Starting phenix.real_space_refine on Thu Feb 15 15:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a69_11667/02_2024/7a69_11667_updated.pdb" } resolution = 3.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8175 2.51 5 N 2090 2.21 5 O 2322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ARG 798": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1024": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1211": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A ARG 1233": "NH1" <-> "NH2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 284 Unusual residues: {'CLR': 8, 'R1Q': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 7.01, per 1000 atoms: 0.55 Number of scatterers: 12637 At special positions: 0 Unit cell: (102.48, 208.32, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2322 8.00 N 2090 7.00 C 8175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 95 " distance=2.05 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.04 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: 5.23 Conformation dependent library (CDL) restraints added in 2.5 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 15 sheets defined 46.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 45 through 80 removed outlier: 3.550A pdb=" N VAL A 52 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 3.752A pdb=" N ASP A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 156 Processing helix chain 'A' and resid 162 through 165 No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.957A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.754A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 236 Processing helix chain 'A' and resid 241 through 259 removed outlier: 4.949A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 323 removed outlier: 3.666A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 370 removed outlier: 3.826A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.528A pdb=" N GLU A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.622A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 533 through 547 removed outlier: 4.377A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 700 through 704 removed outlier: 4.008A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 700 through 704' Processing helix chain 'A' and resid 708 through 738 removed outlier: 4.583A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix Processing helix chain 'A' and resid 745 through 798 Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 812 through 853 removed outlier: 4.526A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.794A pdb=" N ALA A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 880 Processing helix chain 'A' and resid 887 through 902 removed outlier: 4.473A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 4.032A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 965 removed outlier: 4.194A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.804A pdb=" N ILE A 940 " --> pdb=" O HIS A 936 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 981 Processing helix chain 'A' and resid 986 through 994 Processing helix chain 'A' and resid 999 through 1013 Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.749A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 removed outlier: 3.934A pdb=" N TYR A1133 " --> pdb=" O GLU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1159 Processing helix chain 'A' and resid 1171 through 1173 No H-bonds generated for 'chain 'A' and resid 1171 through 1173' Processing helix chain 'A' and resid 1178 through 1192 removed outlier: 3.579A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1222 removed outlier: 3.823A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 removed outlier: 3.890A pdb=" N GLN A1238 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing sheet with id= A, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.897A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 450 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 608 removed outlier: 6.494A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 Processing sheet with id= D, first strand: chain 'A' and resid 1250 through 1256 removed outlier: 7.084A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS A1254 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A1243 " --> pdb=" O HIS A1254 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A1068 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A1114 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N ASP A1200 