYS cc_start: 0.7906 (ttpm) cc_final: 0.7561 (mppt) REVERT: A 1510 LEU cc_start: 0.8329 (tp) cc_final: 0.8110 (tp) REVERT: A 1558 GLN cc_start: 0.6840 (tp40) cc_final: 0.6363 (tp-100) REVERT: A 1559 LEU cc_start: 0.8162 (tm) cc_final: 0.7954 (tt) REVERT: A 1564 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 281 ASP cc_start: 0.8194 (t70) cc_final: 0.7803 (t70) outliers start: 29 outliers final: 16 residues processed: 201 average time/residue: 0.9775 time to fit residues: 218.1298 Evaluate side-chains 190 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1464 TYR Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 334 GLN A 934 ASN A1296 ASN A1524 ASN B 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12503 Z= 0.208 Angle : 0.518 9.710 16888 Z= 0.265 Chirality : 0.039 0.204 1906 Planarity : 0.004 0.043 2048 Dihedral : 15.301 176.204 2103 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.11 % Allowed : 17.88 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.23 (0.23), residues: 1438 helix: 1.91 (0.17), residues: 950 sheet: -0.84 (1.80), residues: 10 loop : -1.47 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1287 HIS 0.005 0.001 HIS A 91 PHE 0.011 0.001 PHE B 352 TYR 0.020 0.001 TYR A1420 ARG 0.002 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6386 (p-90) cc_final: 0.6138 (p-90) REVERT: A 108 CYS cc_start: 0.6924 (m) cc_final: 0.6595 (m) REVERT: A 284 PHE cc_start: 0.7923 (m-80) cc_final: 0.7649 (m-10) REVERT: A 409 GLU cc_start: 0.6615 (pt0) cc_final: 0.6256 (tt0) REVERT: A 880 ASP cc_start: 0.7568 (m-30) cc_final: 0.7035 (t0) REVERT: A 903 MET cc_start: 0.8636 (mtp) cc_final: 0.8235 (ttm) REVERT: A 1003 MET cc_start: 0.8920 (mmm) cc_final: 0.8504 (mmm) REVERT: A 1029 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8038 (tm) REVERT: A 1318 HIS cc_start: 0.8198 (t-170) cc_final: 0.7978 (t-90) REVERT: A 1492 PHE cc_start: 0.7545 (m-80) cc_final: 0.6984 (m-80) REVERT: A 1502 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: A 1509 LYS cc_start: 0.7920 (ttpm) cc_final: 0.7572 (mppt) REVERT: A 1558 GLN cc_start: 0.6855 (tp40) cc_final: 0.6369 (tp-100) REVERT: A 1559 LEU cc_start: 0.8147 (tm) cc_final: 0.7923 (tt) REVERT: A 1564 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 281 ASP cc_start: 0.8265 (t70) cc_final: 0.7816 (t70) outliers start: 27 outliers final: 20 residues processed: 193 average time/residue: 0.9804 time to fit residues: 211.2357 Evaluate side-chains 195 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1225 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 0.0050 chunk 56 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.6976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 334 GLN A 934 ASN A1296 ASN A1524 ASN B 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12503 Z= 0.142 Angle : 0.476 8.758 16888 Z= 0.243 Chirality : 0.037 0.150 1906 Planarity : 0.004 0.042 2048 Dihedral : 14.537 170.253 2103 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.72 % Allowed : 18.58 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.51 (0.23), residues: 1438 helix: 2.14 (0.17), residues: 937 sheet: -0.83 (1.83), residues: 10 loop : -1.31 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1287 HIS 0.005 0.001 HIS A 91 PHE 0.009 0.001 PHE A1250 TYR 0.013 0.001 TYR A1420 ARG 0.002 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 37 TRP cc_start: 0.6375 (p-90) cc_final: 0.6135 (p-90) REVERT: A 59 MET cc_start: 0.7426 (mmm) cc_final: 0.7171 (tpt) REVERT: A 108 CYS cc_start: 0.6947 (m) cc_final: 0.6640 (m) REVERT: A 275 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 284 PHE cc_start: 0.7853 (m-80) cc_final: 0.7607 (m-10) REVERT: A 409 GLU cc_start: 0.6584 (pt0) cc_final: 0.6275 (tt0) REVERT: A 880 ASP cc_start: 0.7584 (m-30) cc_final: 0.7123 (t0) REVERT: A 903 MET cc_start: 0.8634 (mtp) cc_final: 0.8290 (ttm) REVERT: A 1003 MET cc_start: 0.8880 (mmm) cc_final: 0.8495 (mmm) REVERT: A 1029 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7982 (tm) REVERT: A 1318 HIS cc_start: 