Starting phenix.real_space_refine on Tue Nov 19 15:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c3c_45165/11_2024/9c3c_45165.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12347 2.51 5 N 3346 2.21 5 O 3653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19475 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3081 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 23, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1103 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 128} Chain: "D" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2695 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 286} Chain breaks: 1 Chain: "b" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2003 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "d" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2091 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "g" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2025 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1340 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "V" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2341 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.02, per 1000 atoms: 0.57 Number of scatterers: 19475 At special positions: 0 Unit cell: (133.28, 111.52, 295.12, 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 129 16.00 O 3653 8.00 N 3346 7.00 C 12347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS a 209 " - pdb=" SG CYS a 232 " distance=2.03 Simple disulfide: pdb=" SG CYS a 222 " - pdb=" SG CYS a 245 " distance=2.03 Simple disulfide: pdb=" SG CYS b 288 " - pdb=" SG CYS b 307 " distance=2.03 Simple disulfide: pdb=" SG CYS b 290 " - pdb=" SG CYS b 314 " distance=2.03 Simple disulfide: pdb=" SG CYS d 263 " - pdb=" SG CYS d 281 " distance=2.03 Simple disulfide: pdb=" SG CYS d 265 " - pdb=" SG CYS d 288 " distance=2.03 Simple disulfide: pdb=" SG CYS g 265 " - pdb=" SG CYS g 283 " distance=2.03 Simple disulfide: pdb=" SG CYS g 267 " - pdb=" SG CYS g 290 " distance=2.03 Simple disulfide: pdb=" SG CYS n 42 " - pdb=" SG CYS n 45 " distance=2.03 Simple disulfide: pdb=" SG CYS n 150 " - pdb=" SG CYS n 159 " distance=2.03 Simple disulfide: pdb=" SG CYS n 157 " - pdb=" SG CYS n 179 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A1001 " - " ASN A 641 " " NAG C 1 " - " ASN A 649 " " NAG E 1 " - " ASN b 258 " " NAG F 1 " - " ASN b 211 " " NAG G 1 " - " ASN b 158 " " NAG H 1 " - " ASN B 661 " " NAG K 1 " - " ASN a 174 " " NAG O 1 " - " ASN d 108 " " NAG R 1 " - " ASN g 110 " " NAG a 401 " - " ASN a 246 " Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 33 sheets defined 35.8% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 83 through 88 Processing helix chain 'A' and resid 122 through 126 removed outlier: 4.006A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 4.000A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 203 through 219 removed outlier: 3.736A pdb=" N SER A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.665A pdb=" N VAL A 271 " --> pdb=" O GLN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 566 through 570 Processing helix chain 'A' and resid 615 through 622 removed outlier: 4.546A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 637 Processing helix chain 'A' and resid 641 through 643 No H-bonds generated for 'chain 'A' and resid 641 through 643' Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'B' and resid 689 through 697 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.141A pdb=" N TYR B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 758 No H-bonds generated for 'chain 'B' and resid 756 through 758' Processing helix chain 'B' and resid 759 through 773 removed outlier: 3.789A pdb=" N ILE B 763 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3047 removed outlier: 4.097A pdb=" N PHE D3045 " --> pdb=" O ALA D3041 " (cutoff:3.500A) Processing helix chain 'D' and resid 3048 through 3050 No H-bonds generated for 'chain 'D' and resid 3048 through 3050' Processing helix chain 'D' and resid 3078 through 3090 removed outlier: 3.766A pdb=" N ASP D3090 " --> pdb=" O GLN D3086 " (cutoff:3.500A) Processing helix chain 'D' and resid 3096 through 3112 removed outlier: 3.722A pdb=" N ARG D3100 " --> pdb=" O PHE D3096 " (cutoff:3.500A) Processing helix chain 'D' and resid 3113 through 3117 Processing helix chain 'D' and resid 3118 through 3129 Processing helix chain 'D' and resid 3139 through 3158 removed outlier: 3.790A pdb=" N ARG D3153 " --> pdb=" O THR D3149 " (cutoff:3.500A) Processing helix chain 'D' and resid 3163 through 3180 Processing helix chain 'D' and resid 3189 through 3200 Processing helix chain 'D' and resid 3203 through 3216 Processing helix chain 'D' and resid 3223 through 3236 Processing helix chain 'D' and resid 3237 through 3242 removed outlier: 3.782A pdb=" N LEU D3241 " --> pdb=" O ILE D3237 " (cutoff:3.500A) Processing helix chain 'D' and resid 3244 through 3248 Processing helix chain 'D' and