Starting phenix.real_space_refine on Wed Sep 25 20:34:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/09_2024/7s62_24847.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/09_2024/7s62_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_24847/09_2024/7s62_24847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/09_2024/7s62_24847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/09_2024/7s62_24847.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s62_24847/09_2024/7s62_24847.cif" } 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. Time to flip 16 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11013 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1382, 10775 Classifications: {'peptide': 1382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1320} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 6.73, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 2.73 Conformation dependent library (CDL) restraints added in 1.5 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: 1.54 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: 5.23 Time building geometry restraints manager: 3.23 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: 0.00 - 4.62: 15254 4.62 - 9.24: 28 9.24 - 13.86: 1 13.86 - 18.48: 0 18.48 - 23.10: 1 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 3.120 nonbonded pdb=" O GLY A 453 " pdb=" OG SER A 480 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU A 324 " pdb=" OG1 THR A 327 " model vdw 2.200 3.040 ... (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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- 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 : 1.269 Fit side-chains REVERT: A 1343 TYR cc_start: 0.8147 (t80) cc_final: 0.7920 (t80) REVERT: A 1409 ILE cc_start: 0.8192 (tt) cc_final: 0.7931 (tt) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.2151 time to fit residues: 55.0137 Evaluate side-chains 137 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.0370 chunk 125 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 GLN A1217 GLN ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11238 Z= 0.213 Angle : 0.662 13.087 15284 Z= 0.322 Chirality : 0.049 0.343 1800 Planarity : 0.005 0.148 1945 Dihedral : 11.322 104.840 1853 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.78 % Favored : 92.08 % Rotamer: Outliers : 0.74 % Allowed : 9.48 % Favored : 89.78 % 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: -1.18 (0.23), residues: 1376 helix: 1.83 (0.38), residues: 193 sheet: -0.25 (0.25), residues: 479 loop : -2.00 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.020 0.001 PHE A1245 TYR 0.014 0.001 TYR A 449 ARG 0.004 0.000 ARG A1304 *********************** 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 170 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 161 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 1309 VAL cc_start: 0.8546 (t) cc_final: 0.8307 (m) outliers start: 9 outliers final: 5 residues processed: 164 average time/residue: 0.2236 time to fit residues: 56.1766 Evaluate side-chains 144 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1217 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 125 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS A 512 HIS A1217 GLN A1218 GLN ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11238 Z= 0.234 Angle : 0.648 17.176 15284 Z= 0.318 Chirality : 0.048 0.356 1800 Planarity : 0.006 0.163 1945 Dihedral : 8.739 104.530 1853 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.58 % Favored : 91.28 % Rotamer: Outliers : 1.40 % Allowed : 15.09 % Favored : 83.51 % 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: -1.14 (0.23), residues: 1376 helix: 1.88 (0.38), residues: 193 sheet: -0.23 (0.25), residues: 493 loop : -2.00 (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 0.020 0.001 PHE A1245 TYR 0.020 0.001 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 166 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7763 (m-80) cc_final: 0.7483 (m-80) REVERT: A 430 TYR cc_start: 0.7122 (m-80) cc_final: 0.6766 (m-10) REVERT: A 1309 VAL cc_start: 0.8652 (t) cc_final: 0.8437 (m) REVERT: A 1343 TYR cc_start: 0.7920 (t80) cc_final: 0.7650 (t80) outliers start: 17 outliers final: 11 residues processed: 159 average time/residue: 0.1953 time to fit residues: 47.7893 Evaluate side-chains 146 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1425 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 A1217 GLN A1218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11238 Z= 0.259 Angle : 0.645 18.610 15284 Z= 0.320 Chirality : 0.048 0.325 1800 Planarity : 0.006 0.166 1945 Dihedral : 8.410 103.995 1853 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.92 % Favored : 91.93 % Rotamer: Outliers : 2.31 % Allowed : 16.57 % Favored : 81.12 % 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: -1.19 (0.23), residues: 1376 helix: 1.76 (0.38), residues: 194 sheet: -0.26 (0.25), residues: 493 loop : -2.01 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1015 HIS 0.004 0.001 HIS A1250 PHE 0.025 0.002 PHE A 765 TYR 0.014 0.001 TYR A 449 ARG 0.003 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 181 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7750 (m-80) cc_final: 0.7359 (m-80) REVERT: A 1158 LEU cc_start: 0.8140 (mt) cc_final: 0.7918 (mt) REVERT: A 1188 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8386 (m-10) REVERT: A 1278 LEU cc_start: 0.8369 (tt) cc_final: 0.8154 (mp) REVERT: A 1309 VAL cc_start: 0.8681 (t) cc_final: 0.8467 (m) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.2010 time to fit residues: 52.5215 Evaluate side-chains 163 