0.8185 (t-170) cc_final: 0.7976 (t-90) REVERT: A 1492 PHE cc_start: 0.7565 (m-80) cc_final: 0.7014 (m-80) REVERT: A 1502 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6162 (tp30) REVERT: A 1509 LYS cc_start: 0.7727 (ttpm) cc_final: 0.7420 (mppt) REVERT: A 1558 GLN cc_start: 0.6834 (tp40) cc_final: 0.6354 (tp-100) REVERT: B 281 ASP cc_start: 0.8186 (t70) cc_final: 0.7773 (t70) outliers start: 22 outliers final: 16 residues processed: 189 average time/residue: 1.0084 time to fit residues: 211.3840 Evaluate side-chains 192 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1029 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1502 GLU Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.0050 chunk 95 optimal weight: 0.9990 chunk 143 optimal weight: 0.0020 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 88 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 overall best weight: 0.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 135 GLN A 334 GLN A 934 ASN ** A1514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN B 226 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12503 Z= 0.123 Angle : 0.462 9.052 16888 Z= 0.235 Chirality : 0.036 0.146 1906 Planarity : 0.004 0.042 2048 Dihedral : 13.680 169.485 2101 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.56 % Allowed : 18.81 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.69 (0.23), residues: 1438 helix: 2.29 (0.17), residues: 936 sheet: -0.93 (1.87), residues: 10 loop : -1.23 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1090 HIS 0.005 0.001 HIS A 91 PHE 0.007 0.001 PHE A1031 TYR 0.009 0.001 TYR A1426 ARG 0.002 0.000 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 59 MET cc_start: 0.7485 (mmm) cc_final: 0.7230 (tpt) REVERT: A 80 PHE cc_start: 0.7085 (m-80) cc_final: 0.6559 (m-10) REVERT: A 108 CYS cc_start: 0.6914 (m) cc_final: 0.6575 (m) REVERT: A 141 MET cc_start: 0.8612 (mtp) cc_final: 0.8386 (mtp) REVERT: A 275 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6915 (mt-10) REVERT: A 388 MET cc_start: 0.6799 (mtt) cc_final: 0.6368 (mpp) REVERT: A 409 GLU cc_start: 0.6594 (pt0) cc_final: 0.6269 (tt0) REVERT: A 880 ASP cc_start: 0.7511 (m-30) cc_final: 0.7009 (t0) REVERT: A 903 MET cc_start: 0.8613 (mtp) cc_final: 0.8311 (ttm) REVERT: A 1003 MET cc_start: 0.8790 (mmm) cc_final: 0.8521 (mmm) REVERT: A 1318 HIS cc_start: 0.8160 (t-170) cc_final: 0.7930 (t-90) REVERT: A 1492 PHE cc_start: 0.7591 (m-80) cc_final: 0.7057 (m-80) REVERT: A 1509 LYS cc_start: 0.7616 (ttpm) cc_final: 0.7237 (mptt) REVERT: A 1558 GLN cc_start: 0.6801 (tp40) cc_final: 0.6320 (tp-100) REVERT: B 281 ASP cc_start: 0.8167 (t70) cc_final: 0.7761 (t70) outliers start: 20 outliers final: 12 residues processed: 196 average time/residue: 0.9406 time to fit residues: 205.8296 Evaluate side-chains 184 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1312 PHE Chi-restraints excluded: chain A residue 1315 CYS Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain B residue 190 CYS Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain B residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 334 GLN A 934 ASN A1419 ASN A1514 HIS A1524 ASN B 226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.105614 restraints weight = 20151.257| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.62 r_work: 0.3053 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12503 Z= 0.247 Angle : 0.543 8.936 16888 Z= 0.280 Chirality : 0.040 0.183 1906 Planarity : 0.004 0.043 2048 Dihedral : 14.352 175.068 2100 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.56 % Allowed : 18.58 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.23), residues: 1438 helix: 1.98 (0.17), residues: 943 sheet: -0.88 (1.72), residues: 10 loop : -1.36 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1085 HIS 0.003 0.001 HIS A 228 PHE 0.013 0.002 PHE B 352 TYR 0.023 0.002 TYR A1426 ARG 0.003 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4563.21 seconds wall clock time: 82 minutes 38.72 seconds (4958.72 seconds total)