Starting phenix.real_space_refine (version: dev) on Tue Apr 5 02:03:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/04_2022/3jd8_6640_updated.pdb" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 1188": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 8050 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8050 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1158, 8049 Unusual residues: {'BMA': 2, 'NAG': 21, 'CLR': 1, 'MAN': 1} Classifications: {'undetermined': 25, 'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PTRANS': 56, 'CIS': 5, 'TRANS': 1068, None: 25, 'PCIS': 3} Not linked: pdbres="ILE A1251 " pdbres="NAG A1301 " Not linked: pdbres="NAG A1301 " pdbres="NAG A1302 " Not linked: pdbres="NAG A1302 " pdbres="NAG A1303 " Not linked: pdbres="NAG A1303 " pdbres="NAG A1304 " Not linked: pdbres="NAG A1304 " pdbres="NAG A1305 " ... (remaining 20 not shown) Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1295 Unresolved non-hydrogen angles: 1691 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 Conformer: "B" Number of residues, atoms: 1158, 8049 Unusual residues: {'BMA': 2, 'NAG': 21, 'CLR': 1, 'MAN': 1} Classifications: {'undetermined': 25, 'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PTRANS': 56, 'CIS': 5, 'TRANS': 1068, None: 25, 'PCIS': 3} Not linked: pdbres="ILE A1251 " pdbres="NAG A1301 " Not linked: pdbres="NAG A1301 " pdbres="NAG A1302 " Not linked: pdbres="NAG A1302 " pdbres="NAG A1303 " Not linked: pdbres="NAG A1303 " pdbres="NAG A1304 " Not linked: pdbres="NAG A1304 " pdbres="NAG A1305 " ... (remaining 20 not shown) Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1295 Unresolved non-hydrogen angles: 1691 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 bond proxies already assigned to first conformer: 8193 Time building chain proxies: 9.27, per 1000 atoms: 1.15 Number of scatterers: 8050 At special positions: 0 Unit cell: (84.9251, 97.9905, 169.85, 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 42 16.00 O 1597 8.00 N 1336 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.05 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.06 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=1.91 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=1.79 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.10 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.07 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 ALPHA1-6 " BMA A1314 " - " MAN A1315 " BETA1-4 " NAG A1301 " - " NAG A1302 " " NAG A1304 " - " NAG A1305 " " NAG A1306 " - " NAG A1307 " " NAG A1307 " - " BMA A1308 " " NAG A1310 " - " NAG A1311 " " NAG A1312 " - " NAG A1313 " " NAG A1313 " - " BMA A1314 " " NAG A1318 " - " NAG A1319 " NAG-ASN " NAG A1301 " - " ASN A 222 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 524 " " NAG A1306 " - " ASN A 557 " " NAG A1309 " - " ASN A 572 " " NAG A1310 " - " ASN A 598 " " NAG A1316 " - " ASN A 122 " " NAG A1317 " - " ASN A 70 " " NAG A1319 " - " ASN A 185 " " NAG A1320 " - " ASN A1064 " " NAG A1322 " - " ASN A 135 " " NAG A1324 " - " ASN A 459 " Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.4 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 52.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 53 through 62 removed outlier: 5.026A pdb=" N ASP A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.508A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 261 through 287 Processing helix chain 'A' and resid 331 through 349 removed outlier: 4.173A pdb=" N ASN A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 451 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.534A pdb=" N ARG A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 4.051A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.882A pdb=" N THR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 665 Processing helix chain 'A' and resid 676 through 697 Proline residue: A 681 - end of helix removed outlier: 4.523A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.797A pdb=" N VAL A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 removed outlier: 3.869A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.514A pdb=" N ARG A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 742 through 771 removed outlier: 3.521A pdb=" N VAL A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 4.352A pdb=" N SER A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 829 Proline residue: A 827 - end of helix Processing helix