Starting phenix.real_space_refine on Sun Aug 24 11:44:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_45165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_45165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_45165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_45165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3c_45165/08_2025/9c3c_45165.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.88, per 1000 atoms: 0.25 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: 1.89 Conformation dependent library (CDL) restraints added in 896.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.76 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: 4.13 Time building geometry restraints manager: 2.43 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.840 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- 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 19919 Z= 0.175 Angle : 0.722 10.310 27083 Z= 0.358 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 : 10.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG D3293 TYR 0.016 0.001 TYR g 37 PHE 0.026 0.002 PHE n 114 TRP 0.038 0.002 TRP b 87 HIS 0.006 0.001 HIS D3232 Details of bonding type rmsd covalent geometry : bond 0.00351 (19881) covalent geometry : angle 0.71178 (26982) SS BOND : bond 0.00156 ( 13) SS BOND : angle 0.93668 ( 26) hydrogen bonds : bond 0.15883 ( 797) hydrogen bonds : angle 6.63374 ( 2247) link_BETA1-4 : bond 0.00611 ( 15) link_BETA1-4 : angle 1.82934 ( 45) link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 3.03826 ( 30) *********************** 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 : 0.742 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: symmetry clash REVERT: A 202 MET cc_start: -0.0214 (mtp) cc_final: -0.0644 (mtm) REVERT: A 286 MET cc_start: -0.5623 (ttm) cc_final: -0.6010 (mtp) REVERT: A 621 ASN cc_start: 0.8623 (m-40) cc_final: 0.8388 (p0) REVERT: D 3124 ASP cc_start: 0.8793 (m-30) cc_final: 0.8591 (t0) REVERT: D 3204 LEU cc_start: 0.8564 (tp) cc_final: 0.7902 (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: 0.9106 (tt) REVERT: a 124 ILE cc_start: 0.6998 (mt) cc_final: 0.6159 (mt) REVERT: d 64 ASP cc_start: 0.7216 (m-30) cc_final: 0.6667 (m-30) REVERT: d 139 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6972 (mp0) REVERT: d 225 ARG cc_start: 0.8338 (tpt-90) cc_final: 0.7966 (tpp80) REVERT: g 36 LEU cc_start: 0.8957 (mt) cc_final: 0.8568 (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: 0.8024 (pp30) REVERT: g 132 MET cc_start: 0.7611 (ppp) cc_final: 0.7398 (ptm) REVERT: g 204 ASP cc_start: 0.7484 (t0) cc_final: 0.7262 (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: 0.6814 (ptp) REVERT: n 182 ILE cc_start: 0.5639 (mm) cc_final: 0.5280 (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: -0.3589 (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: 0.1728 time to fit residues: 91.5945 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 : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 648 GLN ** D3043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 26 GLN ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 GLN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 103 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.162911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.154813 restraints weight = 34525.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.154195 restraints weight = 44370.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.153187 restraints weight = 38868.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.152986 restraints weight = 35974.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.152749 restraints weight = 29618.301| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 19919 Z= 0.342 Angle : 0.871 9.605 27083 Z= 0.442 Chirality : 0.051 0.277 3182 Planarity : 0.006 0.068 3422 Dihedral : 9.680 65.896 3145 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 0.56 % Allowed : 7.00 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2436 helix: 1.01 (0.19), residues: 761 sheet: -0.51 (0.28), residues: 302 loop : -1.59 (0.16), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 70 TYR 0.039 0.002 TYR d 134 PHE 0.036 0.003 PHE d 138 TRP 0.019 0.002 TRP A 509 HIS 0.013 0.002 HIS b 103 Details of bonding type rmsd covalent geometry : bond 0.00758 (19881) covalent geometry : angle 0.86188 (26982) SS BOND : bond 0.00374 ( 13) SS BOND : angle 0.74018 ( 26) hydrogen bonds : bond 0.05210 ( 797) hydrogen bonds : angle 5.86924 ( 2247) link_BETA1-4 : bond 0.00851 ( 15) link_BETA1-4 : angle 2.59930 ( 45) link_NAG-ASN : bond 0.00988 ( 10) link_NAG-ASN : angle 2.52137 ( 30) *********************** 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 230 