Starting phenix.real_space_refine on Wed Feb 14 15:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r3q_4719/02_2024/6r3q_4719_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6130 2.51 5 N 1599 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9529 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6687 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 20, 'TRANS': 820} Chain breaks: 6 Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2842 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'peptide': 341, 'undetermined': 2} Link IDs: {'PTRANS': 13, 'TRANS': 327, None: 2} Not linked: pdbres="GLN B 390 " pdbres="GSP B 501 " Not linked: pdbres="GSP B 501 " pdbres=" MG B 502 " Chain breaks: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.60 Number of scatterers: 9529 At special positions: 0 Unit cell: (162.8, 105.006, 105.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 3 15.00 Mg 1 11.99 O 1727 8.00 N 1599 7.00 C 6130 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.7 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 55.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.725A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 136 Processing helix chain 'A' and resid 146 through 164 removed outlier: 4.378A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 220 through 236 removed outlier: 3.834A pdb=" N SER A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 280 through 335 removed outlier: 3.615A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 403 through 406 No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 414 through 433 Processing helix chain 'A' and resid 458 through 480 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.950A pdb=" N TYR A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 806 Processing helix chain 'A' and resid 818 through 843 Processing helix chain 'A' and resid 851 through 859 removed outlier: 3.529A pdb=" N TRP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 883 Proline residue: A 876 - end of helix removed outlier: 4.584A pdb=" N HIS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 906 Processing helix chain 'A' and resid 917 through 936 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 979 through 1036 removed outlier: 3.596A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1046 Processing helix chain 'A' and resid 1066 through 1068 No H-bonds generated for 'chain 'A' and resid 1066 through 1068' Processing helix chain 'A' and resid 1080 through 1098 removed outlier: 3.704A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1155 removed outlier: 3.794A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1200 Processing helix chain 'A' and resid 1211 through 1217 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 90 through 111 removed outlier: 4.374A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 157 through 165 removed outlier: 4.031A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 4.042A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.637A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 238 removed outlier: 3.615A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 235 through 238' Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.886A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.625A pdb=" N ARG B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 386 through 390 removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN A 485 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 570 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1052 through 1055 removed outlier: 3.533A pdb=" N LYS A1053 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1058 through 1065 Processing sheet with id= E, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1225 through 1232 removed outlier: 7.084A pdb=" N THR A1240 " --> pdb=" O ARG A1227 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR A1229 " --> pdb=" O MET A1238 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N MET A1238 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN A1231 " --> pdb=" O GLY A1236 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY A1236 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 44 Processing sheet with id= H, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.796A pdb=" N LEU B 289 " --> pdb=" O TYR B 360 