Starting phenix.real_space_refine on Thu Jul 18 23:07:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jle_36394/07_2024/8jle_36394.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 15 5.16 5 C 2819 2.51 5 N 735 2.21 5 O 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 532": "OE1" <-> "OE2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B GLU 1203": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 905 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.13, per 1000 atoms: 0.71 Number of scatterers: 4408 At special positions: 0 Unit cell: (88.81, 83.83, 87.98, 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 15 16.00 O 839 8.00 N 735 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM 4406 O5 NAG A 602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 498 " " NAG A 602 " - " ASN A 548 " " NAG E 1 " - " ASN A 573 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 737.8 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 7.8% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.759A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1210 through 1215 removed outlier: 3.812A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY B1215 " --> pdb=" O PRO B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 removed outlier: 6.248A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR A 500 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 523 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'A' and resid 550 through 552 removed outlier: 6.220A pdb=" N PHE A 551 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.085A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 545 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR A 500 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 523 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 512 current: chain 'A' and resid 555 through 559 Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.588A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.520A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.204A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.588A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.520A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.204A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B1072 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER B 944 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B1074 " --> pdb=" O SER B 942 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 942 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA6, first strand: chain 'B' and resid 962 through 966 removed outlier: 6.682A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA8, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.100A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.490A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.639A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 16.033A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B1204 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.100A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 348 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: 1.30 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 734 1.31 - 1.46: 1688 1.46 - 1.60: 2056 1.60 - 1.74: 0 1.74 - 1.88: 23 Bond restraints: 4501 Sorted by residual: bond pdb=" C ILE B1182 " pdb=" O ILE B1182 " ideal model delta sigma weight residual 1.238 1.172 0.066 1.10e-02 8.26e+03 3.55e+01 bond pdb=" C TYR B1001 " pdb=" O TYR B1001 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.14e-02 7.69e+03 1.65e+01 bond pdb=" C LYS A 515 " pdb=" O LYS A 515 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" C MET B1134 " pdb=" O MET B1134 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.22e-02 6.72e+03 1.51e+01 bond pdb=" CA SER B1281 " pdb=" CB SER B1281 " ideal model delta sigma weight residual 1.532 1.474 0.058 1.58e-02 4.01e+03 1.36e+01 ... (remaining 4496 not shown) Histogram