Starting phenix.real_space_refine on Sat Dec 9 12:04:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/12_2023/7s62_24847.pdb" } resolution = 3.65 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7000 2.51 5 N 1768 2.21 5 O 2191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 914": "OE1" <-> "OE2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A TYR 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A TYR 1426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11013 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1399, 11013 Unusual residues: {'NAG': 17} Inner-chain residues flagged as termini: ['pdbres="CYS A1441 "'] Classifications: {'peptide': 1382, 'undetermined': 17} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1320, None: 17} Not linked: pdbres="CYS A1441 " pdbres="NAG A2101 " Not linked: pdbres="NAG A2101 " pdbres="NAG A2102 " Not linked: pdbres="NAG A2102 " pdbres="NAG A2103 " Not linked: pdbres="NAG A2103 " pdbres="NAG A2104 " Not linked: pdbres="NAG A2104 " pdbres="NAG A2105 " ... (remaining 12 not shown) Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.24, per 1000 atoms: 0.57 Number of scatterers: 11013 At special positions: 0 Unit cell: (126.42, 132.3, 107.31, 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 54 16.00 O 2191 8.00 N 1768 7.00 C 7000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 80 " distance=2.04 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 283 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 758 " distance=2.04 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A1327 " - pdb=" SG CYS A1441 " 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=1, symmetry=0 Links applied NAG-ASN " NAG A2101 " - " ASN A 64 " " NAG A2102 " - " ASN A 81 " " NAG A2103 " - " ASN A 242 " " NAG A2104 " - " ASN A 285 " " NAG A2105 " - " ASN A 415 " " NAG A2106 " - " ASN A 472 " " NAG A2107 " - " ASN A 526 " " NAG A2108 " - " ASN A 578 " " NAG A2109 " - " ASN A 721 " " NAG A2110 " - " ASN A 773 " " NAG A2111 " - " ASN A 918 " " NAG A2112 " - " ASN A 977 " " NAG A2113 " - " ASN A1096 " " NAG A2114 " - " ASN A1266 " " NAG A2115 " - " ASN A1286 " " NAG A2116 " - " ASN A1292 " " NAG A2117 " - " ASN A1348 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.3 seconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2582 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 26 sheets defined 15.3% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 942 through 946 removed outlier: 3.579A pdb=" N LEU A 945 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 946 " --> pdb=" O LEU A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 968 through 979 Processing helix chain 'A' and resid 983 through 1002 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1022 through 1036 Processing helix chain 'A' and resid 1043 through 1057 removed outlier: 3.654A pdb=" N GLN A1047 " --> pdb=" O ASP A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1095 Processing helix chain 'A' and resid 1101 through 1113 removed outlier: 3.851A pdb=" N ALA A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1134 removed outlier: 3.669A pdb=" N SER A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A1126 " --> pdb=" O TYR A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1150 removed outlier: 3.712A pdb=" N SER A1149 " --> pdb=" O ASN A1145 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 3.982A pdb=" N GLU A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A1185 " --> pdb=" O ALA A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1217 removed outlier: 3.894A pdb=" N THR A1205 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP A1213 " --> pdb=" O GLN A1209 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A1217 " --> pdb=" O TRP A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1243 removed outlier: 4.020A pdb=" N VAL A1232 " --> pdb=" O GLN A1228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A1243 " --> pdb=" O PHE A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1376 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 8.856A pdb=" N ARG A 40 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 29 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.684A pdb=" N LEU A 33 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 95 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'A' and resid 170 through 171 removed outlier: 3.770A pdb=" N VAL A 158 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 233 removed outlier: 6.325A pdb=" N ILE A 232 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 348 Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB5, first strand: chain 'A' and resid 454 through 458 Processing sheet with id=AB6, first strand: chain 'A' and resid 503 through 512 removed outlier: 5.187A pdb=" N GLN A 505 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 497 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR A 492 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE A 542 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 573 Processing sheet with id=AB8, first strand: chain 'A' and resid 578 through 583 Processing sheet with id=AB9, first strand: chain 'A' and resid 590 through 596 Processing sheet with id=AC1, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AC2, first strand: chain 'A' and resid 780 through 785 removed outlier: 3.659A pdb=" N SER A 785 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS A 799 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 802 " --> pdb=" O