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A1116 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.264A pdb=" N LYS B 108 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 13 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU B 110 " --> pdb=" O VAL B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 18 through 22 Processing sheet with id= G, first strand: chain 'B' and resid 89 through 95 Processing sheet with id= H, first strand: chain 'B' and resid 119 through 123 Processing sheet with id= I, first strand: chain 'B' and resid 153 through 155 removed outlier: 4.343A pdb=" N TRP B 153 " --> pdb=" O GLN B 161 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 196 through 201 Processing sheet with id= K, first strand: chain 'C' and resid 2 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 112 through 114 removed outlier: 5.781A pdb=" N ARG C 37 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TRP C 46 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.513A pdb=" N LEU C 129 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C 183 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.369A pdb=" N ILE C 198 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 174 through 176 642 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 5.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2018 1.31 - 1.44: 3412 1.44 - 1.57: 7369 1.57 - 1.70: 33 1.70 - 1.83: 83 Bond restraints: 12915 Sorted by residual: bond pdb=" C50 R1Q A1400 " pdb=" C51 R1Q A1400 " ideal model delta sigma weight residual 1.116 1.604 -0.488 2.00e-02 2.50e+03 5.94e+02 bond pdb=" C53 R1Q A1400 " pdb=" N49 R1Q A1400 " ideal model delta sigma weight residual 1.020 1.419 -0.399 2.00e-02 2.50e+03 3.98e+02 bond pdb=" C43 R1Q A1400 " pdb=" C53 R1Q A1400 " ideal model delta sigma weight residual 1.220 1.525 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C48 R1Q A1400 " pdb=" N49 R1Q A1400 " ideal model delta sigma weight residual 1.629 1.324 0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C47 R1Q A1400 " pdb=" C48 R1Q A1400 " ideal model delta sigma weight residual 1.252 1.548 -0.296 2.00e-02 2.50e+03 2.19e+02 ... (remaining 12910 not shown) Histogram of bond angle deviations from ideal: 81.65 - 92.86: 1 92.86 - 104.08: 193 104.08 - 115.29: 8179 115.29 - 126.50: 9023 126.50 - 137.72: 152 Bond angle restraints: 17548 Sorted by residual: angle pdb=" C24 R1Q A1400 " pdb=" C25 R1Q A1400 " pdb=" O26 R1Q A1400 " ideal model delta sigma weight residual 87.19 119.62 -32.43 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C20 R1Q A1400 " pdb=" C25 R1Q A1400 " pdb=" O26 R1Q A1400 " ideal model delta sigma weight residual 150.43 120.27 30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C15 R1Q A1400 " pdb=" C07 R1Q A1400 " pdb=" N08 R1Q A1400 " ideal model delta sigma weight residual 103.15 130.70 -27.55 3.00e+00 1.11e-01 8.43e+01 angle pdb=" C05 R1Q A1400 " pdb=" C06 R1Q A1400 " pdb=" C07 R1Q A1400 " ideal model delta sigma weight residual 111.01 137.72 -26.71 3.00e+00 1.11e-01 7.93e+01 angle pdb=" N TYR B 54 " pdb=" CA TYR B 54 " pdb=" C TYR B 54 " ideal model delta sigma weight residual 113.15 119.98 -6.83 1.19e+00 7.06e-01 3.30e+01 ... (remaining 17543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 7858 34.81 - 69.63: 189 69.63 - 104.44: 9 104.44 - 139.25: 1 139.25 - 174.07: 1 Dihedral angle restraints: 8058 sinusoidal: 3472 harmonic: 4586 Sorted by residual: dihedral pdb=" CA ASN B 216 " pdb=" C ASN B 216 " pdb=" N ARG B 217 " pdb=" CA ARG B 217 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ALA B 99 " pdb=" C ALA B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 8055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.105: 2028 1.105 - 2.209: 1 2.209 - 3.314: 0 3.314 - 4.419: 0 4.419 - 5.523: 2 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C15 R1Q A1400 " pdb=" C07 R1Q A1400 " pdb=" C20 R1Q A1400 " pdb=" C54 R1Q A1400 " both_signs ideal model delta sigma weight residual False 2.79 -2.73 5.52 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C32 R1Q A1400 " pdb=" C31 R1Q A1400 " pdb=" C34 R1Q A1400 " pdb=" C38 R1Q A1400 " both_signs ideal model delta sigma weight residual False 2.42 -2.76 5.19 2.00e-01 2.50e+01 6.73e+02 chirality pdb=" C53 R1Q A1400 " pdb=" C43 R1Q A1400 " pdb=" C52 R1Q A1400 " pdb=" N49 R1Q A1400 " both_signs ideal model delta sigma weight residual False -1.34 -2.48 1.13 2.00e-01 2.50e+01 3.22e+01 ... (remaining 2028 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 744 