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1425 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS A1217 GLN A1375 ASN ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11238 Z= 0.290 Angle : 0.659 20.812 15284 Z= 0.328 Chirality : 0.048 0.331 1800 Planarity : 0.006 0.174 1945 Dihedral : 8.278 103.457 1853 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.43 % Favored : 91.42 % Rotamer: Outliers : 2.97 % Allowed : 17.89 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1376 helix: 1.62 (0.37), residues: 195 sheet: -0.33 (0.24), residues: 495 loop : -2.05 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.020 0.002 PHE A1245 TYR 0.021 0.002 TYR A 449 ARG 0.004 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 181 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7779 (m-80) cc_final: 0.7372 (m-80) REVERT: A 479 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 1188 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8422 (m-10) REVERT: A 1215 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 1278 LEU cc_start: 0.8381 (tt) cc_final: 0.8177 (mp) outliers start: 36 outliers final: 26 residues processed: 170 average time/residue: 0.1950 time to fit residues: 50.6910 Evaluate side-chains 170 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1425 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 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 426 HIS A1217 GLN ** A1388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1678 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= 0.188 Angle : 0.620 21.591 15284 Z= 0.304 Chirality : 0.047 0.325 1800 Planarity : 0.006 0.177 1945 Dihedral : 7.907 103.238 1853 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.85 % Favored : 92.01 % Rotamer: Outliers : 3.05 % Allowed : 18.14 % Favored : 78.81 % 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: -1.15 (0.23), residues: 1376 helix: 1.83 (0.38), residues: 196 sheet: -0.23 (0.25), residues: 479 loop : -1.98 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 728 HIS 0.004 0.001 HIS A1250 PHE 0.021 0.001 PHE A1245 TYR 0.025 0.001 TYR A 449 ARG 0.003 0.000 ARG A 897 *********************** 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 193 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7761 (m-80) cc_final: 0.7362 (m-80) REVERT: A 456 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 479 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7270 (mp) REVERT: A 484 MET cc_start: 0.6128 (ppp) cc_final: 0.4960 (ppp) REVERT: A 667 GLN cc_start: 0.7887 (mp10) cc_final: 0.7463 (mp10) REVERT: A 1188 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8527 (m-10) REVERT: A 1215 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8595 (tt) REVERT: A 1217 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7511 (mt0) outliers start: 37 outliers final: 20 residues processed: 184 average time/residue: 0.1987 time to fit residues: 55.8492 Evaluate side-chains 167 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 4.9990 chunk 76 optimal weight: 0.0060 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 GLN A1242 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: 0.7598 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11238 Z= 0.215 Angle : 0.642 22.774 15284 Z= 0.311 Chirality : 0.047 0.328 1800 Planarity : 0.006 0.179 1945 Dihedral : 7.937 104.831 1853 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 3.13 % Allowed : 18.71 % Favored : 78.15 % 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: -1.17 (0.23), residues: 1376 helix: 1.77 (0.38), residues: 197 sheet: -0.26 (0.25), residues: 492 loop : -1.99 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 845 HIS 0.004 0.001 HIS A1250 PHE 0.021 0.002 PHE A1245 TYR 0.020 0.001 TYR A 449 ARG 0.006 0.000 ARG A 897 *********************** 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 187 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7549 (mm) REVERT: A 235 LEU cc_start: 0.7732 (pt) cc_final: 0.7340 (pp) REVERT: A 297 TYR cc_start: 0.5947 (t80) cc_final: 0.5623 (t80) REVERT: A 456 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7159 (tp) REVERT: A 479 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7253 (mp) REVERT: A 484 MET cc_start: 0.6148 (ppp) cc_final: 0.5017 (ppp) REVERT: A 542 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7193 (pt) REVERT: A 667 GLN cc_start: 0.7899 (mp10) cc_final: 0.7441 (mp10) REVERT: A 1158 LEU cc_start: 0.8172 (mt) cc_final: 0.7699 (mt) REVERT: A 1188 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: A 1217 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7075 (mt0) outliers start: 38 outliers final: 30 residues processed: 179 average time/residue: 0.1950 time to fit residues: 53.2114 Evaluate side-chains 179 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 0.0770 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS 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: 0.7624 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11238 Z= 0.257 Angle : 0.650 17.557 15284 Z= 0.323 Chirality : 0.048 0.332 1800 Planarity : 0.005 0.159 1945 Dihedral : 7.977 104.061 1853 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 3.63 % Allowed : 19.13 % Favored : 77.25 % 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: -1.20 (0.23), residues: 1376 helix: 1.70 (0.38), residues: 198 sheet: -0.26 (0.25), residues: 482 loop : -2.01 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 845 HIS 0.004 0.001 HIS A1250 PHE 0.021 0.002 PHE A1245 TYR 0.028 0.001 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 192 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 222 PHE