Starting phenix.real_space_refine on Mon Mar 11 01:26:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pdf_13336/03_2024/7pdf_13336_updated.pdb" } resolution = 3.8 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= 0.002 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 46 5.16 5 C 4055 2.51 5 N 1107 2.21 5 O 1215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1030": "OD1" <-> "OD2" Residue "A TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A PHE 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1190": "OD1" <-> "OD2" Residue "A ARG 1197": "NH1" <-> "NH2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "A PHE 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 188": "OD1" <-> "OD2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 240": "OD1" <-> "OD2" Residue "B PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6427 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3585 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 443} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 4.02, per 1000 atoms: 0.63 Number of scatterers: 6427 At special positions: 0 Unit cell: (109.35, 105.3, 102.06, 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 46 16.00 P 3 15.00 Mg 1 11.99 O 1215 8.00 N 1107 7.00 C 4055 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: 2.44 Conformation dependent library (CDL) restraints added in 1.3 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 7 sheets defined 43.7% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 321 through 336 Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 353 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 477 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.994A pdb=" N TYR A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1036 Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 3.758A pdb=" N LYS A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) 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: 3.699A pdb=" N ASP A1092 " --> pdb=" O GLU A1088 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1155 removed outlier: 3.976A pdb=" N HIS A1135 " --> pdb=" O PRO A1132 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1136 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A1139 " --> pdb=" O LEU A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1200 Processing helix chain 'A' and resid 1211 through 1220 removed outlier: 4.089A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 90 through 111 removed outlier: 4.588A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.818A pdb=" N PHE B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.623A pdb=" N ARG B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.650A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' 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 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 332 through 348 removed outlier: 4.155A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.854A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 387 through 390 Processing sheet with id= B, first strand: chain 'A' and resid 486 through 493 removed outlier: 3.771A pdb=" N SER A 439 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL A 448 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS A 437 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 529 through 531 Processing sheet with id= D, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id= E, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 7.214A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.253A 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: 6.981A pdb=" N THR A1240 " --> pdb=" O ARG A1227 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A1229 " --> pdb=" O MET A1238 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N MET A1238 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN A1231 " --> pdb=" O GLY A1236 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY A1236 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 243 through 246 removed outlier: 7.307A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 666 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: 1.70 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1988 1.33 - 1.45: 969 1.45 - 1.57: 3514 1.57 - 1.69: 5 1.69 - 1.81: 72 Bond restraints: 6548 Sorted by residual: bond pdb=" CB GLU A1088 " pdb=" CG GLU A1088 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.53e+00 bond pdb=" CB GLN B 59 " pdb=" CG GLN B 59 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CG1 ILE B 288 " pdb=" CD1 ILE B 288 