chain 'A' and resid 832 through 850 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'A' and resid 931 through 939 Proline residue: A 939 - end of helix Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.527A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1085 through 1091 removed outlier: 4.429A pdb=" N GLN A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR A1091 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1112 Processing helix chain 'A' and resid 1122 through 1143 removed outlier: 3.595A pdb=" N THR A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1132 " --> pdb=" O CYS A1128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1173 removed outlier: 3.828A pdb=" N VAL A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1212 removed outlier: 3.643A pdb=" N HIS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1250 removed outlier: 3.773A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A1227 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A1230 " --> pdb=" O PHE A1226 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 204 through 209 removed outlier: 3.552A pdb=" N LEU A 144 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 561 through 567 Processing sheet with id= D, first strand: chain 'A' and resid 454 through 457 390 hydrogen bonds defined for protein. 1125 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: 2.58 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 3489 1.44 - 1.67: 4645 1.67 - 1.90: 60 1.90 - 2.13: 0 2.13 - 2.36: 1 Bond restraints: 8195 Sorted by residual: bond pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 2.360 -1.026 2.34e-02 1.83e+03 1.92e+03 bond pdb=" C SER A 940 " pdb=" N SER A 941 " ideal model delta sigma weight residual 1.332 1.657 -0.325 1.40e-02 5.10e+03 5.38e+02 bond pdb=" C LEU A 469 " pdb=" N ALA A 470 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.77e+01 bond pdb=" C LEU A1060 " pdb=" N ILE A1061 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.25e-02 6.40e+03 7.33e+01 bond pdb=" C GLN A 881 " pdb=" N TYR A 882 " ideal model delta sigma weight residual 1.331 1.221 0.111 1.33e-02 5.65e+03 6.93e+01 ... (remaining 8190 not shown) Histogram of bond angle deviations from ideal: 86.79 - 98.15: 2 98.15 - 109.50: 951 109.50 - 120.86: 7447 120.86 - 132.22: 2814 132.22 - 143.58: 20 Bond angle restraints: 11234 Sorted by residual: angle pdb=" CA VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 118.88 86.79 32.09 1.54e+00 4.22e-01 4.34e+02 angle pdb=" O VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 121.10 143.58 -22.48 1.14e+00 7.69e-01 3.89e+02 angle pdb=" C VAL A 959 " pdb=" N PRO A 984 " pdb=" CA PRO A 984 " ideal model delta sigma weight residual 119.84 98.82 21.02 1.25e+00 6.40e-01 2.83e+02 angle pdb=" N GLN A 881 " pdb=" CA GLN A 881 " pdb=" C GLN A 881 " ideal model delta sigma weight residual 108.86 123.53 -14.67 1.41e+00 5.03e-01 1.08e+02 angle pdb=" N PHE A 995 " pdb=" CA PHE A 995 " pdb=" C PHE A 995 " ideal model delta sigma weight residual 108.34 121.88 -13.54 1.31e+00 5.83e-01 1.07e+02 ... (remaining 11229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 4488 23.14 - 46.27: 213 46.27 - 69.41: 90 69.41 - 92.55: 17 92.55 - 115.69: 1 Dihedral angle restraints: 4809 sinusoidal: 1526 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 13.01 79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C SER A 602 " pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" CB SER A 602 " ideal model delta harmonic sigma weight residual -122.60 -102.74 -19.86 0 2.50e+00 1.60e-01 6.31e+01 dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N PHE A 603 " pdb=" CA PHE A 603 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 4806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1394 0.409 - 0.817: 10 0.817 - 1.226: 4 1.226 - 1.634: 2 1.634 - 2.043: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C1 NAG A1318 " pdb=" C2 NAG A1318 " pdb=" O5 NAG A1318 " pdb=" O4 NAG A1319 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-02 2.50e+03 6.11e+03 chirality pdb=" C1 NAG A1311 " pdb=" O4 NAG A1310 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-02 2.50e+03 5.85e+03 chirality pdb=" C1 BMA A1314 " pdb=" O4 NAG A1313 " pdb=" C2 BMA A1314 " pdb=" O5 BMA A1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.95e+02 ... (remaining 1408 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 572 " 0.132 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 572 