of bond angle deviations from ideal: 94.32 - 102.34: 15 102.34 - 110.36: 941 110.36 - 118.38: 2573 118.38 - 126.41: 2519 126.41 - 134.43: 33 Bond angle restraints: 6081 Sorted by residual: angle pdb=" OD1 ASN A 498 " pdb=" CG ASN A 498 " pdb=" ND2 ASN A 498 " ideal model delta sigma weight residual 122.60 116.40 6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" OD1 ASN A 573 " pdb=" CG ASN A 573 " pdb=" ND2 ASN A 573 " ideal model delta sigma weight residual 122.60 118.39 4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA GLY B1141 " pdb=" C GLY B1141 " pdb=" O GLY B1141 " ideal model delta sigma weight residual 122.47 118.79 3.68 1.08e+00 8.57e-01 1.16e+01 angle pdb=" CA TYR B1107 " pdb=" C TYR B1107 " pdb=" O TYR B1107 " ideal model delta sigma weight residual 121.47 117.66 3.81 1.15e+00 7.56e-01 1.10e+01 angle pdb=" NH1 ARG A 547 " pdb=" CZ ARG A 547 " pdb=" NH2 ARG A 547 " ideal model delta sigma weight residual 119.30 123.55 -4.25 1.30e+00 5.92e-01 1.07e+01 ... (remaining 6076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 2469 14.90 - 29.81: 202 29.81 - 44.71: 52 44.71 - 59.62: 7 59.62 - 74.52: 6 Dihedral angle restraints: 2736 sinusoidal: 1180 harmonic: 1556 Sorted by residual: dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N MET B1054 " pdb=" CA MET B1054 " ideal model delta harmonic sigma weight residual 180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASP B1246 " pdb=" C ASP B1246 " pdb=" N ILE B1247 " pdb=" CA ILE B1247 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS B1204 " pdb=" C LYS B1204 " pdb=" N ILE B1205 " pdb=" CA ILE B1205 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 663 0.223 - 0.447: 5 0.447 - 0.670: 1 0.670 - 0.894: 0 0.894 - 1.117: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" C1 FUC E 3 " pdb=" O6 NAG E 1 " pdb=" C2 FUC E 3 " pdb=" O5 FUC E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.09e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.59e+01 ... (remaining 667 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.052 2.00e-02 2.50e+03 5.90e-02 4.35e+01 pdb=" CG ASN A 573 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.057 2.00e-02 2.50e+03 4.73e-02 2.79e+01 pdb=" C7 NAG A 602 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1014 " -0.061 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP B1014 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B1014 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B1014 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B1014 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP B1014 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1014 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1014 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1014 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B1014 " -0.017 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 399 2.74 - 3.28: 4285 3.28 - 3.82: 7135 3.82 - 4.36: 9175 4.36 - 4.90: 15367 Nonbonded interactions: 36361 Sorted by model distance: nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.204 2.440 nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.208 2.520 nonbonded pdb=" O GLU B1203 " pdb=" OH TYR B1255 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR A 484 " pdb=" OD1 ASN A 503 " model vdw 2.291 2.440 nonbonded pdb=" NH1 ARG A 507 " pdb=" OE1 GLU A 527 " model vdw 2.295 2.520 ... (remaining 36356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.010 0.081 4501 Z= 0.661 Angle : 1.213 6.862 6081 Z= 0.761 Chirality : 0.096 1.117 670 Planarity : 0.010 0.090 772 Dihedral : 12.340 74.519 1740 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.36), residues: 524 helix: 2.06 (1.09), residues: 23 sheet: -0.20 (0.33), residues: 244 loop : -1.35 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.015 TRP B1014 HIS 0.008 0.004 HIS B1253 PHE 0.057 0.012 PHE A 576 TYR 0.051 0.011 TYR B1111 ARG 0.017 0.003 