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.774 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: A 238 MET cc_start: -0.0024 (mtt) cc_final: -0.2447 (pmm) REVERT: A 577 MET cc_start: 0.7962 (mtt) cc_final: 0.7723 (mtp) REVERT: a 124 ILE cc_start: 0.5317 (mt) cc_final: 0.4933 (mt) REVERT: b 116 MET cc_start: 0.8066 (mmm) cc_final: 0.7607 (mmm) REVERT: b 153 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7754 (tt) REVERT: d 175 LYS cc_start: 0.8475 (mttt) cc_final: 0.8218 (mtpp) REVERT: d 202 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6815 (tm-30) REVERT: g 106 GLN cc_start: 0.8746 (pt0) cc_final: 0.8240 (pp30) REVERT: n 182 ILE cc_start: 0.4176 (mm) cc_final: 0.3928 (mp) REVERT: V 1 MET cc_start: 0.1808 (tpt) cc_final: 0.0559 (mpp) outliers start: 12 outliers final: 7 residues processed: 230 average time/residue: 0.1635 time to fit residues: 57.2713 Evaluate side-chains 170 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 221 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 216 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 196 optimal weight: 0.0270 chunk 171 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D3043 GLN D3302 HIS 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 139 GLN g 210 HIS n 158 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.178176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.177980 restraints weight = 34672.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.177958 restraints weight = 43125.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.177941 restraints weight = 46351.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.177934 restraints weight = 41536.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.177928 restraints weight = 36469.653| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4807 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19919 Z= 0.130 Angle : 0.646 11.014 27083 Z= 0.313 Chirality : 0.046 0.293 3182 Planarity : 0.004 0.056 3422 Dihedral : 7.711 50.235 3145 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.17), residues: 2436 helix: 1.19 (0.19), residues: 768 sheet: -0.38 (0.27), residues: 328 loop : -1.39 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 169 TYR 0.027 0.001 TYR g 37 PHE 0.027 0.002 PHE d 37 TRP 0.013 0.001 TRP g 62 HIS 0.004 0.001 HIS a 334 Details of bonding type rmsd covalent geometry : bond 0.00287 (19881) covalent geometry : angle 0.63734 (26982) SS BOND : bond 0.00164 ( 13) SS BOND : angle 0.71553 ( 26) hydrogen bonds : bond 0.03813 ( 797) hydrogen bonds : angle 5.30552 ( 2247) link_BETA1-4 : bond 0.00582 ( 15) link_BETA1-4 : angle 2.24164 ( 45) link_NAG-ASN : bond 0.00326 ( 10) link_NAG-ASN : angle 1.98906 ( 30) *********************** 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 231 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.807 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: A 238 MET cc_start: 0.0604 (mtt) cc_final: -0.2090 (pmm) REVERT: A 554 PHE cc_start: 0.4298 (t80) cc_final: 0.3930 (t80) REVERT: a 124 ILE cc_start: 0.5065 (mt) cc_final: 0.4822 (mt) REVERT: b 116 MET cc_start: 0.7973 (mmm) cc_final: 0.7224 (mmm) REVERT: d 37 PHE cc_start: 0.7097 (m-80) cc_final: 0.6697 (m-10) REVERT: d 202 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6646 (tm-30) REVERT: n 94 TYR cc_start: 0.3800 (t80) cc_final: 0.3422 (t80) REVERT: n 182 ILE cc_start: 0.3716 (mm) cc_final: 0.3460 (mp) REVERT: V 1 MET cc_start: 0.2038 (tpt) cc_final: 0.1033 (mpp) REVERT: V 145 MET cc_start: 0.4531 (mmp) cc_final: 0.3827 (mmt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1472 time to fit residues: 52.8849 Evaluate side-chains 170 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 197 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 103 optimal weight: 0.2980 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 26 GLN a 219 HIS a 338 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN g 96 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.165552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.157082 restraints weight = 34179.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.155948 restraints weight = 43320.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.154572 restraints weight = 41680.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.154161 restraints weight = 38828.