resid 3252 through 3263 Processing helix chain 'D' and resid 3270 through 3280 Processing helix chain 'D' and resid 3286 through 3298 Processing helix chain 'D' and resid 3331 through 3335 Processing helix chain 'D' and resid 3357 through 3374 Processing helix chain 'a' and resid 42 through 47 Processing helix chain 'a' and resid 94 through 98 removed outlier: 3.789A pdb=" N ARG a 98 " --> pdb=" O PRO a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 149 removed outlier: 3.758A pdb=" N VAL a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 163 removed outlier: 3.541A pdb=" N ALA a 154 " --> pdb=" O PRO a 150 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 182 Processing helix chain 'a' and resid 207 through 214 Processing helix chain 'a' and resid 215 through 224 Processing helix chain 'a' and resid 287 through 314 Proline residue: a 297 - end of helix removed outlier: 3.845A pdb=" N TYR a 310 " --> pdb=" O LEU a 306 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS a 314 " --> pdb=" O TYR a 310 " (cutoff:3.500A) Processing helix chain 'a' and resid 319 through 326 Processing helix chain 'a' and resid 327 through 343 Processing helix chain 'a' and resid 343 through 350 Processing helix chain 'b' and resid 58 through 90 removed outlier: 3.738A pdb=" N ILE b 90 " --> pdb=" O ILE b 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 60 Processing helix chain 'g' and resid 29 through 60 Processing helix chain 'g' and resid 283 through 287 removed outlier: 4.109A pdb=" N SER g 287 " --> pdb=" O GLN g 284 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 73 removed outlier: 3.909A pdb=" N PHE n 47 " --> pdb=" O CYS n 43 " (cutoff:3.500A) Proline residue: n 48 - end of helix removed outlier: 3.854A pdb=" N SER n 73 " --> pdb=" O MET n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 105 Processing helix chain 'n' and resid 109 through 146 Processing helix chain 'n' and resid 179 through 184 Processing helix chain 'n' and resid 184 through 216 Processing helix chain 'V' and resid 2 through 25 Processing helix chain 'V' and resid 32 through 48 Processing helix chain 'V' and resid 49 through 53 Processing helix chain 'V' and resid 54 through 65 removed outlier: 3.641A pdb=" N VAL V 58 " --> pdb=" O ASP V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 96 removed outlier: 3.554A pdb=" N LEU V 85 " --> pdb=" O LEU V 81 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE V 88 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG V 95 " --> pdb=" O GLN V 91 " (cutoff:3.500A) Processing helix chain 'V' and resid 105 through 120 removed outlier: 3.636A pdb=" N LEU V 110 " --> pdb=" O GLN V 106 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU V 111 " --> pdb=" O SER V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 140 Processing helix chain 'V' and resid 143 through 155 removed outlier: 3.541A pdb=" N LYS V 147 " --> pdb=" O LYS V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 175 Processing helix chain 'V' and resid 175 through 181 removed outlier: 4.034A pdb=" N THR V 179 " --> pdb=" O LEU V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 192 through 198 Processing helix chain 'V' and resid 205 through 214 Processing helix chain 'V' and resid 219 through 222 Processing helix chain 'V' and resid 223 through 234 removed outlier: 3.816A pdb=" N LEU V 227 " --> pdb=" O VAL V 223 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS V 229 " --> pdb=" O LEU V 225 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73 removed outlier: 6.842A pdb=" N GLN A 137 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 148 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 229 removed outlier: 6.971A pdb=" N THR A 189 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET A 242 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA7, first strand: chain 'A' and resid 645 through 652 removed outlier: 7.241A pdb=" N GLU B 658 " --> pdb=" O GLN A 648 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 650 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 656 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 608 " --> pdb=" O TRP B 659 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN B 661 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 606 " --> pdb=" O ASN B 661 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 3065 through 3068 Processing sheet with id=AA9, first strand: chain 'D' and resid 3137 through 3138 Processing sheet with id=AB1, first strand: chain 'D' and resid 3301 through 3302 Processing sheet with id=AB2, first strand: chain 'D' and resid 3328 through 3330 Processing sheet with id=AB3, first strand: chain 'a' and resid 26 through 29 Processing sheet with id=AB4, first strand: chain 'a' and resid 36 through 40 removed outlier: 3.694A pdb=" N LEU a 89 " --> pdb=" O HIS a 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 171 through 177 removed outlier: 6.379A pdb=" N LYS a 199 " --> pdb=" O