cc_start: 0.7849 (m-80) cc_final: 0.7563 (m-80) REVERT: A 235 LEU cc_start: 0.7748 (pt) cc_final: 0.7366 (pp) REVERT: A 297 TYR cc_start: 0.5917 (t80) cc_final: 0.5603 (t80) REVERT: A 456 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7361 (tp) REVERT: A 479 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 667 GLN cc_start: 0.7919 (mp10) cc_final: 0.7457 (mp10) REVERT: A 1158 LEU cc_start: 0.8131 (mt) cc_final: 0.7640 (mt) REVERT: A 1188 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8563 (m-10) outliers start: 44 outliers final: 33 residues processed: 181 average time/residue: 0.1945 time to fit residues: 53.8761 Evaluate side-chains 180 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1425 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 81 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7594 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11238 Z= 0.209 Angle : 0.669 26.200 15284 Z= 0.320 Chirality : 0.049 0.524 1800 Planarity : 0.006 0.189 1945 Dihedral : 8.056 103.680 1853 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.14 % Favored : 91.72 % Rotamer: Outliers : 3.22 % Allowed : 19.70 % Favored : 77.08 % 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: -1.14 (0.23), residues: 1376 helix: 1.84 (0.38), residues: 196 sheet: -0.24 (0.25), residues: 489 loop : -1.99 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 845 HIS 0.006 0.001 HIS A1250 PHE 0.020 0.001 PHE A1245 TYR 0.025 0.001 TYR A 449 ARG 0.002 0.000 ARG A1304 *********************** 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 182 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 222 PHE cc_start: 0.7812 (m-80) cc_final: 0.7494 (m-80) REVERT: A 235 LEU cc_start: 0.7816 (pt) cc_final: 0.7398 (pp) REVERT: A 297 TYR cc_start: 0.6048 (t80) cc_final: 0.5741 (t80) REVERT: A 456 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7213 (tp) REVERT: A 479 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 667 GLN cc_start: 0.7879 (mp10) cc_final: 0.7407 (mp10) REVERT: A 1158 LEU cc_start: 0.8102 (mt) cc_final: 0.7546 (mt) REVERT: A 1188 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8533 (m-10) REVERT: A 1217 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.7366 (mt0) REVERT: A 1244 LEU cc_start: 0.7945 (mt) cc_final: 0.7532 (pp) outliers start: 39 outliers final: 33 residues processed: 175 average time/residue: 0.1922 time to fit residues: 51.3343 Evaluate side-chains 177 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 HIS ** A1250 HIS ** 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: 0.7645 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11238 Z= 0.281 Angle : 0.683 23.578 15284 Z= 0.335 Chirality : 0.049 0.402 1800 Planarity : 0.006 0.180 1945 Dihedral : 7.968 102.994 1853 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.65 % Favored : 91.21 % Rotamer: Outliers : 3.38 % Allowed : 19.54 % Favored : 77.08 % 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: 1.71 (0.38), residues: 195 sheet: -0.32 (0.24), residues: 503 loop : -2.07 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 845 HIS 0.006 0.001 HIS A1250 PHE 0.021 0.002 PHE A 726 TYR 0.023 0.002 TYR A 449 ARG 0.005 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 183 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7527 (mm) REVERT: A 222 PHE cc_start: 0.7860 (m-80) cc_final: 0.7629 (m-80) REVERT: A 235 LEU cc_start: 0.7784 (pt) cc_final: 0.7399 (pp) REVERT: A 297 TYR cc_start: 0.6110 (t80) cc_final: 0.5809 (t80) REVERT: A 456 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7430 (tp) REVERT: A 479 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7242 (mp) REVERT: A 667 GLN cc_start: 0.7931 (mp10) cc_final: 0.7458 (mp10) REVERT: A 1158 LEU cc_start: 0.8262 (mt) cc_final: 0.7851 (mt) REVERT: A 1188 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: A 1217 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6108 (mp-120) REVERT: A 1244 LEU cc_start: 0.7948 (mt) cc_final: 0.7556 (pp) outliers start: 41 outliers final: 33 residues processed: 175 average time/residue: 0.1878 time to fit residues: 51.2278 Evaluate side-chains 174 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 333 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 758 CYS Chi-restraints excluded: chain A residue 765 PHE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 859 VAL Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1188 TYR Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1217 GLN Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1437 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.167117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148311 restraints weight = 15106.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146772 restraints weight = 25509.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.147428 restraints weight = 26385.171| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11238 Z= 0.196 Angle : 0.638 21.741 15284 Z= 0.311 Chirality : 0.047 0.328 1800 Planarity : 0.006 0.172 1945 Dihedral : 7.713 102.550 1853 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.92 % Favored : 91.86 % Rotamer: Outliers : 3.38 % Allowed : 20.03 % Favored : 76.59 % 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: -1.14 (0.23), residues: 1376 helix: 1.87 (0.38), residues: 193 sheet: -0.23 (0.25), residues: 485 loop : -1.97 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 728 HIS 0.005 0.001 HIS A1250 PHE 0.020 0.001 PHE A1245 TYR 0.023 0.001 TYR A 449 ARG 0.003 0.000 ARG A1304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.31 seconds wall clock time: 40 minutes 45.49 seconds (2445.49 seconds total)