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A 572 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 572 " -0.530 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " -0.329 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG A1306 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " -0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG A1307 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " -0.030 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 40 2.05 - 2.76: 1323 2.76 - 3.47: 12474 3.47 - 4.19: 18775 4.19 - 4.90: 31123 Nonbonded interactions: 63735 Sorted by model distance: nonbonded pdb=" O TRP A 942 " pdb=" CB CYS A1011 " model vdw 1.335 3.440 nonbonded pdb=" CD2 LEU A 656 " pdb=" CB PRO A 755 " model vdw 1.371 3.860 nonbonded pdb=" CG1 VAL A 727 " pdb=" CG1 VAL A1165 " model vdw 1.411 3.880 nonbonded pdb=" CD2 LEU A 680 " pdb=" CE2 TYR A1229 " model vdw 1.470 3.760 nonbonded pdb=" O LEU A 656 " pdb=" CD1 LEU A 751 " model vdw 1.483 3.460 ... (remaining 63730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5075 2.51 5 N 1336 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 2.420 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.080 Process input model: 29.470 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.015 1.026 8195 Z= 0.992 Angle : 1.544 32.094 11234 Z= 1.044 Chirality : 0.127 2.043 1411 Planarity : 0.016 0.285 1453 Dihedral : 16.743 115.687 2658 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 78.00 Ramachandran Plot: Outliers : 8.36 % Allowed : 11.91 % Favored : 79.73 % Rotamer Outliers : 11.82 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.27 (0.23), residues: 1125 helix: -1.35 (0.20), residues: 546 sheet: -0.69 (0.56), residues: 85 loop : -3.45 (0.27), residues: 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 248 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 25 residues processed: 290 average time/residue: 0.1993 time to fit residues: 77.2484 Evaluate side-chains 173 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.909 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 3 residues processed: 25 average time/residue: 0.1304 time to fit residues: 6.0374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 150 GLN A 154 ASN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.109 8195 Z= 0.380 Angle : 1.015 15.789 11234 Z= 0.525 Chirality : 0.068 1.024 1411 Planarity : 0.006 0.076 1453 Dihedral : 7.370 105.682 1349 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 1.86 % Allowed : 9.67 % Favored : 88.46 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.73 (0.26), residues: 1127 helix: 0.21 (0.22), residues: 565 sheet: 0.37 (0.61), residues: 72 loop : -3.15 (0.27), residues: 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1663 time to fit residues: 45.9893 Evaluate side-chains 134 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 8195 Z= 0.410 Angle : 0.916 11.674 11234 Z= 0.473 Chirality : 0.060 0.864 1411 Planarity : 0.008 0.196 1453 Dihedral : 7.068 103.640 1349 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 1.60 % Allowed : 10.03 % Favored : 88.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.26), residues: 1127 helix: 0.48 (0.22), residues: 580 sheet: -0.37 (0.59), residues: 80 loop : -2.75 (0.29), residues: 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1593 time to fit residues: 36.9316 Evaluate side-chains 116 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 8195 Z= 0.291 Angle : 0.819 11.531 11234 Z= 0.422 Chirality : 0.056 0.807 1411 Planarity : 0.005 0.083 1453 Dihedral : 6.886 101.053 1349 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.85 % Favored : 88.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.96 (0.26), residues: 1127 helix: 0.81 (0.23), residues: 573 sheet: -1.08 (0.55), residues: 80 loop : -2.47 (0.29), residues: 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1548 time to fit residues: 35.3036 Evaluate side-chains 112 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 40.0000 chunk 37 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 8195 Z= 0.278 Angle : 0.770 11.818 11234 Z= 0.400 Chirality : 0.053 0.735 1411 Planarity : 0.005 0.054 1453 Dihedral : 6.694 100.052 1349 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.32 % Favored : 89.