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 2.02e+00 bond pdb=" CB TRP A1188 " pdb=" CG TRP A1188 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.77e+00 ... (remaining 6543 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.82: 86 104.82 - 112.13: 3209 112.13 - 119.44: 2236 119.44 - 126.75: 3232 126.75 - 134.06: 67 Bond angle restraints: 8830 Sorted by residual: angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 123.16 118.62 4.54 1.06e+00 8.90e-01 1.83e+01 angle pdb=" C TYR A 445 " pdb=" N TYR A 446 " pdb=" CA TYR A 446 " ideal model delta sigma weight residual 121.75 115.52 6.23 1.73e+00 3.34e-01 1.30e+01 angle pdb=" N ILE A1178 " pdb=" CA ILE A1178 " pdb=" C ILE A1178 " ideal model delta sigma weight residual 110.74 113.98 -3.24 9.10e-01 1.21e+00 1.27e+01 angle pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sigma weight residual 116.30 128.21 -11.91 3.50e+00 8.16e-02 1.16e+01 angle pdb=" C1' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C3' GSP B 501 " ideal model delta sigma weight residual 111.00 102.48 8.52 3.00e+00 1.11e-01 8.07e+00 ... (remaining 8825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 3469 17.01 - 34.02: 398 34.02 - 51.03: 75 51.03 - 68.05: 10 68.05 - 85.06: 5 Dihedral angle restraints: 3957 sinusoidal: 1643 harmonic: 2314 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 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA SER A 511 " pdb=" C SER A 511 " pdb=" N ASN A 512 " pdb=" CA ASN A 512 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA VAL A1177 " pdb=" C VAL A1177 " pdb=" N ILE A1178 " pdb=" CA ILE A1178 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 3954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 540 0.037 - 0.073: 293 0.073 - 0.110: 102 0.110 - 0.146: 21 0.146 - 0.183: 3 Chirality restraints: 959 Sorted by residual: chirality pdb=" C2' GSP B 501 " pdb=" C1' GSP B 501 " pdb=" C3' GSP B 501 " pdb=" O2' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C3' GSP B 501 " pdb=" C2' GSP B 501 " pdb=" C4' GSP B 501 " pdb=" O3' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB ILE B 235 " pdb=" CA ILE B 235 " pdb=" CG1 ILE B 235 " pdb=" CG2 ILE B 235 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 956 not shown) Planarity restraints: 1140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A1038 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.006 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE A 385 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.006 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=" C VAL B 114 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 115 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.020 5.00e-02 4.00e+02 ... (remaining 1137 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 72 2.49 - 3.09: 5050 3.09 - 3.69: 10061 3.69 - 4.30: 14424 4.30 - 4.90: 23477 Nonbonded interactions: 53084 Sorted by model distance: nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 1.885 2.170 nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.916 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.074 2.440 nonbonded pdb=" OE2 GLU A1211 " pdb=" NH2 ARG A1215 " model vdw 2.142 2.520 nonbonded pdb=" O1B GSP B 501 " pdb="MG MG B 502 " model vdw 2.151 2.170 ... (remaining 53079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 6.130 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.370 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.008 0.055 6548 Z= 0.532 Angle : 0.829 11.913 8830 Z= 0.465 Chirality : 0.048 0.183 959 Planarity : 0.004 0.047 1140 Dihedral : 14.632 85.056 2463 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.29 % Allowed : 12.36 % Favored : 87.36 % 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: -4.24 (0.24), residues: 782 helix: -2.27 (0.21), residues: 368 sheet: -2.71 (0.40), residues: 121 loop : -3.38 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 277 HIS 0.010 0.002 HIS B 220 PHE 0.025 0.002 PHE A 385 TYR 0.020 0.002 TYR A1083 ARG 0.006 0.001 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 MET cc_start: 0.8712 (tpp) cc_final: 0.8231 (mmt) REVERT: A 413 HIS cc_start: 0.8168 (t70) cc_final: 0.7753 (t-90) REVERT: A 1094 ASP cc_start: 0.8101 (m-30) cc_final: 0.7700 (m-30) REVERT: A 1106 GLU cc_start: 0.8256 (mp0) cc_final: 0.7773 (mp0) REVERT: A 1136 LEU cc_start: 0.9520 (mt) cc_final: 0.9212 (mt) REVERT: A 1157 MET cc_start: 0.8314 (tpp) cc_final: 0.7724 (tpp) REVERT: B 151 LYS cc_start: 0.7686 (mmpt) cc_final: 0.7471 (mmtt) outliers start: 2 outliers final: 2 residues processed: 125 average