LEU a 173 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE a 175 " --> pdb=" O TYR a 197 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR a 197 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU a 139 " --> pdb=" O ASN a 246 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ASN a 246 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 100 through 102 removed outlier: 3.660A pdb=" N GLU b 101 " --> pdb=" O ARG b 109 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG b 109 " --> pdb=" O GLU b 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU d 83 " --> pdb=" O LEU b 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE b 110 " --> pdb=" O GLU d 83 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER d 82 " --> pdb=" O TYR g 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'd' and resid 88 through 89 removed outlier: 6.311A pdb=" N SER b 114 " --> pdb=" O TYR d 89 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU g 78 " --> pdb=" O VAL b 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 118 through 119 removed outlier: 6.286A pdb=" N ILE b 119 " --> pdb=" O GLN d 94 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL b 145 " --> pdb=" O LEU g 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 131 through 134 removed outlier: 4.870A pdb=" N THR d 122 " --> pdb=" O ILE d 113 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE b 137 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN d 112 " --> pdb=" O ILE b 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY b 139 " --> pdb=" O ASN d 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU d 114 " --> pdb=" O GLY b 139 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE g 95 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN b 140 " --> pdb=" O ILE g 95 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER g 97 " --> pdb=" O ASN b 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 169 through 170 Processing sheet with id=AC2, first strand: chain 'd' and resid 140 through 141 removed outlier: 6.141A pdb=" N VAL d 140 " --> pdb=" O LEU d 148 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG g 166 " --> pdb=" O VAL d 156 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL g 167 " --> pdb=" O ASN b 199 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU b 198 " --> pdb=" O GLU d 178 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE d 177 " --> pdb=" O THR g 185 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 203 through 204 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 203 through 204 current: chain 'b' and resid 295 through 300 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 295 through 300 current: chain 'd' and resid 269 through 274 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 269 through 274 current: chain 'g' and resid 272 through 276 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'd' and resid 171 through 172 removed outlier: 6.694A pdb=" N THR d 171 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG b 207 " --> pdb=" O VAL g 179 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER g 202 " --> pdb=" O LEU d 190 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL b 232 " --> pdb=" O GLU d 217 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR d 219 " --> pdb=" O VAL b 232 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE b 234 " --> pdb=" O THR d 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 216 through 219 removed outlier: 6.041A pdb=" N LEU b 216 " --> pdb=" O VAL d 200 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLU d 202 " --> pdb=" O LEU b 216 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE b 218 " --> pdb=" O GLU d 202 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU d 199 " --> pdb=" O HIS g 210 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLU g 212 " --> pdb=" O LEU d 199 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET d 201 " --> pdb=" O GLU g 212 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU b 240 " --> pdb=" O ILE g 211 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA g 213 " --> pdb=" O GLU b 240 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS b 242 " --> pdb=" O ALA g 213 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE b 239 " --> pdb=" O ARG d 225 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLU d 227 " --> pdb=" O ILE b 239 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE b 241 " --> pdb=" O GLU d 227 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 260 through 261 removed outlier: 7.415A pdb=" N THR b 260 " --> pdb=" O LEU g 235 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'd' and resid 61 through 62 removed outlier: 3.604A pdb=" N GLY d 65 " --> pdb=" O THR d 62 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'd' and resid 69 through 71 Processing sheet with id=AC9, first strand: chain 'd' and resid 102 through 103 removed outlier: 6.269A pdb=" N PHE d 103 " --> pdb=" O ASN g 114 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ARG g 116 " --> pdb=" O PHE d 103 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY g 124 " --> pdb=" O ALA g 115 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'd' and resid 162 through 164 Processing sheet with id=AD2, first strand: chain 'g' and resid 152 through 153 Processing sheet with id=AD3, first strand: chain 'n' and resid 149 through 153 Processing sheet with id=AD4, first strand: chain 'V' and resid 75 through 76 removed outlier: 3.701A pdb=" N ILE V 127 " --> pdb=" O LEU V 76 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 238 through 239 removed outlier: 3.505A pdb=" N MET V 251 " --> pdb=" O HIS V 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 265 through 266 removed outlier: 3.668A pdb=" N TYR V 256 " --> pdb=" O LEU V 266 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2247 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: 6.90 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5562 1.33 - 1.46: 3626 1.46 - 1.58: 10507 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 19881 Sorted by residual: bond pdb=" C ALA n 153 " pdb=" N PRO n 154 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.53e+00 bond pdb=" N ILE B 769 " pdb=" CA ILE B 769 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.10e+00 bond pdb=" N ASP n 107 " pdb=" CA ASP n 107 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.81e+00 bond pdb=" N THR V 98 " pdb=" CA THR V 98 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 5.10e+00 bond pdb=" C MET V 96 " pdb=" N PRO V 97 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.20e-02 6.94e+03 4.50e+00 ... (remaining 19876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 26361 2.06 - 4.12: 501 4.12 - 6.19: 101 6.19 - 8.25: 18 8.25 - 10.31: 1 Bond angle restraints: 26982 Sorted by residual: angle pdb=" N GLY b 167 " pdb=" CA GLY b 167 " pdb=" C GLY b 167 " ideal model delta sigma weight residual 110.60 116.39 -5.79 1.46e+00 4.69e-01 1.57e+01 angle pdb=" C GLN n 113 " pdb=" N PHE n 114 " pdb=" CA PHE n 114 " ideal model delta sigma weight residual 121.14 114.38 6.76 1.75e+00 3.27e-01 1.49e+01 angle pdb=" N ARG a 319 " pdb=" CA ARG a 319 " pdb=" C ARG a 319 " ideal model delta sigma weight residual 114.56 110.13 4.43 1.27e+00 6.20e-01 1.22e+01 angle pdb=" C LEU g 36 " pdb=" N TYR g 37 " pdb=" CA TYR g 37 " ideal model delta sigma weight residual 121.58 114.93 6.65 1.95e+00 2.63e-01 1.16e+01 angle pdb=" CA ARG a 315 " pdb=" C ARG a 315 " pdb=" O ARG a 315 " ideal model delta sigma weight residual 122.14 118.22 3.92 1.24e+00 6.50e-01 9.99e+00 ... (remaining 26977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 11556 22.16 - 44.31: 659 44.31 - 66.47: 57 66.47 - 88.62: 55 88.62 - 110.78: 29 Dihedral angle restraints: 12356 sinusoidal: 5247 harmonic: 7109 Sorted by residual: dihedral pdb=" CB CYS n 157 " pdb=" SG CYS n 157 " pdb=" SG CYS n 179 " pdb=" CB CYS n 179 " ideal model delta sinusoidal sigma weight residual -86.00 -127.14 41.14 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CB CYS n 42 " pdb=" SG CYS n 42 " pdb=" SG CYS n 45 " pdb=" CB CYS n 45 " ideal model delta sinusoidal sigma weight residual 93.00 52.85 40.15 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" CA LYS B 743 " pdb=" C LYS B 743 " pdb=" N SER B 744 " pdb=" CA SER B 744 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 3163 0.165 - 0.331: 16 0.331 - 0.496: 2 0.496 - 0.662: 0 0.662 - 0.827: 1 Chirality restraints: 3182 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 649 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN b 258 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 661 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 3179 not shown) Planarity restraints: 3432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 649 " 0.028 2.00e-02 2.50e+03 2.63e-02 8.62e+00 pdb=" CG ASN A 649 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 649 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 649 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP b 87 " -0.016 2.00e-02 2.50e+03 1.42e-02 5.07e+00 pdb=" CG TRP b 87 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP b 87 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP b 87 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP b 87 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP b 87 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP b 87 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP b 87 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP b 87 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP b 87 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D3078 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO D3079 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D3079 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D3079 " 0.027 5.00e-02 4.00e+02 ... (remaining 3429 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2021 