SER A 841 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 839 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 846 " --> pdb=" O ILE A 825 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.242A pdb=" N LEU A 790 " --> pdb=" O GLN A 892 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 815 " --> pdb=" O SER A 860 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 896 through 913 removed outlier: 3.751A pdb=" N SER A1301 " --> pdb=" O SER A 902 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A1293 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN A 912 " --> pdb=" O ILE A1291 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A1291 " --> pdb=" O ASN A 912 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A1263 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER A1257 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP A1261 " --> pdb=" O SER A1257 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 896 through 913 removed outlier: 3.751A pdb=" N SER A1301 " --> pdb=" O SER A 902 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A1293 " --> pdb=" O ASP A 910 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN A 912 " --> pdb=" O ILE A1291 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A1291 " --> pdb=" O ASN A 912 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A1298 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA A 932 " --> pdb=" O LEU A1280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1152 through 1153 Processing sheet with id=AC7, first strand: chain 'A' and resid 1317 through 1324 removed outlier: 3.984A pdb=" N GLN A1364 " --> pdb=" O LEU A1408 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1381 through 1385 removed outlier: 3.583A pdb=" N LYS A1381 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A1420 " --> pdb=" O GLN A1358 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3526 1.34 - 1.46: 2633 1.46 - 1.58: 5002 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 11238 Sorted by residual: bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1 NAG A2109 " pdb=" O5 NAG A2109 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N PRO A 74 " pdb=" CA PRO A 74 " ideal model delta sigma weight residual 1.465 1.505 -0.040 2.03e-02 2.43e+03 3.88e+00 bond pdb=" C1 NAG A2102 " pdb=" O5 NAG A2102 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" CB PRO A 893 " pdb=" CG PRO A 893 " ideal model delta sigma weight residual 1.492 1.581 -0.089 5.00e-02 4.00e+02 3.13e+00 ... (remaining 11233 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.14: 259 106.14 - 113.12: 6170 113.12 - 120.09: 3735 120.09 - 127.07: 5031 127.07 - 134.05: 89 Bond angle restraints: 15284 Sorted by residual: angle pdb=" C GLN A 73 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 125.00 101.90 23.10 4.10e+00 5.95e-02 3.18e+01 angle pdb=" CA PRO A 893 " pdb=" N PRO A 893 " pdb=" CD PRO A 893 " ideal model delta sigma weight residual 112.00 105.71 6.29 1.40e+00 5.10e-01 2.02e+01 angle pdb=" N PRO A 74 " pdb=" CA PRO A 74 " pdb=" C PRO A 74 " ideal model delta sigma weight residual 110.70 116.08 -5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" N GLY A 867 " pdb=" CA GLY A 867 " pdb=" C GLY A 867 " ideal model delta sigma weight residual 112.73 117.33 -4.60 1.20e+00 6.94e-01 1.47e+01 angle pdb=" CB MET A1359 " pdb=" CG MET A1359 " pdb=" SD MET A1359 " ideal model delta sigma weight residual 112.70 102.76 9.94 3.00e+00 1.11e-01 1.10e+01 ... (remaining 15279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.87: 6403 23.87 - 47.75: 417 47.75 - 71.62: 77 71.62 - 95.49: 40 95.49 - 119.36: 23 Dihedral angle restraints: 6960 sinusoidal: 2926 harmonic: 4034 Sorted by residual: dihedral pdb=" CB CYS A1327 " pdb=" SG CYS A1327 " pdb=" SG CYS A1441 " pdb=" CB CYS A1441 " ideal model delta sinusoidal sigma weight residual -86.00 -157.26 71.26 1 1.00e+01 1.00e-02 6.52e+01 dihedral pdb=" CA LEU A 590 " pdb=" C LEU A 590 " pdb=" N CYS A 591 " pdb=" CA CYS A 591 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 80 " pdb=" CB CYS A 80 " ideal model delta sinusoidal sigma weight residual -86.00 -45.51 -40.49 1 1.00e+01 1.00e-02 2.30e+01 ... (remaining 6957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1497 0.065 - 0.131: 284 0.131 - 0.196: 16 0.196 - 0.262: 1 0.262 - 0.327: 2 Chirality restraints: 1800 Sorted by residual: chirality pdb=" C1 NAG A2108 " pdb=" ND2 ASN A 578 " pdb=" C2 NAG A2108 " pdb=" O5 NAG A2108 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C1 NAG A2114 " pdb=" ND2 ASN A1266 " pdb=" C2 NAG A2114 " pdb=" O5 NAG A2114 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C1 NAG A2101 " pdb=" ND2 ASN A 64 " pdb=" C2 NAG A2101 " pdb=" O5 NAG A2101 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1797 not shown) Planarity restraints: 1962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 73 " 0.118 5.00e-02 4.00e+02 1.82e-01 5.28e+01 pdb=" N PRO A 74 " -0.314 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.110 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 892 " 0.084 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO A 893 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO A 893 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 893 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 73 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C GLN A 73 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN A 73 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 74 " -0.016 2.00e-02 2.50e+03 ... (remaining 1959 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 19 2.34 - 2.98: 5503 2.98 - 3.62: 15351 3.62 - 4.26: 22838 4.26 - 4.90: 39111 Nonbonded interactions: 82822 Sorted by model distance: nonbonded pdb=" SG CYS A 958 " pdb=" CD GLN A 961 " model vdw 1.694 3.630 nonbonded pdb=" SG CYS A 958 " pdb=" CG GLN A 961 " model vdw 2.059 3.800 nonbonded pdb=" ND2 ASN A1219 " pdb=" O GLY A1223 " model vdw 2.181 2.520 nonbonded pdb=" O GLY A 453 " pdb=" OG SER A 480 " model vdw 2.198 2.440 nonbonded pdb=" OE1 GLU A 324 " pdb=" OG1 THR A 327 " model vdw 2.200 2.440 ... (remaining 82817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.180 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.620 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 11238 Z= 0.301 Angle : 0.715 23.104 15284 Z= 0.357 Chirality : 0.049 0.327 1800 Planarity : 0.006 0.182 1945 Dihedral : 19.021 119.364 4357 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.87 % Favored : 90.99 % Rotamer: Outliers : 0.08 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1376 helix: 1.58 (0.37), residues: 194 sheet: -0.45 (0.25), residues: 488 loop : -2.05 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1160 HIS 0.005 0.001 HIS A1250 PHE 0.021 0.002 PHE A 765 TYR 0.023 0.001 TYR A 449 ARG 0.004 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.199 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1915 time to fit residues: 48.2022 Evaluate side-chains 137 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 126 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 GLN ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11238 Z= 0.324 Angle : 0.709 13.773 15284 Z= 0.348 Chirality : 0.051 0.353 1800 Planarity : 0.006 0.151 1945 Dihedral : 11.735 105.623 1853 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.79 % Favored : 91.06 % Rotamer: Outliers : 1.15 % Allowed : 11.13 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1376 helix: 1.63 (0.38), residues: 193 sheet: -0.45 (0.24), residues: 505 loop : -2.14 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1015 HIS 0.004 0.001 HIS A1250 PHE 0.019 0.002 PHE A1245 TYR 0.017 0.002 TYR A 956 ARG 0.004 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 1.161 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 158 average time/residue: 0.2054 time to fit residues: 49.7780 Evaluate side-chains 147 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1102 time to fit residues: 3.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11238 Z= 0.301 Angle : 0.697 17.184 15284 Z= 0.339 Chirality : 0.053 0.756 1800 Planarity : 0.006 0.163 1945 Dihedral : 9.332 105.595 1853 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.45 % Favored : 90.41 % Rotamer: Outliers : 1.40 % Allowed : 17.07 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1376 helix: 1.62 (0.38), residues: 194 sheet: -0.38 (0.25), residues: 492 loop : -2.13 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.017 0.002 PHE A1245 TYR 0.018 0.002 TYR A 449 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.2028 time to fit residues: 51.3191 Evaluate side-chains 154 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1066 time to fit residues: 4.1461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11238 Z= 0.282 Angle : 0.661 18.895 15284 Z= 0.326 Chirality : 0.048 0.330 1800 Planarity : 0.006 0.169 1945 Dihedral : 8.739 106.320 1853 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.74 % Favored : 90.12 % Rotamer: Outliers : 2.72 % Allowed : 18.63 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1376 helix: 1.69 (0.38), residues: 194 sheet: -0.46 (0.24), residues: 495 loop : -2.13 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.018 0.002 PHE A1245 TYR 0.021 0.002 TYR A 449 ARG 0.004 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.483 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 175 average time/residue: 0.1997 time to fit residues: 53.4358 Evaluate side-chains 157 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1124 time to fit residues: 5.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 GLN ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11238 Z= 0.302 Angle : 0.672 19.375 15284 Z= 0.332 Chirality : 0.049 0.343 1800 Planarity : 0.006 0.170 1945 Dihedral : 8.420 105.481 1853 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.25 % Favored : 89.61 % Rotamer: Outliers : 2.72 % Allowed : 19.54 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1376 helix: 1.59 (0.37), residues: 198 sheet: -0.60 (0.24), residues: 501 loop : -2.17 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1015 HIS 0.004 0.001 HIS A1250 PHE 0.018 0.002 PHE A1245 TYR 0.020 0.002 TYR A 449 ARG 0.005 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 183 average time/residue: 0.1886 time to fit residues: 53.6523 Evaluate side-chains 162 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1046 time to fit residues: 5.6702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.0970 chunk 120 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 210 GLN A1300 GLN ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11238 Z= 0.195 Angle : 0.634 22.115 15284 Z= 0.306 Chirality : 0.047 0.333 1800 Planarity : 0.006 0.179 1945 Dihedral : 8.124 105.465 1853 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.14 % Favored : 91.72 % Rotamer: Outliers : 2.31 % Allowed : 21.35 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1376 helix: 1.84 (0.38), residues: 195 sheet: -0.50 (0.25), residues: 