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 513 ASN cc_start: 0.7366 (t0) cc_final: 0.7130 (t0) REVERT: A 532 GLU cc_start: 0.7623 (tt0) cc_final: 0.6899 (tm-30) REVERT: A 572 ILE cc_start: 0.7827 (mt) cc_final: 0.7616 (mt) REVERT: B 913 GLN cc_start: 0.7056 (pt0) cc_final: 0.6828 (pt0) REVERT: B 940 ASN cc_start: 0.5482 (m-40) cc_final: 0.5168 (m-40) REVERT: B 955 LYS cc_start: 0.7396 (pptt) cc_final: 0.7174 (pttt) REVERT: B 982 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 988 GLN cc_start: 0.7010 (tt0) cc_final: 0.6779 (tt0) REVERT: B 1000 LYS cc_start: 0.8190 (tptp) cc_final: 0.7745 (mttp) REVERT: B 1083 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6721 (mt-10) REVERT: B 1085 LYS cc_start: 0.6078 (tptm) cc_final: 0.5806 (mmtt) REVERT: B 1089 ASP cc_start: 0.6994 (m-30) cc_final: 0.6718 (m-30) REVERT: B 1106 GLN cc_start: 0.7631 (mt0) cc_final: 0.7375 (mt0) REVERT: B 1117 PHE cc_start: 0.6115 (m-10) cc_final: 0.5286 (t80) REVERT: B 1158 THR cc_start: 0.8314 (m) cc_final: 0.8043 (p) REVERT: B 1165 TYR cc_start: 0.5874 (t80) cc_final: 0.5477 (t80) REVERT: B 1173 ILE cc_start: 0.7717 (mt) cc_final: 0.7415 (mp) REVERT: B 1179 ARG cc_start: 0.6833 (mtt180) cc_final: 0.5966 (mtp-110) REVERT: B 1189 LYS cc_start: 0.6324 (tppt) cc_final: 0.5843 (mtpm) REVERT: B 1206 LEU cc_start: 0.7066 (mp) cc_final: 0.6862 (mt) REVERT: B 1237 MET cc_start: 0.8903 (mtm) cc_final: 0.8499 (mtm) REVERT: B 1246 ASP cc_start: 0.7648 (p0) cc_final: 0.7181 (m-30) REVERT: B 1256 ASP cc_start: 0.7481 (m-30) cc_final: 0.7003 (p0) REVERT: B 1265 ASN cc_start: 0.7146 (m-40) cc_final: 0.6883 (m-40) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 1.0102 time to fit residues: 142.9946 Evaluate side-chains 93 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1091 GLN B1093 ASN B1106 GLN B1257 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4501 Z= 0.193 Angle : 0.570 6.680 6081 Z= 0.307 Chirality : 0.053 0.479 670 Planarity : 0.003 0.030 772 Dihedral : 7.140 59.073 684 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.67 % Allowed : 10.70 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.36), residues: 524 helix: 2.52 (1.10), residues: 23 sheet: -0.19 (0.33), residues: 254 loop : -1.13 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1014 HIS 0.003 0.001 HIS A 494 PHE 0.015 0.002 PHE A 516 TYR 0.010 0.001 TYR B 962 ARG 0.002 0.000 ARG B1034 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.471 Fit side-chains REVERT: A 513 ASN cc_start: 0.7415 (t0) cc_final: 0.7191 (t0) REVERT: A 532 GLU cc_start: 0.7551 (tt0) cc_final: 0.6869 (tm-30) REVERT: A 581 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: B 913 GLN cc_start: 0.7165 (pt0) cc_final: 0.6956 (pt0) REVERT: B 988 GLN cc_start: 0.7098 (tt0) cc_final: 0.6808 (tt0) REVERT: B 1000 LYS cc_start: 0.8208 (tptp) cc_final: 0.7782 (mttp) REVERT: B 1052 LYS cc_start: 0.7232 (mttt) cc_final: 0.6989 (ttpt) REVERT: B 1083 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6797 (mt-10) REVERT: B 1085 LYS cc_start: 0.5929 (tptm) cc_final: 0.5701 (mmtt) REVERT: B 1089 ASP cc_start: 0.6887 (m-30) cc_final: 0.6626 (m-30) REVERT: B 1117 PHE cc_start: 0.6081 (m-10) cc_final: 0.5233 (t80) REVERT: B 1173 ILE cc_start: 0.7847 (mt) cc_final: 0.7583 (mp) REVERT: B 1179 ARG cc_start: 0.6905 (mtt180) cc_final: 0.6292 (mtm-85) REVERT: B 1189 LYS cc_start: 0.6377 (tppt) cc_final: 0.5891 (mtpm) REVERT: B 1237 MET cc_start: 0.8752 (mtm) cc_final: 0.8382 (mtm) REVERT: B 1246 ASP cc_start: 0.7741 (p0) cc_final: 0.7250 (m-30) REVERT: B 1256 ASP cc_start: 0.7507 (m-30) cc_final: 0.7067 (p0) outliers start: 13 outliers final: 5 residues processed: 103 average time/residue: 1.0794 time to fit residues: 115.5686 Evaluate side-chains 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 13 optimal weight: 0.0870 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.2032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 ASN B 970 