Starting phenix.real_space_refine on Thu Feb 15 18:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o9w_12765/02_2024/7o9w_12765_updated.pdb" } resolution = 3.5 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 526 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 8101 2.51 5 N 2118 2.21 5 O 2347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 459": "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 GLU 707": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A ARG 958": "NH1" <-> "NH2" Residue "A GLU 1013": "OE1" <-> "OE2" 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 66": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "C GLU 1": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 220": "OE1" <-> "OE2" Residue "C ARG 222": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12618 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9089 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 27, 'TRANS': 1141} Chain breaks: 2 Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1710 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 207} Chain: "C" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1717 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 211} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'V5Q': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.62, per 1000 atoms: 0.52 Number of scatterers: 12618 At special positions: 0 Unit cell: (147.84, 139.92, 162.36, 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 52 16.00 O 2347 8.00 N 2118 7.00 C 8101 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 140 " - pdb=" SG CYS B 200 " distance=2.47 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 204 " distance=2.03 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: 5.38 Conformation dependent library (CDL) restraints added in 2.4 seconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2978 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 14 sheets defined 46.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 36 through 39 No H-bonds generated for 'chain 'A' and resid 36 through 39' Processing helix chain 'A' and resid 45 through 88 removed outlier: 4.736A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 106 through 156 removed outlier: 3.798A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.580A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.533A pdb=" N ASN A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'A' and resid 212 through 237 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 241 through 259 removed outlier: 4.436A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.732A pdb=" N ILE A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 267 " --> pdb=" O VAL A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 267' Processing helix chain 'A' and resid 270 through 322 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 349 through 370 removed outlier: 4.507A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (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: 4.758A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 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: 4.706A 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 616 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 705 through 740 Proline residue: A 709 - end of helix removed outlier: 3.583A pdb=" N VAL A 713 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 724 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 725 " --> pdb=" O GLY A 722 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.501A pdb=" N PHE A 732 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 738 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 797 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 811 through 853 removed outlier: 3.999A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ARG A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 885 through 892 Processing helix chain 'A' and resid 895 through 902 Processing helix chain 'A' and resid 904 through 910 removed outlier: 3.592A pdb=" N SER A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 966 removed outlier: 4.855A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 4.375A pdb=" N TYR A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 954 " --> pdb=" O TYR A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 994 removed outlier: 4.311A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) 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: 3.632A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1134 removed outlier: 4.461A pdb=" N GLY A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1151 Processing helix chain 'A' and resid 1155 through 1160 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: 