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.88 (0.26), residues: 1127 helix: 0.88 (0.22), residues: 588 sheet: -1.86 (0.50), residues: 90 loop : -2.35 (0.30), residues: 449 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1683 time to fit residues: 35.4545 Evaluate side-chains 117 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 8195 Z= 0.312 Angle : 0.774 9.642 11234 Z= 0.402 Chirality : 0.052 0.721 1411 Planarity : 0.005 0.053 1453 Dihedral : 6.649 98.254 1349 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.43 % Favored : 90.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.96 (0.26), residues: 1127 helix: 0.75 (0.22), residues: 599 sheet: -2.31 (0.47), residues: 89 loop : -2.27 (0.31), residues: 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1705 time to fit residues: 32.1522 Evaluate side-chains 105 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8195 Z= 0.224 Angle : 0.745 9.729 11234 Z= 0.375 Chirality : 0.048 0.593 1411 Planarity : 0.004 0.047 1453 Dihedral : 6.421 97.179 1349 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.34 % Favored : 90.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1127 helix: 1.05 (0.22), residues: 592 sheet: -2.12 (0.49), residues: 86 loop : -2.30 (0.30), residues: 449 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1448 time to fit residues: 28.8316 Evaluate side-chains 108 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8195 Z= 0.249 Angle : 0.727 9.725 11234 Z= 0.372 Chirality : 0.048 0.582 1411 Planarity : 0.004 0.049 1453 Dihedral : 6.482 97.384 1349 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.98 % Allowed : 8.61 % Favored : 90.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1127 helix: 1.05 (0.22), residues: 592 sheet: -2.30 (0.46), residues: 99 loop : -2.34 (0.30), residues: 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1501 time to fit residues: 28.2214 Evaluate side-chains 101 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 8.9990 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 97 optimal weight: 0.0010 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.0000 chunk 109 optimal weight: 1.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8195 Z= 0.210 Angle : 0.727 9.060 11234 Z= 0.364 Chirality : 0.048 0.567 1411 Planarity : 0.004 0.044 1453 Dihedral : 6.328 96.366 1349 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.99 % Favored : 91.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.70 (0.26), residues: 1127 helix: 1.15 (0.22), residues: 590 sheet: -2.37 (0.44), residues: 107 loop : -2.29 (0.31), residues: 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1581 time to fit residues: 31.1747 Evaluate side-chains 105 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 0.0670 chunk 9 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 overall best weight: 3.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8195 Z= 0.251 Angle : 0.728 8.984 11234 Z= 0.370 Chirality : 0.048 0.568 1411 Planarity : 0.005 0.050 1453 Dihedral : 6.331 96.967 1349 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.78 % Favored : 90.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.72 (0.26), residues: 1127 helix: 1.10 (0.22), residues: 597 sheet: -2.55 (0.43), residues: 108 loop : -2.26 (0.31), residues: 422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1539 time to fit residues: 29.5412 Evaluate side-chains 98 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 50.0000 chunk 91 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 0.0020 chunk 5 optimal weight: 5.9990 overall best weight: 3.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.078891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064075 restraints weight = 52573.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.065193 restraints weight = 38798.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.066003 restraints weight = 30814.712| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.8188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 8195 Z= 0.252 Angle : 0.732 8.983 11234 Z= 0.370 Chirality : 0.048 0.562 1411 Planarity : 0.004 0.051 1453 Dihedral : 6.334 96.614 1349 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.61 % Favored : 90.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.80 (0.26), residues: 1127 helix: 0.99 (0.22), residues: 607 sheet: -2.56 (0.43), residues: 110 loop : -2.31 (0.32), residues: 410 =============================================================================== Job complete usr+sys time: 1591.91 seconds wall clock time: 29 minutes 54.26 seconds (1794.26 seconds total)