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.153934 restraints weight = 31194.924| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5296 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19919 Z= 0.206 Angle : 0.689 12.191 27083 Z= 0.343 Chirality : 0.046 0.292 3182 Planarity : 0.005 0.055 3422 Dihedral : 6.690 48.427 3145 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.17), residues: 2436 helix: 1.21 (0.19), residues: 770 sheet: -0.39 (0.27), residues: 312 loop : -1.50 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 322 TYR 0.026 0.002 TYR g 37 PHE 0.025 0.002 PHE n 114 TRP 0.014 0.001 TRP g 62 HIS 0.008 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00463 (19881) covalent geometry : angle 0.68120 (26982) SS BOND : bond 0.00351 ( 13) SS BOND : angle 0.70932 ( 26) hydrogen bonds : bond 0.03990 ( 797) hydrogen bonds : angle 5.24512 ( 2247) link_BETA1-4 : bond 0.00594 ( 15) link_BETA1-4 : angle 2.18395 ( 45) link_NAG-ASN : bond 0.00566 ( 10) link_NAG-ASN : angle 1.96141 ( 30) *********************** 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 209 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.646 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: A 238 MET cc_start: -0.0348 (mtt) cc_final: -0.2728 (pmm) REVERT: a 124 ILE cc_start: 0.5553 (mt) cc_final: 0.5279 (mt) REVERT: g 106 GLN cc_start: 0.8557 (pt0) cc_final: 0.8051 (pp30) REVERT: n 116 MET cc_start: 0.4661 (ptt) cc_final: 0.4174 (ptt) REVERT: V 1 MET cc_start: 0.1252 (tpt) cc_final: 0.0033 (mpp) outliers start: 1 outliers final: 1 residues processed: 209 average time/residue: 0.1403 time to fit residues: 45.8696 Evaluate side-chains 161 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 12 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 20 optimal weight: 40.0000 chunk 42 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 673 GLN B 788 GLN ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 68 ASN ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.162109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.154168 restraints weight = 34637.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.153058 restraints weight = 43644.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.152034 restraints weight = 39566.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.151680 restraints weight = 40034.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.151348 restraints weight = 35581.287| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5379 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 19919 Z= 0.287 Angle : 0.800 11.104 27083 Z= 0.407 Chirality : 0.049 0.306 3182 Planarity : 0.006 0.058 3422 Dihedral : 6.705 49.106 3145 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2436 helix: 0.95 (0.19), residues: 775 sheet: -0.65 (0.27), residues: 317 loop : -1.77 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 598 TYR 0.029 0.002 TYR g 37 PHE 0.034 0.003 PHE b 146 TRP 0.017 0.002 TRP A 509 HIS 0.011 0.001 HIS b 103 Details of bonding type rmsd covalent geometry : bond 0.00642 (19881) covalent geometry : angle 0.79321 (26982) SS BOND : bond 0.00301 ( 13) SS BOND : angle 0.83943 ( 26) hydrogen bonds : bond 0.04488 ( 797) hydrogen bonds : angle 5.44141 ( 2247) link_BETA1-4 : bond 0.00573 ( 15) link_BETA1-4 : angle 2.14686 ( 45) link_NAG-ASN : bond 0.00837 ( 10) link_NAG-ASN : angle 2.16506 ( 30) *********************** 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 204 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.811 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: A 238 MET cc_start: 0.0054 (mtt) cc_final: -0.2573 (pmm) REVERT: A 577 MET cc_start: 0.7895 (mtt) cc_final: 0.7675 (mtp) REVERT: b 116 MET cc_start: 0.7979 (mmm) cc_final: 0.7446 (mtp) REVERT: g 106 GLN cc_start: 0.8760 (pt0) cc_final: 0.8306 (pp30) REVERT: n 94 TYR cc_start: 0.4497 (t80) cc_final: 0.4060 (t80) REVERT: n 99 MET cc_start: 0.5181 (ttt) cc_final: 0.4615 (ttt) REVERT: n 116 MET cc_start: 0.4686 (ptt) cc_final: 0.4133 (ptt) REVERT: V 1 MET cc_start: 0.1533 (tpt) cc_final: 0.0320 (mpp) REVERT: V 145 MET cc_start: 0.4415 (mmp) cc_final: 0.3600 (mmt) outliers start: 2 outliers final: 1 residues processed: 204 average time/residue: 0.1560 time to fit residues: 49.3054 Evaluate side-chains 160 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 38 optimal weight: 8.9990 chunk 161 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 220 optimal weight: 0.0980 chunk 221 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS g 106 GLN g 214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.177703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.167811 restraints weight = 351067.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.169521 restraints weight = 158832.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.169362 restraints weight = 139086.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.169309 restraints weight = 127508.