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO A 745 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 39 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO C 40 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.020 2.00e-02 2.50e+03 1.48e-02 3.84e+00 pdb=" CG PHE B 94 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.007 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 138 2.61 - 3.19: 11358 3.19 - 3.76: 18870 3.76 - 4.33: 26071 4.33 - 4.90: 43663 Nonbonded interactions: 100100 Sorted by model distance: nonbonded pdb=" OD1 ASP A 47 " pdb=" NH1 ARG A 142 " model vdw 2.042 2.520 nonbonded pdb=" NE1 TRP A 803 " pdb=" NZ LYS A1014 " model vdw 2.073 3.200 nonbonded pdb=" CD1 ILE B 53 " pdb=" O ASN B 58 " model vdw 2.128 3.460 nonbonded pdb=" O TYR A 490 " pdb=" NE2 GLN A 912 " model vdw 2.131 2.520 nonbonded pdb=" O GLY A 269 " pdb=" OH TYR A1133 " model vdw 2.171 2.440 ... (remaining 100095 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.300 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 38.780 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 58.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.014 0.488 12915 Z= 0.864 Angle : 1.060 32.425 17548 Z= 0.506 Chirality : 0.181 5.523 2031 Planarity : 0.004 0.064 2162 Dihedral : 14.537 174.066 5103 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.20 % Rotamer: Outliers : 4.42 % Allowed : 12.58 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.83 (0.18), residues: 1584 helix: -1.46 (0.16), residues: 751 sheet: -1.19 (0.28), residues: 295 loop : -2.66 (0.22), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 46 HIS 0.004 0.001 HIS A 918 PHE 0.033 0.003 PHE B 94 TYR 0.026 0.003 TYR C 94 ARG 0.005 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 166 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 232 TRP cc_start: 0.7404 (t60) cc_final: 0.7139 (t60) REVERT: A 520 PHE cc_start: 0.3302 (OUTLIER) cc_final: 0.2188 (m-80) REVERT: A 628 MET cc_start: 0.0608 (tpp) cc_final: 0.0325 (tpp) REVERT: A 983 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8218 (m-10) REVERT: A 1019 ASP cc_start: 0.1068 (OUTLIER) cc_final: -0.0010 (t0) REVERT: A 1027 MET cc_start: 0.3161 (tpp) cc_final: 0.2457 (tpt) REVERT: A 1056 LEU cc_start: 0.4830 (OUTLIER) cc_final: 0.4556 (tp) REVERT: B 36 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8576 (t) REVERT: B 52 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6814 (mp) REVERT: B 143 ASN cc_start: 0.7741 (m110) cc_final: 0.7493 (m-40) REVERT: B 148 ASP cc_start: 0.1997 (m-30) cc_final: 0.1643 (m-30) REVERT: C 110 GLN cc_start: 0.7289 (pt0) cc_final: 0.7011 (pt0) outliers start: 59 outliers final: 33 residues processed: 223 average time/residue: 0.2661 time to fit residues: 84.1011 Evaluate side-chains 149 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 983 PHE Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 398 HIS A 438 GLN A 537 GLN A 750 GLN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN A1054 GLN ** A1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN B 58 ASN B 129 GLN C 56 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12915 Z= 0.185 Angle : 0.761 24.757 17548 Z= 0.332 Chirality : 0.083 2.375 2031 Planarity : 0.004 0.038 2162 Dihedral : 8.474 139.977 2329 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 3.67 % Allowed : 16.63 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.80 (0.20), residues: 1584 helix: 0.57 (0.18), residues: 763 sheet: -0.48 (0.30), residues: 286 loop : -2.14 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 46 HIS 0.004 0.001 HIS A 612 PHE 0.014 0.001 PHE A 732 TYR 0.014 0.001 TYR B 197 ARG 0.004 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 119 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 497 MET cc_start: 0.5228 (mmp) cc_final: 0.4998 (mtt) REVERT: A 520 PHE cc_start: 0.3324 (OUTLIER) cc_final: 0.2244 (m-80) REVERT: A 628 MET cc_start: 0.0691 (tpp) cc_final: 0.0479 (tpp) REVERT: A 983 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: A 986 MET cc_start: 0.8219 (mtt) cc_final: 0.7943 (mtm) REVERT: A 1019 ASP cc_start: 0.1049 (OUTLIER) cc_final: -0.0030 (t0) REVERT: A 1027 MET cc_start: 0.3243 (tpp) cc_final: 0.2571 (tpt) REVERT: A 1056 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4820 (tp) outliers start: 49 outliers final: 24 residues processed: 165 average time/residue: 0.2807 time to fit residues: 68.2028 Evaluate side-chains 125 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 850 SER