2.75 - 3.29: 19420 3.29 - 3.82: 33320 3.82 - 4.36: 37550 4.36 - 4.90: 62849 Nonbonded interactions: 155160 Sorted by model distance: nonbonded pdb=" O ILE a 337 " pdb=" OG1 THR a 341 " model vdw 2.212 3.040 nonbonded pdb=" O GLY b 245 " pdb=" OG SER d 228 " model vdw 2.264 3.040 nonbonded pdb=" NZ LYS B 794 " pdb=" O VAL B 796 " model vdw 2.264 3.120 nonbonded pdb=" O CYS n 45 " pdb=" OH TYR n 104 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASP V 168 " pdb=" OH TYR V 189 " model vdw 2.272 3.040 ... (remaining 155155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.780 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.090 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 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 : 0.004 0.048 19881 Z= 0.230 Angle : 0.712 10.310 26982 Z= 0.356 Chirality : 0.052 0.827 3182 Planarity : 0.005 0.049 3422 Dihedral : 15.490 110.779 7717 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -0.49 (0.17), residues: 2436 helix: 1.01 (0.19), residues: 767 sheet: -0.33 (0.29), residues: 313 loop : -1.14 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 87 HIS 0.006 0.001 HIS D3232 PHE 0.026 0.002 PHE n 114 TYR 0.016 0.001 TYR g 37 ARG 0.014 0.000 ARG D3293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.0214 (mtp) cc_final: -0.0657 (mtm) REVERT: A 286 MET cc_start: -0.5623 (ttm) cc_final: -0.6027 (mtp) REVERT: A 621 ASN cc_start: 0.8623 (m-40) cc_final: 0.8390 (p0) REVERT: D 3124 ASP cc_start: 0.8793 (m-30) cc_final: 0.8590 (t0) REVERT: D 3204 LEU cc_start: 0.8564 (tp) cc_final: 0.7903 (pt) REVERT: D 3227 LEU cc_start: 0.7474 (tp) cc_final: 0.7061 (tp) REVERT: D 3288 LEU cc_start: 0.9355 (tp) cc_final: 0.9105 (tt) REVERT: a 124 ILE cc_start: 0.6998 (mt) cc_final: 0.6163 (mt) REVERT: d 64 ASP cc_start: 0.7216 (m-30) cc_final: 0.6666 (m-30) REVERT: d 139 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6970 (mp0) REVERT: d 175 LYS cc_start: 0.8560 (mttt) cc_final: 0.8139 (mtpp) REVERT: d 225 ARG cc_start: 0.8338 (tpt-90) cc_final: 0.7969 (tpp80) REVERT: g 36 LEU cc_start: 0.8957 (mt) cc_final: 0.8569 (mt) REVERT: g 45 ILE cc_start: 0.8942 (pt) cc_final: 0.8720 (mm) REVERT: g 106 GLN cc_start: 0.8454 (pt0) cc_final: 0.8000 (pp30) REVERT: g 132 MET cc_start: 0.7611 (ppp) cc_final: 0.7397 (ptm) REVERT: g 204 ASP cc_start: 0.7484 (t0) cc_final: 0.7259 (t0) REVERT: n 95 LEU cc_start: 0.9038 (tt) cc_final: 0.8680 (mt) REVERT: n 116 MET cc_start: 0.7049 (mtt) cc_final: 0.6816 (ptp) REVERT: n 182 ILE cc_start: 0.5639 (mm) cc_final: 0.5279 (mp) REVERT: n 194 MET cc_start: 0.7504 (ppp) cc_final: 0.7164 (ppp) REVERT: V 1 MET cc_start: -0.3316 (tpt) cc_final: -0.3594 (mmm) REVERT: V 16 ARG cc_start: 0.7589 (tpt90) cc_final: 0.7200 (ttp80) REVERT: V 251 MET cc_start: 0.2291 (mpp) cc_final: 0.1556 (mpp) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3536 time to fit residues: 186.7598 Evaluate side-chains 187 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 0.0070 chunk 189 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 26 GLN a 338 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19881 Z= 0.276 Angle : 0.671 8.860 26982 Z= 0.337 Chirality : 0.046 0.276 3182 Planarity : 0.005 0.051 3422 Dihedral : 10.090 72.521 3145 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2436 helix: 1.16 (0.19), residues: 776 sheet: -0.34 (0.28), residues: 312 loop : -1.22 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 212 HIS 0.008 0.001 HIS a 333 PHE 0.025 0.002 PHE d 138 TYR 0.030 0.002 TYR g 37 ARG 0.005 0.000 ARG d 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 3053 PRO cc_start: 0.7007 (Cg_endo) cc_final: 0.6523 (Cg_exo) REVERT: D 3171 CYS cc_start: 0.9231 (t) cc_final: 0.9008 (t) REVERT: a 124 ILE cc_start: 0.6412 (mt) cc_final: 0.6035 (mt) REVERT: a 212 MET cc_start: 0.8230 (mmp) cc_final: 0.7244 (tpt) REVERT: b 126 THR cc_start: 0.7966 (m) cc_final: 0.7685 (p) REVERT: d 175 LYS cc_start: 0.8626 (mttt) cc_final: 0.8354 (mtpp) REVERT: g 36 LEU cc_start: 0.8875 (mt) cc_final: 0.8643 (mt) REVERT: n 95 LEU cc_start: 0.9073 (tt) cc_final: 0.8778 (mt) REVERT: n 116 MET cc_start: 0.7156 (mtt) cc_final: 0.6876 (ptp) REVERT: n 182 ILE cc_start: 0.5728 (mm) cc_final: 0.5403 (mp) REVERT: n 194 MET cc_start: 0.7519 (ppp) cc_final: 0.7206 (ppp) REVERT: V 1 MET cc_start: -0.2950 (tpt) cc_final: -0.3498 (mpp) REVERT: V 162 MET cc_start: 0.1956 (ttt) cc_final: 0.1675 (tpp) REVERT: V 164 TYR cc_start: 0.7723 (t80) cc_final: 0.7284 (t80) outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.3371 time to fit residues: 121.6773 Evaluate side-chains 175 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 220 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 GLN a 338 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 210 HIS n 158 GLN V 51 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19881 Z= 0.219 Angle : 0.626 12.407 26982 Z= 0.309 Chirality : 0.045 0.273 3182 Planarity : 