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.169251 restraints weight = 125318.265| |-----------------------------------------------------------------------------| r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19919 Z= 0.126 Angle : 0.641 12.478 27083 Z= 0.313 Chirality : 0.045 0.273 3182 Planarity : 0.005 0.072 3422 Dihedral : 5.856 45.330 3145 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.17), residues: 2436 helix: 1.09 (0.19), residues: 783 sheet: -0.53 (0.27), residues: 335 loop : -1.54 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 221 TYR 0.030 0.001 TYR D3347 PHE 0.031 0.002 PHE d 37 TRP 0.019 0.001 TRP D3287 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00276 (19881) covalent geometry : angle 0.63519 (26982) SS BOND : bond 0.00438 ( 13) SS BOND : angle 0.99644 ( 26) hydrogen bonds : bond 0.03480 ( 797) hydrogen bonds : angle 5.10525 ( 2247) link_BETA1-4 : bond 0.00601 ( 15) link_BETA1-4 : angle 1.77965 ( 45) link_NAG-ASN : bond 0.00257 ( 10) link_NAG-ASN : angle 1.69445 ( 30) *********************** 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 211 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.771 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: A 238 MET cc_start: -0.1176 (mtt) cc_final: -0.3157 (pmm) REVERT: b 116 MET cc_start: 0.7797 (mmm) cc_final: 0.7056 (mtp) REVERT: d 37 PHE cc_start: 0.7680 (m-80) cc_final: 0.7374 (m-10) REVERT: g 106 GLN cc_start: 0.8522 (pt0) cc_final: 0.8296 (pp30) REVERT: n 94 TYR cc_start: 0.4594 (t80) cc_final: 0.4142 (t80) REVERT: n 99 MET cc_start: 0.5431 (ttp) cc_final: 0.5101 (ttt) REVERT: n 116 MET cc_start: 0.5119 (ptt) cc_final: 0.4526 (ptt) REVERT: V 1 MET cc_start: 0.1134 (tpt) cc_final: -0.0062 (mpp) REVERT: V 251 MET cc_start: 0.6119 (mpp) cc_final: 0.2671 (tmm) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1424 time to fit residues: 47.4687 Evaluate side-chains 163 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 18 optimal weight: 30.0000 chunk 198 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 89 optimal weight: 0.0030 chunk 210 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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** g 106 GLN V 51 HIS V 169 GLN V 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.167901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.159107 restraints weight = 33674.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.158033 restraints weight = 44387.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.157220 restraints weight = 38824.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.156860 restraints weight = 38137.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.156832 restraints weight = 31710.219| |-----------------------------------------------------------------------------| r_work (final): 0.4762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5218 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19919 Z= 0.135 Angle : 0.637 11.922 27083 Z= 0.310 Chirality : 0.045 0.359 3182 Planarity : 0.005 0.078 3422 Dihedral : 5.490 44.140 3145 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.17), residues: 2436 helix: 1.14 (0.19), residues: 783 sheet: -0.32 (0.28), residues: 326 loop : -1.49 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 319 TYR 0.023 0.001 TYR D3347 PHE 0.026 0.002 PHE d 149 TRP 0.020 0.001 TRP D3287 HIS 0.004 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00304 (19881) covalent geometry : angle 0.62986 (26982) SS BOND : bond 0.00311 ( 13) SS BOND : angle 0.92313 ( 26) hydrogen bonds : bond 0.03443 ( 797) hydrogen bonds : angle 5.02908 ( 2247) link_BETA1-4 : bond 0.00583 ( 15) link_BETA1-4 : angle 1.76930 ( 45) link_NAG-ASN : bond 0.00350 ( 10) link_NAG-ASN : angle 2.01430 ( 30) *********************** 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 205 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.813 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: 0.0103 (mtt) cc_final: -0.2472 (pmm) REVERT: A 242 MET cc_start: 0.2753 (ttt) cc_final: 0.2428 (ttt) REVERT: b 116 MET cc_start: 0.7742 (mmm) cc_final: 0.7037 (mtp) REVERT: b 225 ILE cc_start: 0.8900 (mp) cc_final: 0.8679 (mt) REVERT: d 37 PHE cc_start: 0.7720 (m-80) cc_final: 0.7249 (m-10) REVERT: g 106 GLN cc_start: 0.8431 (pt0) cc_final: 0.8216 (pp30) REVERT: n 94 TYR cc_start: 0.4383 (t80) cc_final: 0.3941 (t80) REVERT: n 99 MET cc_start: 0.5313 (ttp) cc_final: 0.4938 (ttt) REVERT: n 116 MET cc_start: 0.5020 (ptt) cc_final: 0.4551 (ptt) REVERT: V 1 MET cc_start: 0.0896 (tpt) cc_final: 0.0060 (mpp) REVERT: V 251 MET cc_start: 0.6192 (mpp) cc_final: 0.2675 (tmm) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1421 time to fit residues: 46.0625 Evaluate side-chains 158 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 104 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** a 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 112 GLN b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS g 106 GLN V 51 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.166724 restraints weight = 349885.