ASN B 988 GLN B 992 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4501 Z= 0.138 Angle : 0.493 4.869 6081 Z= 0.270 Chirality : 0.050 0.379 670 Planarity : 0.003 0.029 772 Dihedral : 6.793 59.439 684 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.26 % Allowed : 14.61 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.37), residues: 524 helix: 2.52 (1.08), residues: 23 sheet: 0.00 (0.34), residues: 254 loop : -0.93 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1266 HIS 0.001 0.000 HIS A 506 PHE 0.014 0.001 PHE A 512 TYR 0.013 0.001 TYR B 938 ARG 0.002 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.458 Fit side-chains REVERT: A 513 ASN cc_start: 0.7498 (t0) cc_final: 0.7231 (t0) REVERT: A 532 GLU cc_start: 0.7510 (tt0) cc_final: 0.6797 (tm-30) REVERT: A 581 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 913 GLN cc_start: 0.7095 (pt0) cc_final: 0.6886 (pt0) REVERT: B 940 ASN cc_start: 0.5499 (m-40) cc_final: 0.5209 (m110) REVERT: B 988 GLN cc_start: 0.7075 (tt0) cc_final: 0.6798 (tt0) REVERT: B 993 ASN cc_start: 0.6096 (m110) cc_final: 0.5873 (m110) REVERT: B 1000 LYS cc_start: 0.8190 (tptp) cc_final: 0.7675 (mttp) REVERT: B 1085 LYS cc_start: 0.5995 (tptm) cc_final: 0.5735 (mmtt) REVERT: B 1089 ASP cc_start: 0.6904 (m-30) cc_final: 0.6618 (m-30) REVERT: B 1117 PHE cc_start: 0.5935 (m-10) cc_final: 0.5205 (t80) REVERT: B 1173 ILE cc_start: 0.7869 (mt) cc_final: 0.7608 (mp) REVERT: B 1179 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6293 (mtm-85) REVERT: B 1187 LYS cc_start: 0.7721 (mmpt) cc_final: 0.7513 (mmtm) REVERT: B 1189 LYS cc_start: 0.6330 (tppt) cc_final: 0.5834 (mtpm) REVERT: B 1237 MET cc_start: 0.8730 (mtm) cc_final: 0.8355 (mtm) REVERT: B 1256 ASP cc_start: 0.7577 (m-30) cc_final: 0.7134 (p0) outliers start: 11 outliers final: 3 residues processed: 92 average time/residue: 1.0163 time to fit residues: 97.4424 Evaluate side-chains 87 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1003 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 4501 Z= 0.483 Angle : 0.693 6.983 6081 Z= 0.370 Chirality : 0.058 0.527 670 Planarity : 0.005 0.050 772 Dihedral : 6.570 58.191 684 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.32 % Allowed : 15.23 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.01 (0.35), residues: 524 helix: -0.09 (1.06), residues: 29 sheet: -0.12 (0.37), residues: 174 loop : -1.05 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1266 HIS 0.004 0.001 HIS B1048 PHE 0.019 0.002 PHE A 516 TYR 0.018 0.002 TYR B1135 ARG 0.003 0.001 ARG B1061 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.469 Fit side-chains REVERT: A 493 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6236 (pm20) REVERT: A 513 ASN cc_start: 0.7590 (t0) cc_final: 0.7199 (t0) REVERT: A 532 GLU cc_start: 0.7619 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 581 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 988 GLN cc_start: 0.7213 (tt0) cc_final: 0.7006 (tt0) REVERT: B 1000 LYS cc_start: 0.8122 (tptp) cc_final: 0.7646 (mttp) REVERT: B 1058 ASP cc_start: 0.6284 (t70) cc_final: 0.5946 (t0) REVERT: B 1083 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7081 (mt-10) REVERT: B 1117 PHE cc_start: 0.6913 (m-10) cc_final: 0.5905 (t80) REVERT: B 1133 TYR cc_start: 0.8267 (p90) cc_final: 0.7911 (p90) REVERT: B 1179 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6428 (mtm-85) REVERT: B 1187 LYS cc_start: 0.7756 (mmpt) cc_final: 0.7550 (mmtm) REVERT: B 1189 LYS cc_start: 0.6371 (tppt) cc_final: 0.5912 (mtpm) REVERT: B 1193 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6647 (tp) REVERT: B 1210 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: B 1256 ASP cc_start: 0.7690 (m-30) cc_final: 0.7271 (p0) outliers start: 21 outliers final: 10 residues processed: 105 average time/residue: 0.9810 time to fit residues: 107.4993 Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1193 