0.004 0.053 3422 Dihedral : 7.637 52.446 3145 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -0.39 (0.17), residues: 2436 helix: 1.25 (0.19), residues: 771 sheet: -0.23 (0.27), residues: 334 loop : -1.21 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 62 HIS 0.006 0.001 HIS a 338 PHE 0.028 0.002 PHE d 37 TYR 0.026 0.001 TYR g 37 ARG 0.007 0.000 ARG n 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3979 (mtt) cc_final: -0.4236 (pmm) REVERT: A 560 LEU cc_start: 0.7817 (mt) cc_final: 0.7495 (mt) REVERT: D 3070 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6580 (tm-30) REVERT: D 3287 TRP cc_start: 0.8545 (p-90) cc_final: 0.8335 (p-90) REVERT: a 124 ILE cc_start: 0.6523 (mt) cc_final: 0.6218 (mt) REVERT: a 212 MET cc_start: 0.8294 (mmp) cc_final: 0.7320 (tpt) REVERT: d 175 LYS cc_start: 0.8621 (mttt) cc_final: 0.8320 (mtpp) REVERT: g 28 ILE cc_start: 0.5863 (mm) cc_final: 0.5613 (mm) REVERT: n 95 LEU cc_start: 0.8967 (tt) cc_final: 0.8668 (mt) REVERT: n 182 ILE cc_start: 0.5868 (mm) cc_final: 0.5525 (mp) REVERT: n 194 MET cc_start: 0.7529 (ppp) cc_final: 0.7204 (ppp) REVERT: n 211 MET cc_start: 0.8690 (tmm) cc_final: 0.8475 (tmm) REVERT: V 1 MET cc_start: -0.2982 (tpt) cc_final: -0.3298 (mmm) REVERT: V 22 MET cc_start: 0.3051 (tpp) cc_final: 0.2750 (mmm) REVERT: V 164 TYR cc_start: 0.7704 (t80) cc_final: 0.7268 (t80) REVERT: V 170 PHE cc_start: 0.8986 (t80) cc_final: 0.8729 (t80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3134 time to fit residues: 112.8954 Evaluate side-chains 172 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 8.9990 chunk 165 optimal weight: 0.3980 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 HIS ** B 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 156 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 308 GLN ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS ** g 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 GLN g 223 GLN ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN V 103 HIS ** V 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.178 19881 Z= 0.820 Angle : 1.178 17.933 26982 Z= 0.608 Chirality : 0.061 0.334 3182 Planarity : 0.008 0.078 3422 Dihedral : 8.398 50.829 3145 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.15 % Favored : 90.48 % Rotamer: Outliers : 0.89 % Allowed : 8.12 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.16), residues: 2436 helix: 0.31 (0.18), residues: 763 sheet: -0.95 (0.28), residues: 295 loop : -2.15 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 509 HIS 0.019 0.003 HIS b 103 PHE 0.057 0.005 PHE d 138 TYR 0.034 0.004 TYR g 37 ARG 0.009 0.001 ARG a 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 PHE cc_start: 0.8012 (t80) cc_final: 0.7683 (t80) REVERT: B 664 LEU cc_start: 0.8314 (mm) cc_final: 0.7949 (mt) REVERT: B 772 MET cc_start: 0.8570 (tpp) cc_final: 0.8306 (tpp) REVERT: D 3070 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6518 (tm-30) REVERT: a 124 ILE cc_start: 0.6329 (mt) cc_final: 0.6034 (mt) REVERT: a 212 MET cc_start: 0.8460 (mmp) cc_final: 0.7427 (tpt) REVERT: b 116 MET cc_start: 0.8166 (mmm) cc_final: 0.7879 (mtp) REVERT: b 247 MET cc_start: 0.8239 (tpt) cc_final: 0.7936 (tpt) REVERT: d 40 LEU cc_start: 0.8898 (pp) cc_final: 0.8365 (pp) REVERT: d 59 MET cc_start: 0.8809 (mmm) cc_final: 0.8539 (tpp) REVERT: g 106 GLN cc_start: 0.8982 (pt0) cc_final: 0.8444 (pp30) REVERT: g 218 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6171 (p) REVERT: n 51 LEU cc_start: 0.8841 (mt) cc_final: 0.8595 (tp) REVERT: n 160 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8279 (ttpp) REVERT: n 194 MET cc_start: 0.7760 (ppp) cc_final: 0.7503 (ppp) REVERT: V 1 MET cc_start: -0.3154 (tpt) cc_final: -0.3638 (mpp) REVERT: V 22 MET cc_start: 0.2192 (tpp) cc_final: 0.1988 (mmm) REVERT: V 164 TYR cc_start: 0.7924 (t80) cc_final: 0.7434 (t80) outliers start: 19 outliers final: 10 residues processed: 198 average time/residue: 0.3212 time to fit residues: 99.6316 Evaluate side-chains 168 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 119 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN D3043 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 219 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 308 GLN ** d 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19881 Z= 0.266 Angle : 0.728 9.962 26982 Z= 0.364 Chirality : 0.048 0.297 3182 Planarity : 0.005 0.060 3422 Dihedral : 6.976 49.562 3145 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -1.29 (0.16), residues: 2436 helix: 0.72 (0.19), residues: 772 sheet: -0.85 (0.27), residues: 318 loop : -1.89 (0.16), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 62 HIS 0.008 0.001 HIS a 333 PHE 0.030 0.002 PHE d 149 TYR 0.029 0.002 TYR g 37 ARG 0.015 0.001 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3999 (mtt) cc_final: -0.4284 (pmm) REVERT: D 3070 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6434 (tm-30) REVERT: D 3171 CYS cc_start: 