4.398A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.945A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 4.235A 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 1235 through 1238 No H-bonds generated for 'chain 'A' and resid 1235 through 1238' Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 191 through 194 No H-bonds generated for 'chain 'B' and resid 191 through 194' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing sheet with id= A, first strand: chain 'A' and resid 415 through 417 removed outlier: 3.743A pdb=" N ARG A 395 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 3.585A 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: 6.514A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.551A 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 1066 through 1069 removed outlier: 6.629A pdb=" N LEU A1242 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL A1069 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A1244 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 4.021A pdb=" N LEU A1198 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1116 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A1200 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR A1226 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU A1199 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A1228 " --> pdb=" O LEU A1199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.969A pdb=" N ALA B 19 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 80 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 90 through 95 removed outlier: 6.125A pdb=" N LEU B 42 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N LEU B 51 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 120 through 123 removed outlier: 3.536A pdb=" N ASN B 143 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 183 " --> pdb=" O CYS B 140 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 142 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET B 181 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR B 179 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.804A pdb=" N THR C 119 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 93 through 99 removed outlier: 5.825A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 145 through 148 removed outlier: 4.677A pdb=" N SER C 187 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 175 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 178 through 180 Processing sheet with id= N, first strand: chain 'C' and resid 203 through 206 606 hydrogen bonds defined for protein. 1695 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: 4.65 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2038 1.31 - 1.44: 3511 1.44 - 1.57: 7250 1.57 - 1.70: 4 1.70 - 1.83: 86 Bond restraints: 12889 Sorted by residual: bond pdb=" C09 V5Q A1402 " pdb=" N08 V5Q A1402 " ideal model delta sigma weight residual 1.464 1.285 0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C09 V5Q A1401 " pdb=" N08 V5Q A1401 " ideal model delta sigma weight residual 1.464 1.291 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C46 V5Q A1401 " pdb=" C47 V5Q A1401 " ideal model delta sigma weight residual 1.498 1.584 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C46 V5Q A1402 " pdb=" C47 V5Q A1402 " ideal model delta sigma weight residual 1.498 1.583 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C07 V5Q A1401 " pdb=" N08 V5Q A1401 " ideal model delta sigma weight residual 1.448 1.371 0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 12884 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.69: 290 106.69 - 113.58: 7177 113.58 - 120.48: 5155 120.48 - 127.38: 4732 127.38 - 134.27: 105 Bond angle restraints: 17459 Sorted by residual: angle pdb=" C PRO B 100 " pdb=" N PRO B 101 " pdb=" CA PRO B 101 " ideal model delta sigma weight residual 119.84 131.34 -11.50 1.25e+00 6.40e-01 8.47e+01 angle pdb=" N ILE B 99 " pdb=" CA ILE B 99 " pdb=" C ILE B 99 " ideal model delta sigma weight residual 108.88 121.19 -12.31 2.16e+00 2.14e-01 3.25e+01 angle pdb=" C LYS B 55 " pdb=" CA LYS B 55 " pdb=" CB LYS B 55 " ideal model delta sigma weight residual 116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01 angle pdb=" N LYS B 55 " pdb=" CA LYS B 55 " pdb=" C LYS B 55 " ideal model delta sigma weight residual 108.08 116.69 -8.61 1.69e+00 3.50e-01 2.59e+01 angle pdb=" C ILE B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta sigma weight residual 120.38 115.14 5.24 1.03e+00 9.43e-01 2.58e+01 ... (remaining 17454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.72: 6885 22.72 - 45.43: 639 45.43 - 68.15: 89 68.15 - 90.86: 17 90.86 - 113.58: 4 Dihedral angle restraints: 7634 sinusoidal: 2991 harmonic: 4643 Sorted by residual: dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 