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1210 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1003 GLN B1093 ASN B1115 ASN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4501 Z= 0.226 Angle : 0.552 4.938 6081 Z= 0.299 Chirality : 0.052 0.431 670 Planarity : 0.003 0.035 772 Dihedral : 6.009 56.838 684 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.14 % Allowed : 15.84 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.37), residues: 524 helix: 1.58 (1.15), residues: 23 sheet: 0.08 (0.34), residues: 250 loop : -1.03 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1266 HIS 0.002 0.001 HIS A 494 PHE 0.014 0.001 PHE A 516 TYR 0.025 0.001 TYR B1181 ARG 0.002 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 84 time to evaluate : 0.503 Fit side-chains REVERT: A 513 ASN cc_start: 0.7567 (t0) cc_final: 0.7123 (t0) REVERT: A 532 GLU cc_start: 0.7636 (tt0) cc_final: 0.6952 (tm-30) REVERT: B 988 GLN cc_start: 0.7176 (tt0) cc_final: 0.6960 (tt0) REVERT: B 1000 LYS cc_start: 0.8131 (tptp) cc_final: 0.7655 (mttp) REVERT: B 1058 ASP cc_start: 0.6213 (t70) cc_final: 0.5870 (t0) REVERT: B 1083 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 1117 PHE cc_start: 0.6870 (m-10) cc_final: 0.5910 (t80) REVERT: B 1133 TYR cc_start: 0.8294 (p90) cc_final: 0.7903 (p90) REVERT: B 1179 ARG cc_start: 0.6975 (mtt180) cc_final: 0.6405 (mtm-85) REVERT: B 1189 LYS cc_start: 0.6421 (tppt) cc_final: 0.5960 (mtpm) REVERT: B 1256 ASP cc_start: 0.7832 (m-30) cc_final: 0.7391 (p0) outliers start: 25 outliers final: 14 residues processed: 99 average time/residue: 1.0109 time to fit residues: 104.3688 Evaluate side-chains 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1003 GLN ** B1022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1265 ASN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4501 Z= 0.258 Angle : 0.543 5.411 6081 Z= 0.296 Chirality : 0.052 0.414 670 Planarity : 0.003 0.029 772 Dihedral : 5.919 59.375 684 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.94 % Allowed : 16.87 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.36), residues: 524 helix: 1.57 (1.16), residues: 23 sheet: 0.32 (0.43), residues: 147 loop : -0.89 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1266 HIS 0.002 0.001 HIS B1048 PHE 0.016 0.002 PHE A 516 TYR 0.012 0.001 TYR B 938 ARG 0.002 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.491 Fit side-chains REVERT: A 493 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: A 513 ASN cc_start: 0.7597 (t0) cc_final: 0.7118 (t0) REVERT: A 532 GLU cc_start: 0.7646 (tt0) cc_final: 0.6968 (tm-30) REVERT: B 903 ARG cc_start: 0.6998 (mmm160) cc_final: 0.6786 (mmm160) REVERT: B 988 GLN cc_start: 0.7204 (tt0) cc_final: 0.6989 (tt0) REVERT: B 1000 LYS cc_start: 0.8157 (tptp) cc_final: 0.7680 (mttp) REVERT: B 1058 ASP cc_start: 0.6237 (t70) cc_final: 0.5891 (t0) REVERT: B 1083 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7001 (mt-10) REVERT: B 1117 PHE cc_start: 0.6806 (m-10) cc_final: 0.5859 (t80) REVERT: B 1133 TYR cc_start: 0.8368 (p90) cc_final: 0.7966 (p90) REVERT: B 1179 ARG cc_start: 0.6963 (mtt180) cc_final: 0.6385 (mtm-85) REVERT: B 1189 LYS cc_start: 0.6416 (tppt) cc_final: 0.5939 (mtpm) REVERT: B 1256 ASP cc_start: 0.7775 (m-30) cc_final: 0.7323 (p0) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 1.0142 time to fit residues: 105.7324 Evaluate side-chains 97 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B 993 ASN B1003 GLN B1093 ASN B1219 GLN ** B1270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4501 Z= 0.332 Angle : 0.591 6.144 6081 Z= 0.321 Chirality : 0.054 0.442 670 Planarity : 0.004 0.033 772 Dihedral : 6.059 59.925 684 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 5.56 % Allowed : 17.70 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.36), residues: 524 helix: -0.08 (1.07), residues: 29 sheet: 0.25 (0.42), residues: 156 loop : -0.91 