time/residue: 0.2383 time to fit residues: 37.7622 Evaluate side-chains 90 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 HIS A 389 GLN A 420 ASN A 458 HIS A1040 HIS B 41 HIS B 64 HIS B 98 ASN B 136 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 271 ASN B 362 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.183 Angle : 0.585 8.525 8830 Z= 0.304 Chirality : 0.042 0.133 959 Planarity : 0.004 0.049 1140 Dihedral : 5.358 49.228 884 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.44 % Allowed : 16.24 % Favored : 81.32 % 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: -2.63 (0.27), residues: 782 helix: -0.77 (0.25), residues: 367 sheet: -2.49 (0.40), residues: 123 loop : -2.53 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.003 0.001 HIS B 220 PHE 0.009 0.001 PHE A1168 TYR 0.013 0.001 TYR B 163 ARG 0.003 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8029 (t70) cc_final: 0.7593 (t-90) REVERT: A 464 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 1039 TYR cc_start: 0.7800 (t80) cc_final: 0.7492 (t80) REVERT: A 1094 ASP cc_start: 0.8131 (m-30) cc_final: 0.7696 (m-30) REVERT: A 1136 LEU cc_start: 0.9304 (mt) cc_final: 0.9083 (mt) REVERT: A 1157 MET cc_start: 0.8176 (tpp) cc_final: 0.7511 (tpp) REVERT: B 194 ASP cc_start: 0.8449 (p0) cc_final: 0.8153 (p0) outliers start: 17 outliers final: 8 residues processed: 129 average time/residue: 0.1738 time to fit residues: 30.4006 Evaluate side-chains 98 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.5980 chunk 22 optimal weight: 0.0370 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.170 Angle : 0.578 9.417 8830 Z= 0.296 Chirality : 0.042 0.146 959 Planarity : 0.004 0.046 1140 Dihedral : 4.971 46.801 884 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.87 % Allowed : 20.40 % Favored : 77.73 % 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: -1.96 (0.28), residues: 782 helix: -0.27 (0.26), residues: 369 sheet: -2.28 (0.40), residues: 125 loop : -2.06 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1159 HIS 0.004 0.001 HIS B 149 PHE 0.014 0.001 PHE B 140 TYR 0.015 0.001 TYR A1214 ARG 0.002 0.000 ARG A1026 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8044 (t70) cc_final: 0.7623 (t-90) REVERT: A 457 ASP cc_start: 0.7236 (p0) cc_final: 0.6981 (p0) REVERT: A 1039 TYR cc_start: 0.7786 (t80) cc_final: 0.7424 (t80) REVERT: A 1094 ASP cc_start: 0.8115 (m-30) cc_final: 0.7758 (m-30) REVERT: A 1136 LEU cc_start: 0.9270 (mt) cc_final: 0.9027 (mt) REVERT: A 1157 MET cc_start: 0.8177 (tpp) cc_final: 0.7536 (tpp) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.1614 time to fit residues: 26.4947 Evaluate side-chains 98 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 379 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 0.0370 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 HIS A1055 HIS ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6548 Z= 0.151 Angle : 0.552 9.865 8830 Z= 0.280 Chirality : 0.041 0.147 959 Planarity : 0.003 0.048 1140 Dihedral : 4.710 47.159 882 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.30 % Allowed : 21.84 % Favored : 75.86 % 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: -1.60 (0.29), residues: 782 helix: 0.07 (0.27), residues: 369 sheet: -2.22 (0.39), residues: 131 loop : -1.85 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.011 0.001 HIS B 387 PHE 0.011 0.001 PHE A1168 TYR 0.012 0.001 TYR A 445 ARG 0.004 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8143 (pp20) cc_final: 0.7554 (tm-30) REVERT: A 413 HIS cc_start: 0.8015 (t70) cc_final: 0.7529 (t-90) REVERT: A 457 ASP cc_start: 0.7357 (p0) cc_final: 0.7084 (p0) REVERT: A 1039 TYR cc_start: 0.7768 (t80) cc_final: 0.7354 (t80) REVERT: A 1094 ASP cc_start: 0.8111 (m-30) cc_final: 0.7738 (m-30) REVERT: A 1157 MET cc_start: 0.8140 (tpp) cc_final: 0.7534 (tpp) REVERT: B 59 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7982 (tp40) REVERT: B 374 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7618 (ptp-170) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.1644 time to fit residues: 28.5309 Evaluate side-chains 113 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 98 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6548 Z= 0.206 Angle : 0.575 10.604 8830 Z= 0.295 Chirality : 0.042 0.155 959 Planarity : 0.003 0.049 1140 Dihedral : 4.719 47.257 882 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.30 % Allowed : 22.84 % Favored : 74.86 % 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: -1.50 (0.29), residues: 782 helix: 0.11 (0.27), residues: 