Chi-restraints excluded: chain A residue 983 PHE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 168 TRP Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 0.0980 chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 128 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN A1130 ASN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 196 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12915 Z= 0.262 Angle : 0.779 24.993 17548 Z= 0.342 Chirality : 0.085 2.411 2031 Planarity : 0.003 0.035 2162 Dihedral : 7.709 138.368 2292 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 3.82 % Allowed : 18.20 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.21), residues: 1584 helix: 0.92 (0.19), residues: 773 sheet: -0.18 (0.31), residues: 281 loop : -1.89 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 108 HIS 0.003 0.001 HIS A 612 PHE 0.013 0.001 PHE A 957 TYR 0.019 0.001 TYR C 94 ARG 0.004 0.000 ARG B 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 109 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7924 (tp) REVERT: A 520 PHE cc_start: 0.3282 (OUTLIER) cc_final: 0.2416 (m-10) REVERT: A 840 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 986 MET cc_start: 0.8294 (mtt) cc_final: 0.7988 (mtm) REVERT: A 1019 ASP cc_start: 0.1084 (OUTLIER) cc_final: 0.0204 (t0) REVERT: A 1027 MET cc_start: 0.3173 (tpp) cc_final: 0.2591 (tpt) REVERT: A 1056 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4761 (tp) REVERT: A 1270 MET cc_start: -0.0458 (tpt) cc_final: -0.0929 (tpt) REVERT: B 175 ASP cc_start: 0.8121 (p0) cc_final: 0.7905 (p0) outliers start: 51 outliers final: 36 residues processed: 156 average time/residue: 0.2421 time to fit residues: 56.3229 Evaluate side-chains 131 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 90 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 136 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12915 Z= 0.195 Angle : 0.748 26.516 17548 Z= 0.320 Chirality : 0.080 2.340 2031 Planarity : 0.003 0.035 2162 Dihedral : 7.239 133.726 2284 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 4.12 % Allowed : 19.10 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.16 (0.21), residues: 1584 helix: 1.29 (0.19), residues: 769 sheet: 0.15 (0.32), residues: 275 loop : -1.65 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.003 0.000 HIS B 98 PHE 0.012 0.001 PHE C 171 TYR 0.017 0.001 TYR C 94 ARG 0.003 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 102 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.7772 (mmp) cc_final: 0.7503 (mmp) REVERT: A 490 TYR cc_start: 0.7795 (OUTLIER) cc_final: 0.7015 (m-80) REVERT: A 520 PHE cc_start: 0.3209 (OUTLIER) cc_final: 0.2353 (m-10) REVERT: A 986 MET cc_start: 0.8289 (mtt) cc_final: 0.7954 (mtm) REVERT: A 1019 ASP cc_start: 0.1344 (OUTLIER) cc_final: 0.0420 (t0) REVERT: A 1027 MET cc_start: 0.3243 (tpp) cc_final: 0.2694 (tpt) REVERT: A 1270 MET cc_start: -0.0303 (tpt) cc_final: -0.0616 (tpt) REVERT: B 175 ASP cc_start: 0.8310 (p0) cc_final: 0.7976 (p0) outliers start: 55 outliers final: 34 residues processed: 149 average time/residue: 0.2300 time to fit residues: 52.0654 Evaluate side-chains 137 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 0.0570 chunk 38 optimal weight: 20.0000 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12915 Z= 0.158 Angle : 0.730 26.592 17548 Z= 0.308 Chirality : 0.079 2.330 2031 Planarity : 0.003 0.034 2162 Dihedral : 6.931 131.789 2282 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 3.52 % Allowed : 20.15 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1584 helix: 1.60 (0.19), residues: 761 sheet: 0.28 (0.32), residues: 275 loop : -1.47 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.002 0.000 HIS B 98 PHE 0.011 0.001 PHE A 994 TYR 0.015 0.001 TYR C 94 ARG 0.002 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 279 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7294 (ptpt) REVERT: A 490 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: A 520 PHE cc_start: 0.3072 (OUTLIER) cc_final: 0.2253 (m-10) REVERT: A 840 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8336 (mt) REVERT: A 953 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7453 (t80) REVERT: A 986 MET cc_start: 0.8240 (mtt) cc_final: 0.7885 (mtm) REVERT: A 1019 ASP cc_start: 0.1361 (OUTLIER) cc_final: 0.0478 (t0) REVERT: A 1027 MET cc_start: 0.3201 (tpp) cc_final: 0.2650 (tpt) REVERT: A 1270 MET cc_start: -0.0222 (tpt) cc_final: -0.0547 (tpt) REVERT: B 180 MET cc_start: 0.7481 (tpt) cc_final: 0.6834 (tpt) outliers start: 47 outliers final: 29 residues processed: 147 average time/residue: 0.2508 time to fit residues: 54.4965 Evaluate side-chains 134 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 10.0000 chunk 137 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 152 optimal weight: 0.0270 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12915 Z= 0.149 Angle : 0.725 26.624 17548 Z= 0.305 Chirality : 0.078 2.311 2031 Planarity : 0.003 0.030 2162 Dihedral : 6.673 130.306 2276 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 3.67 % Allowed : 20.15 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.72 (0.21), residues: 1584 helix: 1.76 (0.19), residues: 761 sheet: 0.35 (0.32), residues: 269 loop : -1.29 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 232 HIS 0.002 0.000 HIS B 98 PHE 0.024 0.001 PHE A 994 TYR 0.015 0.001 TYR C 94 ARG 0.005 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7511 (mmp) cc_final: 0.7273 (mmp) REVERT: A 520 PHE cc_start: 0.3046 (OUTLIER) cc_final: 0.2248 (m-10) REVERT: A 840 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8287 (mt) REVERT: A 876 MET cc_start: 0.6408 (mmm) cc_final: 0.6083 (mmm) REVERT: A 953 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 986 MET cc_start: 0.8221 (mtt) cc_final: 0.7873 (mtm) REVERT: A 1019 ASP cc_start: 0.1539 (OUTLIER) cc_final: 0.0583 (t0) REVERT: A 1027 MET cc_start: 0.3275 (tpp) cc_final: 0.2672 (tpt) REVERT: A 1270 MET cc_start: -0.0361 (tpt) cc_final: -0.0581 (tpt) outliers start: 49 outliers final: 33 residues processed: 147 average time/residue: 0.2455 time to fit residues: 53.3180 Evaluate side-chains 129 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 0.0060 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12915 Z= 0.145 Angle : 0.720 26.845 17548 Z= 0.303 Chirality : 0.078 2.304 2031 Planarity : 0.003 0.031 2162 Dihedral : 6.577 130.860 2275 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 20.30 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.92 (0.21), residues: 1584 helix: 1.90 (0.19), residues: 761 sheet: 0.41 (0.32), residues: 271 loop : -1.14 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 232 HIS 0.002 0.000 HIS B 98 PHE 0.015 0.001 PHE A 994 TYR 0.016 0.001 TYR B 197 ARG 0.007 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 97 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7467 (mmp) cc_final: 0.7248 (mmp) REVERT: A 520 PHE cc_start: 0.2963 (OUTLIER) cc_final: 0.2206 (m-10) REVERT: A 840 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 876 MET cc_start: 0.6440 (mmm) cc_final: 0.6171 (mmm) REVERT: A 953 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7550 (t80) REVERT: A 986 MET cc_start: 0.8201 (mtt) cc_final: 0.7827 (mtm) REVERT: A 1019 ASP cc_start: 0.1550 (OUTLIER) cc_final: 0.0545 (t0) REVERT: A 1027 MET cc_start: 0.3242 (tpp) cc_final: 0.2625 (tpt) REVERT: B 168 TRP cc_start: 0.6523 (m-90) cc_final: 0.5618 (m-90) REVERT: B 180 MET cc_start: 0.7450 (tpt) cc_final: 0.6723 (tpt) outliers start: 46 outliers final: 34 residues processed: 138 average time/residue: 0.2472 time to fit residues: 51.0324 Evaluate side-chains 130 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12915 Z= 0.235 Angle : 0.759 25.923 17548 Z= 0.328 Chirality : 0.082 2.374 2031 Planarity : 0.003 0.030 2162 Dihedral : 6.842 133.539 2275 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 3.75 % Allowed : 20.15 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.21), residues: 1584 helix: 1.62 (0.19), residues: 766 sheet: 0.48 (0.32), residues: 277 loop : -1.07 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 232 HIS 0.003 0.001 HIS B 98 PHE 0.019 0.001 PHE A 994 TYR 0.019 0.001 TYR C 94 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 91 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7914 (mmp) cc_final: 0.7629 (mmp) REVERT: A 520 PHE cc_start: 0.3093 (OUTLIER) cc_final: 0.2357 (m-10) REVERT: A 840 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 1019 ASP cc_start: 0.1300 (OUTLIER) cc_final: 0.0388 (t0) REVERT: A 1027 MET cc_start: 0.3407 (tpp) cc_final: 0.2796 (tpt) outliers start: 50 outliers final: 39 residues processed: 136 average time/residue: 0.2292 time to fit residues: 47.7428 Evaluate side-chains 132 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 90 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12915 Z= 0.196 Angle : 0.744 26.232 17548 Z= 0.317 Chirality : 0.080 2.338 2031 Planarity : 0.003 0.032 2162 Dihedral : 6.716 132.635 