499 loop : -2.11 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.017 0.001 PHE A1245 TYR 0.021 0.001 TYR A 449 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.399 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 165 average time/residue: 0.1980 time to fit residues: 50.7013 Evaluate side-chains 156 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1254 time to fit residues: 4.7560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 82 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A1387 ASN A1388 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11238 Z= 0.207 Angle : 0.635 22.826 15284 Z= 0.307 Chirality : 0.047 0.335 1800 Planarity : 0.006 0.180 1945 Dihedral : 8.013 104.411 1853 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.79 % Favored : 91.06 % Rotamer: Outliers : 1.32 % Allowed : 22.26 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.23), residues: 1376 helix: 1.85 (0.38), residues: 198 sheet: -0.39 (0.25), residues: 499 loop : -2.12 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.005 0.001 HIS A1250 PHE 0.019 0.002 PHE A1245 TYR 0.026 0.001 TYR A 449 ARG 0.003 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 150 time to evaluate : 1.287 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 164 average time/residue: 0.1981 time to fit residues: 49.8968 Evaluate side-chains 151 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1163 time to fit residues: 3.6560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.0470 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A1300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11238 Z= 0.261 Angle : 0.662 17.925 15284 Z= 0.324 Chirality : 0.048 0.338 1800 Planarity : 0.006 0.164 1945 Dihedral : 8.031 104.055 1853 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.23 % Favored : 90.62 % Rotamer: Outliers : 1.48 % Allowed : 22.67 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.23), residues: 1376 helix: 1.81 (0.38), residues: 198 sheet: -0.48 (0.25), residues: 498 loop : -2.14 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 845 HIS 0.004 0.001 HIS A1250 PHE 0.017 0.002 PHE A1245 TYR 0.022 0.002 TYR A 449 ARG 0.004 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 151 average time/residue: 0.1989 time to fit residues: 46.3941 Evaluate side-chains 151 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1114 time to fit residues: 3.7754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 118 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A1300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11238 Z= 0.190 Angle : 0.650 26.087 15284 Z= 0.309 Chirality : 0.047 0.335 1800 Planarity : 0.006 0.191 1945 Dihedral : 7.849 103.697 1853 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.72 % Favored : 91.13 % Rotamer: Outliers : 0.49 % Allowed : 23.08 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1376 helix: 1.91 (0.38), residues: 198 sheet: -0.34 (0.25), residues: 495 loop : -2.08 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1160 HIS 0.005 0.001 HIS A1250 PHE 0.018 0.001 PHE A1245 TYR 0.029 0.001 TYR A1343 ARG 0.003 0.000 ARG A1412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.158 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 156 average time/residue: 0.2064 time to fit residues: 48.8605 Evaluate side-chains 146 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 1.245 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1026 time to fit residues: 2.6920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11238 Z= 0.318 Angle : 0.703 23.488 15284 Z= 0.342 Chirality : 0.049 0.347 1800 Planarity : 0.006 0.182 1945 Dihedral : 8.042 103.994 1853 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.74 % Favored : 90.12 % Rotamer: Outliers : 0.82 % Allowed : 23.66 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1376 helix: 1.67 (0.38), residues: 199 sheet: -0.56 (0.24), residues: 505 loop : -2.14 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 845 HIS 0.005 0.001 HIS A1388 PHE 0.017 0.002 PHE A1245 TYR 0.041 0.002 TYR A1343 ARG 0.004 0.000 ARG A 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 156 average time/residue: 0.2033 time to fit residues: 48.5972 Evaluate side-chains 150 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1171 time to fit residues: 3.0206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 16 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN A1300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.167539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.149874 restraints weight = 15132.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.148321 restraints weight = 25332.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.148499 restraints weight = 26105.459| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11238 Z= 0.186 Angle : 0.650 21.350 15284 Z= 0.312 Chirality : 0.047 0.335 1800 Planarity : 0.005 0.172 1945 Dihedral : 7.814 103.480 1853 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.65 % Favored : 91.21 % Rotamer: Outliers : 0.49 % Allowed : 23.91 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1376 helix: 1.87 (0.38), residues: 196 sheet: -0.35 (0.25), residues: 500 loop : -2.10 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 845 HIS 0.005 0.001 HIS A1250 PHE 0.017 0.001 PHE A1245 TYR 0.039 0.001 TYR A1343 ARG 0.003 0.000 ARG A1277 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2172.88 seconds wall clock time: 40 minutes 39.15 seconds (2439.15 seconds total)