204 " pdb=" CB CYS C 204 " ideal model delta sinusoidal sigma weight residual 93.00 32.00 61.00 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CA ASN A1163 " pdb=" C ASN A1163 " pdb=" N LYS A1164 " pdb=" CA LYS A1164 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASP A 997 " pdb=" C ASP A 997 " pdb=" N TYR A 998 " pdb=" CA TYR A 998 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 7631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 1978 0.403 - 0.806: 1 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.015: 1 Chirality restraints: 1981 Sorted by residual: chirality pdb=" C35 V5Q A1401 " pdb=" C33 V5Q A1401 " pdb=" C36 V5Q A1401 " pdb=" O41 V5Q A1401 " both_signs ideal model delta sigma weight residual False -2.49 -0.47 -2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" C35 V5Q A1402 " pdb=" C33 V5Q A1402 " pdb=" C36 V5Q A1402 " pdb=" O41 V5Q A1402 " both_signs ideal model delta sigma weight residual False -2.49 -1.09 -1.40 2.00e-01 2.50e+01 4.88e+01 chirality pdb=" CB VAL B 56 " pdb=" CA VAL B 56 " pdb=" CG1 VAL B 56 " pdb=" CG2 VAL B 56 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 1978 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 97 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C THR B 97 " -0.061 2.00e-02 2.50e+03 pdb=" O THR B 97 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS B 98 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 174 " 0.213 9.50e-02 1.11e+02 9.53e-02 5.57e+00 pdb=" NE ARG A 174 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 174 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 174 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 174 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 109 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C MET C 109 " 0.040 2.00e-02 2.50e+03 pdb=" O MET C 109 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 110 " -0.013 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 403 2.70 - 3.25: 12601 3.25 - 3.80: 20086 3.80 - 4.35: 25348 4.35 - 4.90: 41582 Nonbonded interactions: 100020 Sorted by model distance: nonbonded pdb=" N ASP C 110 " pdb=" OD1 ASP C 110 " model vdw 2.149 2.520 nonbonded pdb=" O GLN A 990 " pdb=" OG SER A 993 " model vdw 2.197 2.440 nonbonded pdb=" O GLY A 854 " pdb=" OG1 THR A 858 " model vdw 2.201 2.440 nonbonded pdb=" O PRO B 8 " pdb=" OG1 THR B 108 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU A 707 " pdb=" NH2 ARG A 787 " model vdw 2.246 2.520 ... (remaining 100015 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: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 19.410 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 37.880 Find NCS groups from input model: 0.340 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 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 : 0.006 0.179 12889 Z= 0.359 Angle : 0.856 12.310 17459 Z= 0.505 Chirality : 0.075 2.015 1981 Planarity : 0.005 0.095 2202 Dihedral : 17.056 113.577 4641 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 4.42 % Allowed : 18.76 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -3.00 (0.18), residues: 1604 helix: -1.45 (0.16), residues: 753 sheet: -1.62 (0.31), residues: 263 loop : -2.71 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.009 0.001 HIS A 145 PHE 0.023 0.002 PHE C 50 TYR 0.016 0.002 TYR C 33 ARG 0.006 0.001 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 130 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7400 (tp) REVERT: A 258 LEU cc_start: 0.6295 (mt) cc_final: 0.5911 (tt) REVERT: A 332 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 440 MET cc_start: 0.2756 (tpt) cc_final: 0.2356 (mtt) REVERT: A 514 MET cc_start: 0.3342 (mtm) cc_final: 0.2660 (ttm) REVERT: A 616 MET cc_start: 0.2662 (mmp) cc_final: 0.0905 (mtp) REVERT: A 703 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5828 (mp) REVERT: A 824 GLN cc_start: 0.5937 (OUTLIER) cc_final: 0.5374 (tt0) REVERT: A 875 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6808 (tm-30) REVERT: A 1027 MET cc_start: 0.1858 (tpp) cc_final: 0.1400 (ttp) REVERT: B 18 GLN cc_start: 0.6907 (mm110) cc_final: 0.4806 (pt0) REVERT: B 146 TYR cc_start: 0.4866 (t80) cc_final: 0.4641 (t80) outliers start: 60 outliers final: 39 residues processed: 188 average time/residue: 0.2436 time to fit residues: 67.3261 Evaluate side-chains 145 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 102 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 752 SER Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 143 GLN A 145 HIS A 158 GLN A 387 ASN A 398 HIS A 438 GLN A 537 GLN A 725 GLN A 750 GLN A 820 ASN A 946 GLN A 966 HIS A1054 GLN A1105 ASN A1153 ASN A1215 GLN A1232 HIS A1248 ASN B 98 HIS B 167 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 102 GLN C 105 