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 974 HIS 0.002 0.001 HIS B1048 PHE 0.016 0.002 PHE A 516 TYR 0.015 0.002 TYR B1135 ARG 0.003 0.001 ARG B1061 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 88 time to evaluate : 0.498 Fit side-chains REVERT: A 493 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: A 513 ASN cc_start: 0.7657 (t0) cc_final: 0.7392 (m-40) REVERT: A 532 GLU cc_start: 0.7653 (tt0) cc_final: 0.6919 (tm-30) REVERT: B 903 ARG cc_start: 0.6956 (mmm160) cc_final: 0.6739 (mmm160) REVERT: B 988 GLN cc_start: 0.7279 (tt0) cc_final: 0.7039 (tt0) REVERT: B 1000 LYS cc_start: 0.8137 (tptp) cc_final: 0.7646 (mttp) REVERT: B 1058 ASP cc_start: 0.6347 (t70) cc_final: 0.5978 (t0) REVERT: B 1083 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6951 (mt-10) REVERT: B 1117 PHE cc_start: 0.6790 (m-10) cc_final: 0.5963 (t80) REVERT: B 1133 TYR cc_start: 0.8472 (p90) cc_final: 0.8082 (p90) REVERT: B 1179 ARG cc_start: 0.7004 (mtt180) cc_final: 0.6728 (mmt90) REVERT: B 1189 LYS cc_start: 0.6493 (tppt) cc_final: 0.5984 (mtpm) REVERT: B 1256 ASP cc_start: 0.7801 (m-30) cc_final: 0.7354 (p0) outliers start: 27 outliers final: 19 residues processed: 104 average time/residue: 1.0230 time to fit residues: 110.8316 Evaluate side-chains 103 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS B 899 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 971 ASN B 992 GLN B1003 GLN B1093 ASN B1219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4501 Z= 0.198 Angle : 0.538 6.209 6081 Z= 0.292 Chirality : 0.051 0.383 670 Planarity : 0.003 0.029 772 Dihedral : 5.880 59.556 684 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.32 % Allowed : 19.14 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.37), residues: 524 helix: 1.58 (1.15), residues: 23 sheet: 0.22 (0.35), residues: 226 loop : -0.91 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.003 0.001 HIS A 494 PHE 0.013 0.001 PHE A 516 TYR 0.018 0.001 TYR A 480 ARG 0.002 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.526 Fit side-chains REVERT: A 493 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: A 532 GLU cc_start: 0.7653 (tt0) cc_final: 0.6928 (tm-30) REVERT: B 903 ARG cc_start: 0.6912 (mmm160) cc_final: 0.6563 (mmm160) REVERT: B 1000 LYS cc_start: 0.8156 (tptp) cc_final: 0.7668 (mttp) REVERT: B 1003 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: B 1004 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7124 (mpt) REVERT: B 1058 ASP cc_start: 0.6283 (t70) cc_final: 0.5918 (t0) REVERT: B 1083 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6935 (mt-10) REVERT: B 1117 PHE cc_start: 0.6788 (m-10) cc_final: 0.5942 (t80) REVERT: B 1133 TYR cc_start: 0.8482 (p90) cc_final: 0.8013 (p90) REVERT: B 1179 ARG cc_start: 0.6985 (mtt180) cc_final: 0.6413 (mtm-85) REVERT: B 1189 LYS cc_start: 0.6504 (tppt) cc_final: 0.5991 (mtpm) REVERT: B 1256 ASP cc_start: 0.7749 (m-30) cc_final: 0.7299 (p0) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 1.2052 time to fit residues: 124.0174 Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1003 GLN B1093 ASN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4501 Z= 0.197 Angle : 0.523 5.767 6081 Z= 0.285 Chirality : 0.050 0.372 670 Planarity : 0.003 0.028 772 Dihedral : 5.810 58.402 684 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.12 % Allowed : 19.55 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.37), residues: 524 helix: 1.66 (1.16), residues: 23 sheet: 0.28 (0.35), residues: 226 loop : -0.84 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.003 0.001 HIS A 494 PHE 0.018 0.001 PHE A 512 TYR 0.012 0.001 TYR A 564 ARG 0.002 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.508 Fit side-chains REVERT: A 493 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6067 (pm20) REVERT: A 513 ASN cc_start: 0.7557 (t0) cc_final: 0.7299 (m-40) REVERT: A 532 GLU cc_start: 0.7669 (tt0) cc_final: 0.6919 (tm-30) REVERT: B 903 ARG cc_start: 0.6879 (mmm160) cc_final: 0.6553 (mmm160) REVERT: B 1000 LYS cc_start: 0.8141 (tptp) cc_final: 0.7659 (mttp) REVERT: B 1003 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: B 1004 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7126 (mpt) REVERT: B 1058 ASP cc_start: 0.6263 (t70) cc_final: 0.5896 (t0) REVERT: B 1083 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6934 (mt-10) REVERT: B 1117 PHE cc_start: 0.6784 (m-10) cc_final: 0.5937 (t80) REVERT: B 1133 TYR cc_start: 0.8479 (p90) cc_final: 0.8010 (p90) REVERT: B 1179 ARG cc_start: 0.6921 (mtt180) cc_final: 0.6331 (mtm-85) REVERT: B 1189 LYS cc_start: 0.6520 (tppt) cc_final: 0.6013 (mtpm) REVERT: B 1256 ASP cc_start: 0.7718 (m-30) cc_final: 0.7271 (p0) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 1.1494 time to fit residues: 113.5421 Evaluate side-chains 101 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1003 GLN B1093 ASN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1233 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4501 Z= 0.212 Angle : 0.528 5.163 6081 Z= 0.288 Chirality : 0.051 0.368 670 Planarity : 0.003 0.026 772 Dihedral : 5.792 59.467 684 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.70 % Allowed : 20.16 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.37), residues: 524 helix: 1.67 (1.16), residues: 23 sheet: 0.33 (0.36), residues: 226 loop : -0.81 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 946 HIS 0.003 0.001 HIS A 494 PHE 0.012 0.001 PHE A 516 TYR 0.010 0.001 TYR B 938 ARG 0.002 0.000 ARG A 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.499 Fit side-chains REVERT: A 493 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.6048 (pm20) REVERT: A 513 ASN cc_start: 0.7545 (t0) cc_final: 0.7295 (m-40) REVERT: A 532 GLU cc_start: 0.7668 (tt0) cc_final: 0.6921 (tm-30) REVERT: B 903 ARG cc_start: 0.6876 (mmm160) cc_final: 0.6549 (mmm160) REVERT: B 1000 LYS cc_start: 0.8143 (tptp) cc_final: 0.7659 (mttp) REVERT: B 1003 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: B 1004 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7138 (mpt) REVERT: B 1058 ASP cc_start: 0.6262 (t70) cc_final: 0.5892 (t0) REVERT: B 1083 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6943 (mt-10) REVERT: B 1117 PHE cc_start: 0.6811 (m-10) cc_final: 0.5939 (t80) REVERT: B 1133 TYR cc_start: 0.8480 (p90) cc_final: 0.8034 (p90) REVERT: B 1179 ARG cc_start: 0.6913 (mtt180) cc_final: 0.6562 (mmt90) REVERT: B 1189 LYS cc_start: 0.6519 (tppt) cc_final: 0.6011 (mtpm) REVERT: B 1256 ASP cc_start: 0.7730 (m-30) cc_final: 0.7274 (p0) outliers start: 18 outliers final: 15 residues processed: 95 average time/residue: 1.1570 time to fit residues: 114.0785 Evaluate side-chains 101 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 GLU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1003 GLN Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 HIS ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1003 GLN B1093 ASN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.171546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131066 restraints weight = 4917.812| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.24 r_work: 0.3262 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4501 Z= 0.261 Angle : 0.554 5.436 6081 Z= 0.300 Chirality : 0.052 0.381 670 Planarity : 0.003 0.024 772 Dihedral : 5.835 59.850 684 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.12 % Allowed : 19.96 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.37), residues: 524 helix: 1.67 (1.17), residues: 23 sheet: 0.35 (0.44), residues: 149 loop : -0.70 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1266 HIS 0.002 0.000 HIS A 494 PHE 0.018 0.001 PHE A 512 TYR 0.012 0.001 TYR B1135 ARG 0.002 0.000 ARG B1061 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.77 seconds wall clock time: 44 minutes 26.20 seconds (2666.20 seconds total)