0.9193 (t) cc_final: 0.8981 (t) REVERT: D 3287 TRP cc_start: 0.8566 (p-90) cc_final: 0.7903 (p-90) REVERT: a 212 MET cc_start: 0.8357 (mmp) cc_final: 0.7353 (tpt) REVERT: b 116 MET cc_start: 0.8162 (mmm) cc_final: 0.7639 (mtp) REVERT: b 262 MET cc_start: 0.7214 (mmp) cc_final: 0.6989 (mmm) REVERT: n 116 MET cc_start: 0.5284 (ptt) cc_final: 0.4610 (mtm) REVERT: n 160 LYS cc_start: 0.8576 (ptpp) cc_final: 0.8074 (ttpp) REVERT: n 194 MET cc_start: 0.7668 (ppp) cc_final: 0.7335 (ppp) REVERT: V 1 MET cc_start: -0.3147 (tpt) cc_final: -0.3653 (mpp) REVERT: V 22 MET cc_start: 0.2859 (tpp) cc_final: 0.2416 (mmm) REVERT: V 162 MET cc_start: 0.1760 (tpt) cc_final: 0.1530 (tpt) REVERT: V 164 TYR cc_start: 0.7735 (t80) cc_final: 0.7238 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3094 time to fit residues: 100.2814 Evaluate side-chains 151 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19881 Z= 0.329 Angle : 0.733 8.316 26982 Z= 0.371 Chirality : 0.048 0.342 3182 Planarity : 0.005 0.075 3422 Dihedral : 6.620 48.505 3145 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -1.17 (0.17), residues: 2436 helix: 0.84 (0.19), residues: 771 sheet: -0.86 (0.27), residues: 317 loop : -1.79 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 509 HIS 0.025 0.001 HIS b 318 PHE 0.037 0.002 PHE d 149 TYR 0.025 0.002 TYR g 37 ARG 0.012 0.001 ARG g 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3999 (mtt) cc_final: -0.4244 (pmm) REVERT: D 3070 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6360 (tm-30) REVERT: D 3349 MET cc_start: 0.5976 (tpt) cc_final: 0.5599 (tpp) REVERT: a 212 MET cc_start: 0.8382 (mmp) cc_final: 0.7285 (tpt) REVERT: b 116 MET cc_start: 0.8133 (mmm) cc_final: 0.7661 (mtp) REVERT: b 262 MET cc_start: 0.7325 (mmp) cc_final: 0.7044 (mmm) REVERT: n 94 TYR cc_start: 0.3985 (t80) cc_final: 0.3534 (t80) REVERT: n 160 LYS cc_start: 0.8448 (ptpp) cc_final: 0.7817 (ttpp) REVERT: n 194 MET cc_start: 0.7648 (ppp) cc_final: 0.7318 (ppp) REVERT: V 1 MET cc_start: -0.3133 (tpt) cc_final: -0.3640 (mpp) REVERT: V 145 MET cc_start: 0.7231 (mmp) cc_final: 0.6957 (mmt) REVERT: V 164 TYR cc_start: 0.7715 (t80) cc_final: 0.7220 (t80) REVERT: V 251 MET cc_start: 0.0413 (tmm) cc_final: -0.0519 (mpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3067 time to fit residues: 95.7478 Evaluate side-chains 151 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 142 optimal weight: 9.9990 chunk 107 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN B 673 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 249 GLN V 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19881 Z= 0.203 Angle : 0.646 8.861 26982 Z= 0.320 Chirality : 0.045 0.281 3182 Planarity : 0.005 0.057 3422 Dihedral : 6.024 46.080 3145 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.17), residues: 2436 helix: 0.93 (0.19), residues: 779 sheet: -0.66 (0.28), residues: 318 loop : -1.61 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3287 HIS 0.019 0.001 HIS b 318 PHE 0.019 0.002 PHE n 114 TYR 0.025 0.002 TYR g 37 ARG 0.013 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3864 (mtt) cc_final: -0.4151 (pmm) REVERT: D 3070 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6321 (tm-30) REVERT: D 3171 CYS cc_start: 0.9120 (t) cc_final: 0.8869 (t) REVERT: D 3349 MET cc_start: 0.5796 (tpt) cc_final: 0.5468 (tpp) REVERT: a 212 MET cc_start: 0.8371 (mmp) cc_final: 0.7354 (tpt) REVERT: b 116 MET cc_start: 0.8017 (mmm) cc_final: 0.7565 (mtp) REVERT: b 262 MET cc_start: 0.7254 (mmp) cc_final: 0.6933 (mmm) REVERT: d 41 LEU cc_start: 0.8968 (tp) cc_final: 0.8430 (tp) REVERT: g 28 ILE cc_start: 0.5860 (mm) cc_final: 0.5659 (mm) REVERT: n 94 TYR cc_start: 0.4110 (t80) cc_final: 0.3860 (t80) REVERT: n 160 LYS cc_start: 0.8509 (ptpp) cc_final: 0.7907 (ttpt) REVERT: n 194 MET cc_start: 0.7631 (ppp) cc_final: 0.7297 (ppp) REVERT: V 1 MET cc_start: -0.3138 (tpt) cc_final: -0.3606 (mpp) REVERT: V 145 MET cc_start: 0.7187 (mmp) cc_final: 0.6942 (mmt) REVERT: V 164 TYR cc_start: 0.7686 (t80) cc_final: 0.7191 (t80) REVERT: V 251 MET cc_start: 0.0452 (tmm) cc_final: -0.0369 (mpp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.3167 time to fit residues: 99.2783 Evaluate side-chains 156 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 212 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 648 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 124 HIS V 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19881 Z= 0.267 Angle : 0.667 8.008 26982 Z= 0.334 Chirality : 0.046 0.280 3182 Planarity : 0.005 0.057 3422 Dihedral : 5.909 45.178 3145 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -0.88 (0.17), residues: 2436 helix: 1.01 (0.19), residues: 775 sheet: -0.61 (0.28), residues: 315 loop : -1.61 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D3287 HIS 0.011 0.001 HIS b 318 PHE 0.021 0.002 PHE n 114 TYR 0.025 0.002 TYR g 37 ARG 0.008 0.000 ARG a 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3679 (mtt) cc_final: -0.3975 (pmm) REVERT: A 592 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7687 (pt0) REVERT: D 3070 GLU cc_start: 0.6801 (mm-30) cc_final: 0.5972 (tm-30) REVERT: D 3171 CYS cc_start: 0.9141 (t) cc_final: 0.8915 (t) REVERT: a 212 MET cc_start: 0.8373 (mmp) cc_final: 0.7383 (tpt) REVERT: b 116 MET cc_start: 0.8082 (mmm) cc_final: 0.7561 (mtp) REVERT: b 262 MET cc_start: 0.7290 (mmp) cc_final: 0.6966 (mmm) REVERT: n 94 TYR cc_start: 0.4082 (t80) cc_final: 0.3816 (t80) REVERT: n 160 LYS cc_start: 0.8542 (ptpp) cc_final: 0.7779 (ptmm) REVERT: n 194 MET cc_start: 0.7729 (ppp) cc_final: 0.7387 (ppp) REVERT: V 1 MET cc_start: -0.3144 (tpt) cc_final: -0.3603 (mpp) REVERT: V 164 TYR cc_start: 0.7684 (t80) cc_final: 0.7181 (t80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2941 time to fit residues: 89.1098 Evaluate side-chains 148 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 196 optimal weight: 0.5980 chunk 205 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19881 Z= 0.249 Angle : 0.670 9.602 26982 Z= 0.335 Chirality : 0.046 0.277 3182 Planarity : 0.005 0.097 3422 Dihedral : 5.781 44.063 3145 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -0.86 (0.17), residues: 2436 helix: 0.95 (0.19), residues: 785 sheet: -0.55 (0.28), residues: 315 loop : -1.56 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3287 HIS 0.009 0.001 HIS b 318 PHE 0.028 0.002 PHE A 635 TYR 0.027 0.002 TYR A 513 ARG 0.007 0.000 ARG a 345 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3684 (mtt) cc_final: -0.3982 (pmm) REVERT: D 3171 CYS cc_start: 0.9192 (t) cc_final: 0.8956 (t) REVERT: D 3349 MET cc_start: 0.5424 (tpt) cc_final: 0.4949 (tpp) REVERT: a 212 MET cc_start: 0.8369 (mmp) cc_final: 0.7331 (tpt) REVERT: b 116 MET cc_start: 0.8064 (mmm) cc_final: 0.7550 (mtp) REVERT: n 94 TYR cc_start: 0.4027 (t80) cc_final: 0.3760 (t80) REVERT: n 160 LYS cc_start: 0.8549 (ptpp) cc_final: 0.7791 (ptmm) REVERT: n 194 MET cc_start: 0.7722 (ppp) cc_final: 0.7388 (ppp) REVERT: V 1 MET cc_start: -0.3430 (tpt) cc_final: -0.3799 (mpp) REVERT: V 145 MET cc_start: 0.7404 (mmp) cc_final: 0.7138 (mmt) REVERT: V 164 TYR cc_start: 0.7670 (t80) cc_final: 0.7169 (t80) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.3059 time to fit residues: 91.4825 Evaluate side-chains 150 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 159 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19881 Z= 0.199 Angle : 0.645 9.181 26982 Z= 0.319 Chirality : 0.045 0.304 3182 Planarity : 0.005 0.092 3422 Dihedral : 5.490 41.946 3145 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2436 helix: 1.04 (0.19), residues: 780 sheet: -0.50 (0.28), residues: 328 loop : -1.48 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 509 HIS 0.009 0.001 HIS a 333 PHE 0.036 0.002 PHE n 47 TYR 0.021 0.001 TYR A 513 ARG 0.007 0.000 ARG a 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: -0.3673 (mtt) cc_final: -0.3982 (pmm) REVERT: D 3171 CYS cc_start: 0.9192 (t) cc_final: 0.8959 (t) REVERT: D 3349 MET cc_start: 0.5338 (tpt) cc_final: 0.4878 (tpp) REVERT: a 212 MET cc_start: 0.8355 (mmp) cc_final: 0.7294 (tpt) REVERT: b 116 MET cc_start: 0.7842 (mmm) cc_final: 0.7539 (mtp) REVERT: d 236 ASP cc_start: 0.7365 (t0) cc_final: 0.7062 (m-30) REVERT: g 28 ILE cc_start: 0.5920 (mm) cc_final: 0.5714 (mm) REVERT: n 160 LYS cc_start: 0.8547 (ptpp) cc_final: 0.7777 (ptmm) REVERT: n 194 MET cc_start: 0.7710 (ppp) cc_final: 0.7381 (ppp) REVERT: V 1 MET cc_start: -0.3434 (tpt) cc_final: -0.3799 (mpp) REVERT: V 164 TYR cc_start: 0.7650 (t80) cc_final: 0.7154 (t80) REVERT: V 251 MET cc_start: 0.0735 (tmm) cc_final: -0.0442 (mtt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2923 time to fit residues: 88.5906 Evaluate side-chains 154 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 3.9990 chunk 58 optimal weight: 0.0050 chunk 177 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 197 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.158895 restraints weight = 33828.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.157732 restraints weight = 41916.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.156521 restraints weight = 40749.101| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5233 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19881 Z= 0.188 Angle : 0.631 8.931 26982 Z= 0.310 Chirality : 0.044 0.260 3182 Planarity : 0.005 0.083 3422 Dihedral : 5.181 40.111 3145 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % 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: -0.58 (0.17), residues: 2436 helix: 1.14 (0.19), residues: 789 sheet: -0.10 (0.30), residues: 296 loop : -1.45 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3287 HIS 0.009 0.001 HIS a 333 PHE 0.024 0.002 PHE n 47 TYR 0.021 0.001 TYR g 37 ARG 0.010 0.000 ARG n 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3331.99 seconds wall clock time: 63 minutes 1.90 seconds (3781.90 seconds total)