ASN C 164 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12889 Z= 0.231 Angle : 0.589 8.256 17459 Z= 0.306 Chirality : 0.042 0.250 1981 Planarity : 0.004 0.043 2202 Dihedral : 9.038 95.028 1819 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.22 % Allowed : 20.90 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -1.54 (0.20), residues: 1604 helix: -0.08 (0.18), residues: 770 sheet: -1.14 (0.33), residues: 260 loop : -2.18 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 232 HIS 0.008 0.001 HIS A 145 PHE 0.024 0.002 PHE C 50 TYR 0.015 0.002 TYR B 54 ARG 0.005 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 105 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7741 (tp) REVERT: A 258 LEU cc_start: 0.6323 (mt) cc_final: 0.6073 (tt) REVERT: A 332 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 450 MET cc_start: 0.4873 (ttp) cc_final: 0.3914 (mtp) REVERT: A 616 MET cc_start: 0.2107 (mmp) cc_final: 0.1699 (mmt) REVERT: A 875 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 1027 MET cc_start: 0.1947 (tpp) cc_final: 0.1472 (ttp) REVERT: B 18 GLN cc_start: 0.6924 (mm110) cc_final: 0.4877 (pt0) REVERT: B 99 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7767 (pp) outliers start: 71 outliers final: 42 residues processed: 164 average time/residue: 0.2257 time to fit residues: 56.2381 Evaluate side-chains 144 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 99 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 157 optimal weight: 0.0060 chunk 129 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 HIS ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12889 Z= 0.226 Angle : 0.573 8.767 17459 Z= 0.298 Chirality : 0.042 0.487 1981 Planarity : 0.004 0.047 2202 Dihedral : 8.541 95.168 1789 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.59 % Allowed : 22.37 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -1.03 (0.21), residues: 1604 helix: 0.33 (0.18), residues: 771 sheet: -0.89 (0.34), residues: 260 loop : -1.91 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 803 HIS 0.004 0.001 HIS A 145 PHE 0.023 0.002 PHE C 50 TYR 0.014 0.002 TYR C 33 ARG 0.003 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 100 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 144 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7828 (tp) REVERT: A 332 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 450 MET cc_start: 0.4897 (ttp) cc_final: 0.3886 (mtp) REVERT: A 606 ILE cc_start: -0.0585 (OUTLIER) cc_final: -0.1147 (pt) REVERT: A 616 MET cc_start: 0.2022 (mmp) cc_final: 0.1602 (mmt) REVERT: A 628 MET cc_start: 0.0843 (ptt) cc_final: -0.0383 (pmm) REVERT: A 758 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 770 PHE cc_start: 0.6059 (OUTLIER) cc_final: 0.5503 (t80) REVERT: A 862 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7431 (mp) REVERT: A 875 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 1027 MET cc_start: 0.2183 (tpp) cc_final: 0.1567 (ttp) REVERT: B 18 GLN cc_start: 0.7039 (mm110) cc_final: 0.4966 (pt0) REVERT: B 84 GLU cc_start: 0.6523 (tp30) cc_final: 0.5824 (tt0) REVERT: B 99 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7876 (pp) outliers start: 76 outliers final: 51 residues processed: 161 average time/residue: 0.2468 time to fit residues: 60.1994 Evaluate side-chains 151 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 93 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 196 ASN B 216 ASN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12889 Z= 0.154 Angle : 0.513 7.648 17459 Z= 0.266 Chirality : 0.040 0.366 1981 Planarity : 0.004 0.045 2202 Dihedral : 8.176 93.586 1789 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.86 % Allowed : 23.69 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.21), residues: 1604 helix: 0.91 (0.19), residues: 759 sheet: -0.69 (0.34), residues: 260 loop : -1.61 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 803 HIS 0.002 0.000 HIS A 145 PHE 0.021 0.001 PHE C 50 TYR 0.017 0.001 TYR B 146 ARG 0.003 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 102 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 441 GLN cc_start: 0.4648 (OUTLIER) cc_final: 0.3908 (mm-40) REVERT: A 450 MET cc_start: 0.5043 (ttp) cc_final: 0.3929 (mtp) REVERT: A 606 ILE cc_start: -0.0462 (OUTLIER) cc_final: -0.1012 (pt) REVERT: A 616 MET cc_start: 0.1999 (mmp) cc_final: 0.1542 (mmt) REVERT: A 628 MET cc_start: 0.0862 (ptt) cc_final: -0.0324 (pmm) REVERT: A 770 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.5339 (t80) REVERT: A 862 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 1027 MET cc_start: 0.2260 (tpp) cc_final: 0.1595 (ttp) REVERT: B 18 GLN cc_start: 0.6877 (mm110) cc_final: 0.4729 (pt0) REVERT: B 84 GLU cc_start: 0.6162 (tp30) cc_final: 0.5568 (tt0) REVERT: B 99 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7829 (pp) REVERT: B 146 TYR cc_start: 0.4966 (t80) cc_final: 0.4509 (t80) outliers start: 66 outliers final: 39 residues processed: 155 average time/residue: 0.2106 time to fit residues: 51.2453 Evaluate side-chains 139 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 200 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A1034 ASN A1180 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12889 Z= 0.397 Angle : 0.712 12.304 17459 Z= 0.374 Chirality : 0.048 0.578 1981 Planarity : 0.005 0.067 2202 Dihedral : 8.936 97.284 1783 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.25 % Allowed : 24.21 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % Cis-general : 0.00 % Twisted Proline : 1.96 % 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: -1.03 (0.20), residues: 1604 helix: 0.20 (0.18), residues: 758 sheet: -0.76 (0.35), residues: 253 loop : -1.72 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 803 HIS 0.009 0.002 HIS A 145 PHE 0.029 0.003 PHE C 50 TYR 0.016 0.002 TYR B 41 ARG 0.010 0.001 ARG A1188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 98 time to evaluate : 1.343 Fit side-chains REVERT: A 332 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 450 MET cc_start: 0.5029 (ttp) cc_final: 0.3945 (mtp) REVERT: A 606 ILE cc_start: -0.0204 (OUTLIER) cc_final: -0.0784 (pt) REVERT: A 616 MET cc_start: 0.2291 (mmp) cc_final: 0.1775 (mmt) REVERT: A 628 MET cc_start: 0.0901 (ptt) cc_final: -0.0242 (pmm) REVERT: A 703 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5869 (mp) REVERT: A 770 PHE cc_start: 0.6069 (OUTLIER) cc_final: 0.5769 (t80) REVERT: A 777 PHE cc_start: 0.6867 (m-80) cc_final: 0.6545 (m-80) REVERT: A 810 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.7067 (m) REVERT: A 862 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (mp) REVERT: A 875 GLU cc_start: 0.7618 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 949 MET cc_start: 0.8012 (tpt) cc_final: 0.7769 (tpt) REVERT: A 1027 MET cc_start: 0.2430 (tpp) cc_final: 0.1577 (ttp) REVERT: B 18 GLN cc_start: 0.7350 (mm110) cc_final: 0.5372 (pt0) REVERT: B 86 GLU cc_start: 0.6567 (tm-30) cc_final: 0.5875 (mt-10) REVERT: B 99 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8046 (pp) outliers start: 85 outliers final: 56 residues processed: 170 average time/residue: 0.2148 time to fit residues: 56.6879 Evaluate side-chains 156 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 93 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 704 ASN Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12889 Z= 0.190 Angle : 0.549 7.856 17459 Z= 0.286 Chirality : 0.041 0.382 1981 Planarity : 0.004 0.067 2202 Dihedral : 8.306 94.323 1783 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.64 % Allowed : 26.05 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 1604 helix: 0.80 (0.19), residues: 755 sheet: -0.67 (0.34), residues: 262 loop : -1.64 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 803 HIS 0.003 0.001 HIS A 145 PHE 0.022 0.001 PHE C 50 TYR 0.024 0.002 TYR B 146 ARG 0.002 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 100 time to evaluate : 1.431 Fit side-chains REVERT: A 450 MET cc_start: 0.5035 (ttp) cc_final: 0.3935 (mtp) REVERT: A 606 ILE cc_start: -0.0197 (OUTLIER) cc_final: -0.0712 (pt) REVERT: A 616 MET cc_start: 0.2161 (mmp) cc_final: 0.1610 (mmt) REVERT: A 628 MET cc_start: 0.1089 (ptt) cc_final: -0.0080 (pmm) REVERT: A 770 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.5644 (t80) REVERT: A 777 PHE cc_start: 0.6701 (m-80) cc_final: 0.6404 (m-80) REVERT: A 1027 MET cc_start: 0.2563 (tpp) cc_final: 0.1787 (ttp) REVERT: B 18 GLN cc_start: 0.7019 (mm110) cc_final: 0.4875 (pt0) REVERT: B 86 GLU cc_start: 0.6344 (tm-30) cc_final: 0.5943 (mt-10) REVERT: B 99 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7919 (pp) REVERT: B 184 THR cc_start: 0.3699 (OUTLIER) cc_final: 0.3495 (m) outliers start: 63 outliers final: 45 residues processed: 150 average time/residue: 0.2053 time to fit residues: 48.4276 Evaluate side-chains 143 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 94 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 809 ASN Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 922 GLN Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** A1180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12889 Z= 0.217 Angle : 0.560 8.118 17459 Z= 0.291 Chirality : 0.042 0.378 1981 Planarity : 0.004 0.062 2202 Dihedral : 8.075 95.100 1781 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.86 % Allowed : 26.20 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -0.42 (0.21), residues: 1604 helix: 0.85 (0.19), residues: 757 sheet: -0.76 (0.33), residues: 276 loop : -1.49 