2275 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 3.52 % Allowed : 20.52 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.85 (0.22), residues: 1584 helix: 1.73 (0.19), residues: 762 sheet: 0.46 (0.32), residues: 270 loop : -1.03 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 232 HIS 0.003 0.001 HIS B 98 PHE 0.016 0.001 PHE A 994 TYR 0.016 0.001 TYR C 94 ARG 0.007 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 102 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7762 (mmp) cc_final: 0.7491 (mmp) REVERT: A 520 PHE cc_start: 0.3237 (OUTLIER) cc_final: 0.2367 (m-10) REVERT: A 628 MET cc_start: 0.2841 (tpp) cc_final: 0.2443 (tpp) REVERT: A 840 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 986 MET cc_start: 0.8218 (mtt) cc_final: 0.7935 (mtm) REVERT: A 1019 ASP cc_start: 0.1462 (OUTLIER) cc_final: 0.0408 (t0) REVERT: A 1027 MET cc_start: 0.3302 (tpp) cc_final: 0.2715 (tpt) REVERT: A 1151 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5793 (mt-10) REVERT: B 150 ASN cc_start: 0.2113 (OUTLIER) cc_final: 0.1792 (t0) REVERT: B 180 MET cc_start: 0.7642 (tpt) cc_final: 0.7028 (tpt) REVERT: C 110 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6682 (pt0) outliers start: 47 outliers final: 40 residues processed: 144 average time/residue: 0.2437 time to fit residues: 52.3263 Evaluate side-chains 144 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 99 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1215 GLN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 133 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1215 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12915 Z= 0.253 Angle : 0.774 26.210 17548 Z= 0.335 Chirality : 0.082 2.377 2031 Planarity : 0.003 0.035 2162 Dihedral : 6.880 133.562 2275 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 3.67 % Allowed : 20.60 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.65 (0.21), residues: 1584 helix: 1.53 (0.19), residues: 767 sheet: 0.48 (0.32), residues: 276 loop : -1.18 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 232 HIS 0.003 0.001 HIS B 98 PHE 0.015 0.001 PHE A 994 TYR 0.019 0.001 TYR C 94 ARG 0.008 0.000 ARG B 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 99 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.7928 (mmp) cc_final: 0.7684 (mmp) REVERT: A 520 PHE cc_start: 0.3214 (OUTLIER) cc_final: 0.2436 (m-10) REVERT: A 840 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8476 (mt) REVERT: A 986 MET cc_start: 0.8233 (mtt) cc_final: 0.7944 (mtm) REVERT: A 1019 ASP cc_start: 0.1342 (OUTLIER) cc_final: 0.0336 (t0) REVERT: A 1027 MET cc_start: 0.3369 (tpp) cc_final: 0.2822 (tpt) REVERT: A 1151 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5824 (mt-10) REVERT: B 36 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8276 (p) REVERT: B 180 MET cc_start: 0.7772 (tpt) cc_final: 0.7078 (tpt) outliers start: 49 outliers final: 43 residues processed: 143 average time/residue: 0.2560 time to fit residues: 53.5400 Evaluate side-chains 144 residues out of total 1335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 97 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 137 CYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 387 ASN Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 829 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 1004 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 30.0000 chunk 115 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 0.0770 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 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 = 0.4499 r_free = 0.4499 target = 0.221378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.176907 restraints weight = 16099.038| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.72 r_work: 0.3682 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12915 Z= 0.190 Angle : 0.748 26.339 17548 Z= 0.319 Chirality : 0.080 2.338 2031 Planarity : 0.003 0.035 2162 Dihedral : 6.712 132.618 2275 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 3.60 % Allowed : 20.90 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.83 (0.22), residues: 1584 helix: 1.70 (0.19), residues: 763 sheet: 0.46 (0.32), residues: 270 loop : -1.03 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 232 HIS 0.003 0.000 HIS A1007 PHE 0.019 0.001 PHE A 163 TYR 0.016 0.001 TYR C 94 ARG 0.008 0.000 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2701.34 seconds wall clock time: 50 minutes 21.22 seconds (3021.22 seconds total)