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.168557 restraints weight = 157380.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.168341 restraints weight = 136445.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.168280 restraints weight = 127081.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.168089 restraints weight = 124310.385| |-----------------------------------------------------------------------------| r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5552 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19919 Z= 0.136 Angle : 0.629 8.678 27083 Z= 0.307 Chirality : 0.045 0.319 3182 Planarity : 0.005 0.076 3422 Dihedral : 5.293 42.863 3145 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.05 % Allowed : 1.27 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.17), residues: 2436 helix: 1.25 (0.19), residues: 776 sheet: -0.17 (0.29), residues: 313 loop : -1.47 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 776 TYR 0.023 0.001 TYR g 37 PHE 0.026 0.002 PHE d 149 TRP 0.021 0.001 TRP D3287 HIS 0.004 0.001 HIS n 214 Details of bonding type rmsd covalent geometry : bond 0.00306 (19881) covalent geometry : angle 0.62260 (26982) SS BOND : bond 0.00236 ( 13) SS BOND : angle 0.96549 ( 26) hydrogen bonds : bond 0.03390 ( 797) hydrogen bonds : angle 4.94121 ( 2247) link_BETA1-4 : bond 0.00547 ( 15) link_BETA1-4 : angle 1.68976 ( 45) link_NAG-ASN : bond 0.00316 ( 10) link_NAG-ASN : angle 1.96218 ( 30) *********************** 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 198 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.830 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: A 238 MET cc_start: -0.0687 (mtt) cc_final: -0.2903 (pmm) REVERT: A 242 MET cc_start: 0.2351 (ttt) cc_final: 0.2077 (ttt) REVERT: b 116 MET cc_start: 0.7688 (mmm) cc_final: 0.7021 (mtp) REVERT: n 94 TYR cc_start: 0.4868 (t80) cc_final: 0.4254 (t80) REVERT: n 116 MET cc_start: 0.5118 (ptt) cc_final: 0.4745 (ptt) REVERT: V 1 MET cc_start: 0.0734 (tpt) cc_final: -0.0151 (mpp) REVERT: V 145 MET cc_start: 0.5698 (mmp) cc_final: 0.4734 (mmt) REVERT: V 251 MET cc_start: 0.6907 (mpp) cc_final: 0.3404 (tmm) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.1414 time to fit residues: 44.6162 Evaluate side-chains 161 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 216 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 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 648 GLN ** a 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 112 GLN b 140 ASN b 169 GLN ** b 299 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.164738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.156423 restraints weight = 34369.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.155186 restraints weight = 43588.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.154612 restraints weight = 40833.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.154255 restraints weight = 36352.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.154027 restraints weight = 32585.115| |-----------------------------------------------------------------------------| r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5329 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19919 Z= 0.203 Angle : 0.699 8.955 27083 Z= 0.345 Chirality : 0.046 0.300 3182 Planarity : 0.005 0.072 3422 Dihedral : 5.560 43.238 3145 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.05 % Allowed : 0.89 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.17), residues: 2436 helix: 1.14 (0.19), residues: 785 sheet: -0.31 (0.28), residues: 315 loop : -1.56 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG n 169 TYR 0.022 0.002 TYR g 37 PHE 0.042 0.002 PHE d 149 TRP 0.022 0.001 TRP D3287 HIS 0.006 0.001 HIS B 752 Details of bonding type rmsd covalent geometry : bond 0.00459 (19881) covalent geometry : angle 0.69252 (26982) SS BOND : bond 0.00249 ( 13) SS BOND : angle 0.91637 ( 26) hydrogen bonds : bond 0.03819 ( 797) hydrogen bonds : angle 5.05601 ( 2247) link_BETA1-4 : bond 0.00521 ( 15) link_BETA1-4 : angle 1.78357 ( 45) link_NAG-ASN : bond 0.00545 ( 10) link_NAG-ASN : angle 2.08893 ( 30) *********************** 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 198 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.603 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: 0.0141 (mtt) cc_final: -0.2436 (pmm) REVERT: A 242 MET cc_start: 0.2324 (ttt) cc_final: 0.2065 (ttt) REVERT: b 116 MET cc_start: 0.7896 (mmm) cc_final: 0.7404 (mtp) REVERT: n 94 TYR cc_start: 0.4374 (t80) cc_final: 0.3943 (t80) REVERT: n 99 MET cc_start: 0.5504 (ttp) cc_final: 0.5143 (ttt) REVERT: n 116 MET cc_start: 0.5051 (ptt) cc_final: 0.4702 (ptt) REVERT: V 1 MET cc_start: 0.0572 (tpt) cc_final: -0.0290 (mpp) REVERT: V 251 MET cc_start: 0.6826 (mpp) cc_final: 0.3488 (tmm) outliers start: 1 outliers final: 1 residues processed: 198 average time/residue: 0.1384 time to fit residues: 43.9504 Evaluate side-chains 153 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 108 optimal weight: 0.7980 chunk 230 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 171 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** a 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 124 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.167779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.159165 restraints weight = 33822.