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 232 HIS 0.005 0.001 HIS A 145 PHE 0.023 0.002 PHE C 50 TYR 0.014 0.002 TYR C 33 ARG 0.003 0.000 ARG A1188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 96 time to evaluate : 1.405 Fit side-chains REVERT: A 440 MET cc_start: 0.3486 (mtt) cc_final: 0.3219 (mtp) REVERT: A 450 MET cc_start: 0.5106 (ttp) cc_final: 0.3915 (mtp) REVERT: A 475 GLN cc_start: 0.2685 (OUTLIER) cc_final: 0.1808 (mm-40) REVERT: A 606 ILE cc_start: -0.0250 (OUTLIER) cc_final: -0.0704 (pt) REVERT: A 616 MET cc_start: 0.2179 (mmp) cc_final: 0.1620 (mmt) REVERT: A 628 MET cc_start: 0.1018 (ptt) cc_final: -0.0112 (pmm) REVERT: A 770 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.5646 (t80) REVERT: A 777 PHE cc_start: 0.6741 (m-80) cc_final: 0.6458 (m-80) REVERT: A 862 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 1027 MET cc_start: 0.2641 (tpp) cc_final: 0.1782 (ttp) REVERT: B 18 GLN cc_start: 0.7071 (mm110) cc_final: 0.4948 (pt0) REVERT: B 86 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5913 (mt-10) REVERT: B 99 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7954 (pp) REVERT: B 184 THR cc_start: 0.3691 (OUTLIER) cc_final: 0.3490 (m) outliers start: 66 outliers final: 49 residues processed: 153 average time/residue: 0.2038 time to fit residues: 49.0975 Evaluate side-chains 148 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 93 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 708 TRP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 824 GLN A1180 GLN C 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12889 Z= 0.159 Angle : 0.517 7.791 17459 Z= 0.267 Chirality : 0.040 0.307 1981 Planarity : 0.004 0.061 2202 Dihedral : 7.745 93.634 1781 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.97 % Allowed : 27.15 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: -0.08 (0.22), residues: 1604 helix: 1.14 (0.19), residues: 763 sheet: -0.58 (0.33), residues: 281 loop : -1.39 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 232 HIS 0.011 0.001 HIS A1112 PHE 0.022 0.001 PHE C 50 TYR 0.014 0.001 TYR C 33 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 100 time to evaluate : 1.406 Fit side-chains REVERT: A 440 MET cc_start: 0.3589 (mtt) cc_final: 0.3315 (mtp) REVERT: A 450 MET cc_start: 0.5125 (ttp) cc_final: 0.3919 (mtp) REVERT: A 616 MET cc_start: 0.2128 (mmp) cc_final: 0.1561 (mmt) REVERT: A 628 MET cc_start: 0.1016 (ptt) cc_final: -0.0101 (pmm) REVERT: A 770 PHE cc_start: 0.5973 (OUTLIER) cc_final: 0.5598 (t80) REVERT: A 824 GLN cc_start: 0.5877 (OUTLIER) cc_final: 0.5494 (tp40) REVERT: A 856 GLN cc_start: 0.8091 (mp10) cc_final: 0.7706 (mt0) REVERT: A 862 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7370 (mp) REVERT: A 1027 MET cc_start: 0.2643 (tpp) cc_final: 0.1790 (ttp) REVERT: B 18 GLN cc_start: 0.6925 (mm110) cc_final: 0.4680 (pt0) REVERT: B 86 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5870 (mt-10) REVERT: B 87 ASP cc_start: 0.6559 (m-30) cc_final: 0.6279 (m-30) REVERT: B 99 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 124 LYS cc_start: 0.6370 (mmmt) cc_final: 0.6147 (mmmt) outliers start: 54 outliers final: 42 residues processed: 146 average time/residue: 0.2415 time to fit residues: 54.9092 Evaluate side-chains 143 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 97 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 94 optimal weight: 0.0970 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 1 GLN B 143 ASN C 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12889 Z= 0.140 Angle : 0.498 7.759 17459 Z= 0.257 Chirality : 0.039 0.266 1981 Planarity : 0.004 0.061 2202 Dihedral : 7.410 93.257 1780 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.68 % Allowed : 27.08 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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 (0.22), residues: 1604 helix: 1.37 (0.19), residues: 762 sheet: -0.51 (0.33), residues: 281 loop : -1.28 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 232 HIS 0.011 0.001 HIS A1112 PHE 0.020 0.001 PHE C 50 TYR 0.014 0.001 TYR C 33 ARG 0.001 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 105 time to evaluate : 1.694 Fit side-chains REVERT: A 111 MET cc_start: 0.7183 (mmm) cc_final: 0.6974 (tmm) REVERT: A 244 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5162 (tt) REVERT: A 440 MET cc_start: 0.3662 (mtt) cc_final: 0.3371 (mtp) REVERT: A 450 MET cc_start: 0.5125 (ttp) cc_final: 0.3901 (mtp) REVERT: A 475 GLN cc_start: 0.2658 (OUTLIER) cc_final: 0.1747 (mm-40) REVERT: A 616 MET cc_start: 0.2177 (mmp) cc_final: 0.1605 (mmt) REVERT: A 628 MET cc_start: 0.1006 (ptt) cc_final: -0.0148 (pmm) REVERT: A 770 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5549 (t80) REVERT: A 777 PHE cc_start: 