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1897 1.32 - 1.44: 2347 1.44 - 1.57: 5380 1.57 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9735 Sorted by residual: bond pdb=" C LYS A 549 " pdb=" N VAL A 550 " ideal model delta sigma weight residual 1.332 1.286 0.046 1.73e-02 3.34e+03 6.96e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" SD MET A 469 " pdb=" CE MET A 469 " ideal model delta sigma weight residual 1.791 1.732 0.059 2.50e-02 1.60e+03 5.48e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.94e+00 ... (remaining 9730 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.92: 141 104.92 - 113.29: 5345 113.29 - 121.65: 5724 121.65 - 130.02: 1886 130.02 - 138.38: 75 Bond angle restraints: 13171 Sorted by residual: angle pdb=" N LEU A 875 " pdb=" CA LEU A 875 " pdb=" C LEU A 875 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 122.97 118.46 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 5253 15.24 - 30.48: 382 30.48 - 45.72: 127 45.72 - 60.95: 15 60.95 - 76.19: 10 Dihedral angle restraints: 5787 sinusoidal: 2329 harmonic: 3458 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 144.43 35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -148.87 -31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1308 0.109 - 0.218: 161 0.218 - 0.328: 13 0.328 - 0.437: 0 0.437 - 0.546: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL A 986 " pdb=" CA VAL A 986 " pdb=" CG1 VAL A 986 " pdb=" CG2 VAL A 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CG LEU B 99 " pdb=" CB LEU B 99 " pdb=" CD1 LEU B 99 " pdb=" CD2 LEU B 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1481 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.016 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 385 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.030 2.00e-02 2.50e+03 2.66e-02 1.24e+01 pdb=" CG PHE A 232 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 115 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.041 5.00e-02 4.00e+02 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 145 2.64 - 3.21: 8621 3.21 - 3.77: 15312 3.77 - 4.34: 19790 4.34 - 4.90: 32262 Nonbonded interactions: 76130 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.124 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.205 2.440 ... (remaining 76125 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.030 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.082 9735 Z= 0.729 Angle : 1.245 13.383 13171 Z= 0.651 Chirality : 0.072 0.546 1484 Planarity : 0.008 0.074 1655 Dihedral : 12.612 76.192 3549 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.20), residues: 1164 helix: -2.14 (0.15), residues: 684 sheet: -2.03 (0.43), residues: 136 loop : -2.85 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 918 HIS 0.016 0.003 HIS A 491 PHE 0.060 0.005 PHE A 232 TYR 0.050 0.004 TYR A 446 ARG 0.016 0.002 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7842 (t80) cc_final: 0.7457 (t80) REVERT: A 138 MET cc_start: 0.6930 (ttt) cc_final: 0.6257 (ttt) REVERT: A 152 PHE cc_start: 0.6885 (t80) cc_final: 0.6632 (t80) REVERT: A 182 LEU cc_start: 0.8690 (mp) cc_final: 0.8428 (mp) REVERT: A 333 MET cc_start: 0.8765 (mmt) cc_final: 0.8547 (mmp) REVERT: A 987 PHE cc_start: 0.8294 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1006 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6473 (mmp-170) REVERT: B 174 CYS cc_start: 0.7864 (p) cc_final: 0.7382 (p) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.2172 time to fit residues: 54.3658 Evaluate side-chains 101 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 HIS A1055 HIS A1154 ASN A1169 ASN A1231 ASN A1237 GLN B 31 GLN B 98 ASN B 112 ASN B 213 GLN B 239 ASN B 264 ASN B 357 HIS B 362 HIS B 371 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9735 Z= 0.178 Angle : 0.660 12.551 13171 Z= 0.328 Chirality : 0.043 0.173 1484 Planarity : 0.005 0.057 1655 Dihedral : 5.593 33.505 1300 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.27 % Allowed : 11.62 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.46 (0.23), residues: 1164 helix: -0.05 (0.19), residues: 675 sheet: -1.72 (0.40), residues: 147 loop : -2.27 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 130 HIS 0.004 0.001 HIS B 220 PHE 0.015 0.001 PHE A 232 TYR 0.024 0.002 TYR A1214 ARG 0.004 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7822 (t80) cc_final: 0.7606 (t80) REVERT: A 129 LEU cc_start: 0.8158 (tp) cc_final: 0.7924 (tp) REVERT: A 145 MET cc_start: 0.6764 (mmm) cc_final: 0.6273 (mmt) REVERT: A 181 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 232 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8481 (m-10) REVERT: A 896 MET cc_start: 0.8002 (mtm) cc_final: 0.7618 (mtp) REVERT: A 1002 GLU cc_start: 0.7640 (pp20) cc_final: 0.7434 (tm-30) REVERT: A 1006 ARG cc_start: 0.6842 (ttm-80) cc_final: 0.6512 (mmp-170) outliers start: 34 outliers final: 14 residues processed: 165 average time/residue: 0.1717 time to fit residues: 42.6160 Evaluate side-chains 125 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9735 Z= 0.218 Angle : 0.652 13.747 13171 Z= 0.321 Chirality : 0.042 0.167 1484 Planarity : 0.004 0.054 1655 Dihedral : 5.131 32.307 1298 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.94 % Allowed : 13.45 % Favored : 82.61 % 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: -0.56 (0.24), residues: 1164 helix: 0.75 (0.20), residues: 681 sheet: -1.56 (0.40), residues: 145 loop : -2.05 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.019 0.002 PHE A 385 TYR 0.020 0.002 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 112 time to evaluate : 1.176 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7343 (ttt) cc_final: 0.7132 (ttt) REVERT: A 145 MET cc_start: 0.6704 (mmm) cc_final: 0.6391 (mmt) REVERT: A 181 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 232 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: A 537 LYS cc_start: 0.8418 (ptpt) cc_final: 0.8085 (ptpp) REVERT: A 784 THR cc_start: 0.8298 (m) cc_final: 0.7988 (t) REVERT: A 1002 GLU cc_start: 0.7693 (pp20) cc_final: 0.7462 (tm-30) REVERT: A 1006 ARG cc_start: 0.6907 (ttm-80) cc_final: 0.6519 (mmp-170) REVERT: B 99 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9317 (tp) outliers start: 41 outliers final: 26 residues processed: 144 average time/residue: 0.1707 time to fit residues: 37.3226 Evaluate side-chains 132 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9735 Z= 0.216 Angle : 0.644 13.829 13171 Z= 0.313 Chirality : 0.042 0.167 1484 Planarity : 0.004 0.053 1655 Dihedral : 4.907 30.587 1298 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.09 % Allowed : 12.68 % Favored : 82.23 % 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: -0.10 (0.25), residues: 1164 helix: 1.18 (0.20), residues: 680 sheet: -1.40 (0.39), residues: 144 loop : -1.99 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.004 0.001 HIS B 220 PHE 0.015 0.001 PHE A 232 TYR 0.019 0.001 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 114 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.6757 (mmm) cc_final: 0.6512 (mmt) REVERT: A 181 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 232 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: A 784 THR cc_start: 0.8224 (m) cc_final: 0.7934 (t) REVERT: A 1002 GLU cc_start: 0.7749 (pp20) cc_final: 0.7486 (tm-30) REVERT: A 1006 ARG cc_start: 0.6903 (ttm-80) cc_final: 0.6507 (mmp-170) REVERT: B 99 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9316 (tp) outliers start: 53 outliers final: 33 residues processed: 156 average time/residue: 0.1726 time to fit residues: 40.7936 Evaluate side-chains 140 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9735 Z= 0.236 Angle : 0.644 14.728 13171 Z= 0.315 Chirality : 0.042 0.173 1484 Planarity : 0.004 0.051 1655 Dihedral : 4.840 30.245 1298 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.90 % Allowed : 14.31 % Favored : 80.79 % 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: 0.12 (0.25), residues: 1164 helix: 1.33 (0.20), residues: 680 sheet: -1.23 (0.39), residues: 147 loop : -1.87 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.016 0.002 PHE A 232 TYR 0.019 0.002 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 110 time to evaluate : 1.184 Fit side-chains REVERT: A 122 TYR cc_start: 0.7886 (t80) cc_final: 0.7568 (t80) REVERT: A 145 MET cc_start: 0.6680 (mmm) cc_final: 0.6423 (mmt) REVERT: A 181 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8062 (mm) REVERT: A 232 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8591 (m-10) REVERT: A 1002 GLU cc_start: 0.7819 (pp20) cc_final: 0.7561 (tm-30) REVERT: A 1006 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6538 (mmp-170) REVERT: B 99 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9325 (tp) outliers start: 51 outliers final: 37 residues processed: 150 average time/residue: 0.1702 time to fit residues: 39.4936 Evaluate side-chains 147 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 354 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9735 Z= 0.187 Angle : 0.638 15.118 13171 Z= 0.305 Chirality : 0.042 0.184 1484 Planarity : 0.004 0.055 1655 Dihedral : 4.729 29.213 1298 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.61 % Allowed : 16.71 % Favored : 78.67 % 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: 0.38 (0.25), residues: 1164 helix: 1.52 (0.20), residues: 679 sheet: -1.06 (0.40), residues: 147 loop : -1.73 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.006 0.001 HIS A 530 PHE 0.015 0.001 PHE A 184 TYR 0.018 0.001 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 114 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7852 (t80) cc_final: 0.7508 (t80) REVERT: A 138 MET cc_start: 0.7417 (ttt) cc_final: 0.7120 (ttm) REVERT: A 145 MET cc_start: 0.6699 (mmm) cc_final: 0.6436 (mmt) REVERT: A 181 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 232 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: A 464 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 465 MET cc_start: 0.9045 (tpp) cc_final: 0.8836 (tpp) REVERT: A 1006 ARG cc_start: 0.6889 (ttm-80) cc_final: 0.6493 (mmp-170) REVERT: B 99 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9337 (tp) REVERT: B 266 LEU cc_start: 0.9070 (tp) cc_final: 0.8768 (tt) outliers start: 48 outliers final: 33 residues processed: 149 average time/residue: 0.1807 time to fit residues: 41.2723 Evaluate side-chains 147 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 0.0370 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9735 Z= 0.150 Angle : 0.631 15.867 13171 Z= 0.295 Chirality : 0.041 0.205 1484 Planarity : 0.004 0.055 1655 Dihedral : 4.403 26.300 1297 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.65 % Allowed : 17.96 % Favored : 78.39 % 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: 0.77 (0.26), residues: 1164 helix: 1.75 (0.20), residues: 675 sheet: -0.86 (0.40), residues: 144 loop : -1.38 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 995 HIS 0.004 0.001 HIS A 530 PHE 0.013 0.001 PHE A 184 TYR 0.016 0.001 TYR A 446 ARG 0.003 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7427 (ttt) cc_final: 0.7172 (ttm) REVERT: A 145 MET cc_start: 0.6681 (mmm) cc_final: 0.6444 (mmt) REVERT: A 181 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (mm) REVERT: A 232 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: A 465 MET cc_start: 0.9030 (tpp) cc_final: 0.8825 (tpp) REVERT: A 537 LYS cc_start: 0.8457 (ptpp) cc_final: 0.8072 (ptpp) REVERT: A 896 MET cc_start: 0.8199 (mtp) cc_final: 0.7519 (mtp) REVERT: A 1002 GLU cc_start: 0.7212 (tp30) cc_final: 0.6785 (tp30) REVERT: A 1006 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.5070 (tpt170) REVERT: A 1145 GLU cc_start: 0.7497 (tp30) cc_final: 0.7272 (tp30) REVERT: B 99 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9354 (tp) outliers start: 38 outliers final: 28 residues processed: 158 average time/residue: 0.1741 time to fit residues: 42.1576 Evaluate side-chains 145 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 0.0030 chunk 77 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9735 Z= 0.163 Angle : 0.640 15.773 13171 Z= 0.300 Chirality : 0.042 0.177 1484 Planarity : 0.004 0.053 1655 Dihedral : 4.313 26.232 1297 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.75 % Allowed : 18.73 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1164 helix: 1.85 (0.20), residues: 675 sheet: -0.68 (0.41), residues: 144 loop : -1.31 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1159 HIS 0.003 0.001 HIS A 530 PHE 0.027 0.001 PHE A 125 TYR 0.018 0.001 TYR A 446 ARG 0.002 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7323 (ttt) cc_final: 0.7032 (ttm) REVERT: A 145 MET cc_start: 0.6699 (mmm) cc_final: 0.6457 (mmt) REVERT: A 181 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8109 (mm) REVERT: A 232 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: A 537 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8188 (ptpp) REVERT: A 896 MET cc_start: 0.8028 (mtp) cc_final: 