370 sheet: -2.00 (0.38), residues: 142 loop : -1.82 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.010 0.001 HIS B 387 PHE 0.015 0.001 PHE A1168 TYR 0.015 0.001 TYR A1214 ARG 0.002 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8063 (t70) cc_final: 0.7583 (t-90) REVERT: A 1039 TYR cc_start: 0.7803 (t80) cc_final: 0.7525 (t80) REVERT: A 1094 ASP cc_start: 0.8092 (m-30) cc_final: 0.7813 (m-30) REVERT: A 1157 MET cc_start: 0.8245 (tpp) cc_final: 0.7521 (tpp) REVERT: B 59 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7880 (tp40) REVERT: B 374 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7625 (ptp-170) outliers start: 16 outliers final: 12 residues processed: 110 average time/residue: 0.1430 time to fit residues: 22.4758 Evaluate side-chains 105 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1183 LEU Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 6 optimal weight: 0.0020 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6548 Z= 0.165 Angle : 0.560 11.067 8830 Z= 0.286 Chirality : 0.041 0.139 959 Planarity : 0.003 0.049 1140 Dihedral : 4.615 47.423 882 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.30 % Allowed : 23.42 % Favored : 74.28 % 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: -1.32 (0.29), residues: 782 helix: 0.22 (0.27), residues: 370 sheet: -1.91 (0.39), residues: 142 loop : -1.67 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.009 0.001 HIS B 387 PHE 0.015 0.001 PHE A1168 TYR 0.016 0.001 TYR A1214 ARG 0.002 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8050 (t70) cc_final: 0.7561 (t-90) REVERT: A 1039 TYR cc_start: 0.7941 (t80) cc_final: 0.7467 (t80) REVERT: A 1094 ASP cc_start: 0.8062 (m-30) cc_final: 0.7753 (m-30) REVERT: A 1157 MET cc_start: 0.8166 (tpp) cc_final: 0.7492 (tpp) REVERT: B 59 GLN cc_start: 0.7968 (tp-100) cc_final: 0.7744 (tp40) REVERT: B 125 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7623 (pt0) REVERT: B 374 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7622 (ptp-170) outliers start: 16 outliers final: 14 residues processed: 122 average time/residue: 0.1518 time to fit residues: 26.0143 Evaluate side-chains 112 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.0040 chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 0.0060 chunk 14 optimal weight: 0.8980 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1137 GLN ** 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: 0.8032 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6548 Z= 0.160 Angle : 0.563 11.805 8830 Z= 0.286 Chirality : 0.041 0.140 959 Planarity : 0.003 0.048 1140 Dihedral : 4.500 47.685 882 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.16 % Allowed : 23.56 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.29), residues: 782 helix: 0.31 (0.27), residues: 370 sheet: -1.86 (0.38), residues: 142 loop : -1.56 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1159 HIS 0.008 0.001 HIS B 387 PHE 0.013 0.001 PHE A1168 TYR 0.016 0.001 TYR A1214 ARG 0.001 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8096 (t70) cc_final: 0.7564 (t-90) REVERT: A 457 ASP cc_start: 0.7280 (p0) cc_final: 0.7011 (p0) REVERT: A 545 MET cc_start: 0.7141 (ppp) cc_final: 0.6925 (tpt) REVERT: A 1039 TYR cc_start: 0.7931 (t80) cc_final: 0.7425 (t80) REVERT: A 1094 ASP cc_start: 0.8083 (m-30) cc_final: 0.7782 (m-30) REVERT: A 1137 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: A 1157 MET cc_start: 0.8173 (tpp) cc_final: 0.7491 (tpp) REVERT: B 59 GLN cc_start: 0.7995 (tp-100) cc_final: 0.7759 (tp40) REVERT: B 125 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7690 (pt0) REVERT: B 374 ARG cc_start: 0.7791 (mtt180) cc_final: 0.7582 (ptp-170) outliers start: 15 outliers final: 11 residues processed: 117 average time/residue: 0.1690 time to fit residues: 27.4156 Evaluate side-chains 111 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.8980 chunk 48 optimal weight: 0.0270 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6548 Z= 0.219 Angle : 0.597 12.438 8830 Z= 0.304 Chirality : 0.042 0.210 959 Planarity : 0.003 0.047 1140 Dihedral : 4.583 47.606 882 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.30 % Allowed : 24.28 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 782 helix: 0.29 (0.27), residues: 370 sheet: -1.72 (0.38), residues: 148 loop : -1.55 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1159 HIS 0.007 0.001 HIS B 387 PHE 0.021 0.001 PHE B 376 TYR 0.018 0.001 TYR A1214 ARG 0.002 0.000 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8072 (t70) cc_final: 0.7567 (t-90) REVERT: A 1039 TYR cc_start: 0.7940 (t80) cc_final: 0.7513 (t80) REVERT: A 1094 ASP cc_start: 0.8107 (m-30) cc_final: 0.7809 (m-30) REVERT: A 1157 MET cc_start: 0.8248 (tpp) cc_final: 0.7491 (tpp) REVERT: B 59 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7680 (tp40) outliers start: 16 outliers final: 14 residues processed: 115 average time/residue: 0.1598 time to fit residues: 25.5334 Evaluate side-chains 109 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1174 THR Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6548 Z= 0.186 Angle : 0.608 12.734 8830 Z= 0.307 Chirality : 0.042 0.266 959 Planarity : 0.003 0.047 1140 Dihedral : 4.504 44.773 882 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.16 % Allowed : 24.86 % Favored : 72.99 % 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: -1.06 (0.29), residues: 782 helix: 0.40 (0.27), residues: 367 sheet: -1.66 (0.38), residues: 147 loop : -1.52 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.008 0.001 HIS B 387 PHE 0.011 0.001 PHE A1168 TYR 0.020 0.001 TYR A1214 ARG 0.003 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8047 (t70) cc_final: 0.7559 (t-90) REVERT: A 457 ASP cc_start: 0.7367 (p0) cc_final: 0.7107 (p0) REVERT: A 1039 TYR cc_start: 0.7953 (t80) cc_final: 0.7539 (t80) REVERT: A 1094 ASP cc_start: 0.8069 (m-30) cc_final: 0.7786 (m-30) REVERT: A 1157 MET cc_start: 0.8179 (tpp) cc_final: 0.7467 (tpp) REVERT: B 59 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7776 (tp40) REVERT: B 125 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7666 (pt0) REVERT: B 374 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7589 (ptp-170) outliers start: 15 outliers final: 12 residues processed: 117 average time/residue: 0.1622 time to fit residues: 26.5505 Evaluate side-chains 112 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 364 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.0980 chunk 72 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1044 GLN A1137 GLN ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 6548 Z= 0.167 Angle : 0.598 13.011 8830 Z= 0.301 Chirality : 0.042 0.187 959 Planarity : 0.003 0.043 1140 Dihedral : 4.377 46.969 882 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.58 % Allowed : 25.57 % Favored : 72.84 % 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: -0.89 (0.30), residues: 782 helix: 0.51 (0.27), residues: 364 sheet: -1.81 (0.38), residues: 143 loop : -1.23 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1159 HIS 0.009 0.001 HIS B 387 PHE 0.019 0.001 PHE B 178 TYR 0.022 0.001 TYR A1214 ARG 0.004 0.000 ARG B 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 HIS cc_start: 0.8025 (t70) cc_final: 0.7487 (t-90) REVERT: A 457 ASP cc_start: 0.7330 (p0) cc_final: 0.7080 (p0) REVERT: A 1039 TYR cc_start: 0.7932 (t80) cc_final: 0.7521 (t80) REVERT: A 1137 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8633 (tm-30) REVERT: A 1157 MET cc_start: 0.8124 (tpp) cc_final: 0.7451 (tpp) REVERT: B 59 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7725 (tp40) REVERT: B 125 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7620 (pt0) REVERT: B 376 PHE cc_start: 0.7810 (t80) cc_final: 0.7233 (t80) outliers start: 11 outliers final: 7 residues processed: 114 average time/residue: 0.1484 time to fit residues: 23.8551 Evaluate side-chains 108 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ASN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1097 LEU Chi-restraints excluded: chain A residue 1110 THR Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain B residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.097316 restraints weight = 14326.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099967 restraints weight = 8258.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.101757 restraints weight = 5828.238| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6548 Z= 0.189 Angle : 0.629 13.272 8830 Z= 0.312 Chirality : 0.043 0.323 959 Planarity : 0.003 0.043 1140 Dihedral : 4.381 45.775 882 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.15 % Allowed : 26.58 % Favored : 72.27 % 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: -0.91 (0.29), residues: 782 helix: 0.43 (0.27), residues: 367 sheet: -1.60 (0.39), residues: 143 loop : -1.30 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1159 HIS 0.008 0.001 HIS B 387 PHE 0.042 0.002 PHE A1142 TYR 0.023 0.001 TYR A1214 ARG 0.004 0.000 ARG B 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.45 seconds wall clock time: 32 minutes 16.04 seconds (1936.04 seconds total)