0.6604 (m-80) cc_final: 0.6322 (m-80) REVERT: A 814 LEU cc_start: 0.6563 (mt) cc_final: 0.6126 (tt) REVERT: A 856 GLN cc_start: 0.8083 (mp10) cc_final: 0.7678 (mt0) REVERT: A 862 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7353 (mp) REVERT: A 1027 MET cc_start: 0.2649 (tpp) cc_final: 0.1773 (ttp) REVERT: B 18 GLN cc_start: 0.6863 (mm110) cc_final: 0.4625 (pt0) REVERT: B 86 GLU cc_start: 0.6193 (tm-30) cc_final: 0.5852 (mt-10) REVERT: B 99 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7865 (pp) REVERT: C 124 LYS cc_start: 0.6510 (mmmt) cc_final: 0.6265 (mmmt) outliers start: 50 outliers final: 39 residues processed: 147 average time/residue: 0.2238 time to fit residues: 50.0769 Evaluate side-chains 142 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 708 TRP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0020 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 126 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 77 optimal weight: 0.3980 chunk 100 optimal weight: 0.0050 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS C 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12889 Z= 0.131 Angle : 0.486 7.747 17459 Z= 0.250 Chirality : 0.039 0.229 1981 Planarity : 0.004 0.066 2202 Dihedral : 6.925 92.985 1772 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 27.52 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 0.35 (0.22), residues: 1604 helix: 1.49 (0.19), residues: 769 sheet: -0.40 (0.33), residues: 281 loop : -1.18 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 232 HIS 0.010 0.001 HIS A1112 PHE 0.019 0.001 PHE C 50 TYR 0.014 0.001 TYR C 33 ARG 0.003 0.000 ARG A 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 103 time to evaluate : 1.502 Fit side-chains REVERT: A 244 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5152 (tt) REVERT: A 450 MET cc_start: 0.5216 (ttp) cc_final: 0.3985 (mtp) REVERT: A 475 GLN cc_start: 0.2670 (OUTLIER) cc_final: 0.1740 (mm-40) REVERT: A 616 MET cc_start: 0.2151 (mmp) cc_final: 0.1600 (mmt) REVERT: A 628 MET cc_start: 0.1041 (ptt) cc_final: -0.0139 (pmm) REVERT: A 770 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5513 (t80) REVERT: A 777 PHE cc_start: 0.6511 (m-80) cc_final: 0.6214 (m-80) REVERT: A 814 LEU cc_start: 0.6539 (mt) cc_final: 0.6058 (tt) REVERT: A 824 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.5523 (mm110) REVERT: A 856 GLN cc_start: 0.8075 (mp10) cc_final: 0.7672 (mt0) REVERT: A 862 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7328 (mp) REVERT: A 948 MET cc_start: 0.7090 (mmm) cc_final: 0.6796 (tpp) REVERT: A 1027 MET cc_start: 0.2710 (tpp) cc_final: 0.1819 (ttp) REVERT: B 18 GLN cc_start: 0.6856 (mm110) cc_final: 0.4575 (pt0) REVERT: B 86 GLU cc_start: 0.6139 (tm-30) cc_final: 0.5821 (mt-10) REVERT: B 87 ASP cc_start: 0.6588 (m-30) cc_final: 0.6325 (m-30) REVERT: B 99 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7790 (pp) REVERT: C 117 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (m) REVERT: C 124 LYS cc_start: 0.6482 (mmmt) cc_final: 0.6245 (mmmt) outliers start: 45 outliers final: 29 residues processed: 140 average time/residue: 0.2202 time to fit residues: 47.7170 Evaluate side-chains 137 residues out of total 1359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 376 ASP Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 708 TRP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 855 TRP Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 876 MET Chi-restraints excluded: chain A residue 904 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1019 ASP Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 220 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 ASN C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.230958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.189904 restraints weight = 16861.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.184546 restraints weight = 33273.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.180113 restraints weight = 33560.312| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12889 Z= 0.191 Angle : 0.533 9.548 17459 Z= 0.274 Chirality : 0.041 0.298 1981 Planarity : 0.004 0.075 2202 Dihedral : 7.051 94.576 1772 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.38 % Allowed : 27.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.84 % 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: 0.24 (0.22), residues: 1604 helix: 1.35 (0.19), residues: 768 sheet: -0.34 (0.34), residues: 276 loop : -1.21 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 232 HIS 0.010 0.001 HIS A1112 PHE 0.021 0.001 PHE C 50 TYR 0.015 0.002 TYR A 510 ARG 0.005 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2611.27 seconds wall clock time: 48 minutes 38.49 seconds (2918.49 seconds total)