0.6682 (mtp) REVERT: A 1002 GLU cc_start: 0.7308 (tp30) cc_final: 0.6765 (tp30) REVERT: A 1006 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.5104 (tpt170) REVERT: A 1145 GLU cc_start: 0.7510 (tp30) cc_final: 0.7303 (tp30) REVERT: B 99 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9356 (tp) outliers start: 39 outliers final: 29 residues processed: 151 average time/residue: 0.2066 time to fit residues: 47.4259 Evaluate side-chains 144 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9735 Z= 0.194 Angle : 0.673 16.520 13171 Z= 0.315 Chirality : 0.043 0.167 1484 Planarity : 0.004 0.044 1655 Dihedral : 4.339 26.872 1297 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.36 % Allowed : 19.21 % Favored : 77.43 % 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: 0.81 (0.25), residues: 1164 helix: 1.76 (0.20), residues: 680 sheet: -0.59 (0.41), residues: 144 loop : -1.48 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.022 0.001 PHE A 125 TYR 0.019 0.001 TYR A 446 ARG 0.003 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.183 Fit side-chains REVERT: A 138 MET cc_start: 0.7303 (ttt) cc_final: 0.7016 (ttm) REVERT: A 145 MET cc_start: 0.6679 (mmm) cc_final: 0.6461 (mmt) REVERT: A 232 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8493 (m-10) REVERT: A 537 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8231 (ptpp) REVERT: A 1002 GLU cc_start: 0.7343 (tp30) cc_final: 0.6788 (tp30) REVERT: A 1006 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.5078 (tpt170) REVERT: A 1145 GLU cc_start: 0.7464 (tp30) cc_final: 0.7105 (tp30) REVERT: B 99 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9356 (tp) outliers start: 35 outliers final: 30 residues processed: 140 average time/residue: 0.1690 time to fit residues: 36.0448 Evaluate side-chains 139 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9735 Z= 0.205 Angle : 0.672 15.047 13171 Z= 0.318 Chirality : 0.043 0.219 1484 Planarity : 0.004 0.043 1655 Dihedral : 4.369 26.567 1297 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.17 % Allowed : 19.31 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1164 helix: 1.71 (0.20), residues: 681 sheet: -0.58 (0.41), residues: 144 loop : -1.47 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.021 0.001 PHE A 125 TYR 0.020 0.001 TYR A 446 ARG 0.003 0.000 ARG A 920 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.262 Fit side-chains REVERT: A 138 MET cc_start: 0.7298 (ttt) cc_final: 0.6980 (ttm) REVERT: A 145 MET cc_start: 0.6627 (mmm) cc_final: 0.6345 (mmm) REVERT: A 232 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: A 537 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8275 (ptpp) REVERT: A 1002 GLU cc_start: 0.7344 (tp30) cc_final: 0.6828 (tp30) REVERT: A 1006 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.5075 (tpt170) REVERT: A 1145 GLU cc_start: 0.7316 (tp30) cc_final: 0.6969 (tp30) REVERT: B 99 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9347 (tp) REVERT: B 230 GLU cc_start: 0.8131 (mp0) cc_final: 0.7848 (mp0) outliers start: 33 outliers final: 30 residues processed: 137 average time/residue: 0.2027 time to fit residues: 43.5378 Evaluate side-chains 142 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 447 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 0.0870 chunk 86 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 96 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.107440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.086818 restraints weight = 26001.941| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.04 r_work: 0.3364 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9735 Z= 0.155 Angle : 0.655 13.377 13171 Z= 0.304 Chirality : 0.042 0.195 1484 Planarity : 0.003 0.042 1655 Dihedral : 4.191 24.542 1297 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.69 % Allowed : 20.08 % Favored : 77.23 % 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: 1.05 (0.26), residues: 1164 helix: 1.87 (0.20), residues: 676 sheet: -0.53 (0.43), residues: 132 loop : -1.10 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 130 HIS 0.003 0.000 HIS B 357 PHE 0.020 0.001 PHE A 125 TYR 0.016 0.001 TYR A 446 ARG 0.002 0.000 ARG A 920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.02 seconds wall clock time: 40 minutes 32.56 seconds (2432.56 seconds total)