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.158285 restraints weight = 41912.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.157242 restraints weight = 40303.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.157168 restraints weight = 36587.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.156876 restraints weight = 31471.465| |-----------------------------------------------------------------------------| r_work (final): 0.4762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5233 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19919 Z= 0.134 Angle : 0.644 8.789 27083 Z= 0.313 Chirality : 0.045 0.279 3182 Planarity : 0.004 0.069 3422 Dihedral : 5.293 41.639 3145 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.17), residues: 2436 helix: 1.21 (0.19), residues: 778 sheet: -0.22 (0.29), residues: 316 loop : -1.44 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.023 0.001 TYR g 37 PHE 0.024 0.002 PHE d 36 TRP 0.022 0.001 TRP D3287 HIS 0.012 0.001 HIS b 318 Details of bonding type rmsd covalent geometry : bond 0.00301 (19881) covalent geometry : angle 0.63817 (26982) SS BOND : bond 0.00193 ( 13) SS BOND : angle 0.85212 ( 26) hydrogen bonds : bond 0.03401 ( 797) hydrogen bonds : angle 4.92211 ( 2247) link_BETA1-4 : bond 0.00542 ( 15) link_BETA1-4 : angle 1.62846 ( 45) link_NAG-ASN : bond 0.00270 ( 10) link_NAG-ASN : angle 1.91439 ( 30) ********************** 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 197 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.500 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: 0.0699 (mtt) cc_final: -0.2124 (pmm) REVERT: A 242 MET cc_start: 0.2521 (ttt) cc_final: 0.2318 (ttt) REVERT: b 116 MET cc_start: 0.7775 (mmm) cc_final: 0.7211 (mtp) REVERT: b 225 ILE cc_start: 0.8917 (mp) cc_final: 0.8675 (mt) REVERT: n 99 MET cc_start: 0.5503 (ttp) cc_final: 0.5147 (ttt) REVERT: n 116 MET cc_start: 0.5190 (ptt) cc_final: 0.4739 (ptt) REVERT: V 1 MET cc_start: 0.0522 (tpt) cc_final: -0.0233 (mpp) REVERT: V 251 MET cc_start: 0.6794 (mpp) cc_final: 0.3333 (tmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.1391 time to fit residues: 43.8280 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 : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 233 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** D3173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 118 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** V 51 HIS V 124 HIS V 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.163536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.155342 restraints weight = 34191.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.153684 restraints weight = 42874.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.153349 restraints weight = 43968.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.152962 restraints weight = 41871.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.152729 restraints weight = 34607.662| |-----------------------------------------------------------------------------| r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 19919 Z= 0.228 Angle : 0.734 9.442 27083 Z= 0.366 Chirality : 0.047 0.278 3182 Planarity : 0.005 0.067 3422 Dihedral : 5.648 42.196 3145 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2436 helix: 1.03 (0.19), residues: 784 sheet: -0.38 (0.28), residues: 315 loop : -1.61 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG n 169 TYR 0.026 0.002 TYR V 90 PHE 0.039 0.002 PHE d 149 TRP 0.022 0.002 TRP D3287 HIS 0.023 0.001 HIS b 318 Details of bonding type rmsd covalent geometry : bond 0.00514 (19881) covalent geometry : angle 0.72763 (26982) SS BOND : bond 0.00274 ( 13) SS BOND : angle 0.89091 ( 26) hydrogen bonds : bond 0.03941 ( 797) hydrogen bonds : angle 5.12750 ( 2247) link_BETA1-4 : bond 0.00552 ( 15) link_BETA1-4 : angle 1.81721 ( 45) link_NAG-ASN : bond 0.00620 ( 10) link_NAG-ASN : angle 2.10373 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2551.73 seconds wall clock time: 45 minutes 46.19 seconds (2746.19 seconds total)