Starting phenix.real_space_refine on Tue Jun 17 06:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c3c_45165/06_2025/9c3c_45165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c3c_45165/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c3c_45165/06_2025/9c3c_45165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c3c_45165/06_2025/9c3c_45165.map" model { file = "/net/cci-nas-00/data/ceres_data/9c3c_45165/06_2025/9c3c_45165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c3c_45165/06_2025/9c3c_45165.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 12347 2.51 5 N 3346 2.21 5 O 3653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19475 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3081 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 23, 'TRANS': 376} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1103 Classifications: {'peptide': 145} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 128} Chain: "D" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2695 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 286} Chain breaks: 1 Chain: "b" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2003 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "d" Number of atoms: 2091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2091 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "g" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2025 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 253} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1340 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "V" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2341 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 280} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.12, per 1000 atoms: 0.62 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: 4.53 Conformation dependent library (CDL) restraints added in 2.6 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 33 sheets defined 35.8% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 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: 7.22 Time building geometry restraints manager: 5.38 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 45.870 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.090 ------------------------------------------------------------------------------- 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 : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2436 helix: 1.01 (0.19), residues: 767 sheet: -0.33 (0.29), residues: 313 loop : -1.14 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 87 HIS 0.006 0.001 HIS D3232 PHE 0.026 0.002 PHE n 114 TYR 0.016 0.001 TYR g 37 ARG 0.014 0.000 ARG D3293 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 10) link_NAG-ASN : angle 3.03826 ( 30) link_BETA1-4 : bond 0.00611 ( 15) link_BETA1-4 : angle 1.82934 ( 45) hydrogen bonds : bond 0.15883 ( 797) hydrogen bonds : angle 6.63374 ( 2247) SS BOND : bond 0.00156 ( 13) SS BOND : angle 0.93668 ( 26) covalent geometry : bond 0.00351 (19881) covalent geometry : angle 0.71178 (26982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: -0.0214 (mtp) cc_final: -0.0657 (mtm) REVERT: A 286 MET cc_start: -0.5623 (ttm) cc_final: -0.6027 (mtp) REVERT: A 621 ASN cc_start: 0.8623 (m-40) cc_final: 0.8390 (p0) REVERT: D 3124 ASP cc_start: 0.8793 (m-30) cc_final: 0.8590 (t0) REVERT: D 3204 LEU cc_start: 0.8564 (tp) cc_final: 0.7903 (pt) REVERT: D 3227 LEU cc_start: 0.7474 (tp) cc_final: 0.7061 (tp) REVERT: D 3288 LEU cc_start: 0.9355 (tp) cc_final: 0.9105 (tt) REVERT: a 124 ILE cc_start: 0.6998 (mt) cc_final: 0.6163 (mt) REVERT: d 64 ASP cc_start: 0.7216 (m-30) cc_final: 0.6666 (m-30) REVERT: d 139 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6970 (mp0) REVERT: d 175 LYS cc_start: 0.8560 (mttt) cc_final: 0.8139 (mtpp) REVERT: d 225 ARG cc_start: 0.8338 (tpt-90) cc_final: 0.7969 (tpp80) REVERT: g 36 LEU cc_start: 0.8957 (mt) cc_final: 0.8569 (mt) REVERT: g 45 ILE cc_start: 0.8942 (pt) cc_final: 0.8720 (mm) REVERT: g 106 GLN cc_start: 0.8454 (pt0) cc_final: 0.8000 (pp30) REVERT: g 132 MET cc_start: 0.7611 (ppp) cc_final: 0.7397 (ptm) REVERT: g 204 ASP cc_start: 0.7484 (t0) cc_final: 0.7259 (t0) REVERT: n 95 LEU cc_start: 0.9038 (tt) cc_final: 0.8680 (mt) REVERT: n 116 MET cc_start: 0.7049 (mtt) cc_final: 0.6816 (ptp) REVERT: n 182 ILE cc_start: 0.5639 (mm) cc_final: 0.5279 (mp) REVERT: n 194 MET cc_start: 0.7504 (ppp) cc_final: 0.7164 (ppp) REVERT: V 1 MET cc_start: -0.3316 (tpt) cc_final: -0.3594 (mmm) REVERT: V 16 ARG cc_start: 0.7589 (tpt90) cc_final: 0.7200 (ttp80) REVERT: V 251 MET cc_start: 0.2291 (mpp) cc_final: 0.1556 (mpp) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3483 time to fit residues: 184.6590 Evaluate side-chains 187 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 0.0070 chunk 189 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 GLN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 26 GLN a 338 HIS ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.169608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.160586 restraints weight = 33273.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.159424 restraints weight = 43567.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.158245 restraints weight = 37305.246| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5159 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19919 Z= 0.192 Angle : 0.681 8.860 27083 Z= 0.339 Chirality : 0.046 0.276 3182 Planarity : 0.005 0.051 3422 Dihedral : 10.090 72.521 3145 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.17), residues: 2436 helix: 1.16 (0.19), residues: 776 sheet: -0.34 (0.28), residues: 312 loop : -1.22 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 212 HIS 0.008 0.001 HIS a 333 PHE 0.025 0.002 PHE d 138 TYR 0.030 0.002 TYR g 37 ARG 0.005 0.000 ARG d 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 10) link_NAG-ASN : angle 2.10093 ( 30) link_BETA1-4 : bond 0.00586 ( 15) link_BETA1-4 : angle 2.30203 ( 45) hydrogen bonds : bond 0.04361 ( 797) hydrogen bonds : angle 5.52010 ( 2247) SS BOND : bond 0.00202 ( 13) SS BOND : angle 0.64849 ( 26) covalent geometry : bond 0.00422 (19881) covalent geometry : angle 0.67138 (26982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 233 time to evaluate : 2.334 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 124 ILE cc_start: 0.5601 (mt) cc_final: 0.5248 (mt) REVERT: b 126 THR cc_start: 0.7860 (m) cc_final: 0.7584 (p) REVERT: V 1 MET cc_start: 0.1573 (tpt) cc_final: 0.0293 (mpp) outliers start: 2 outliers final: 1 residues processed: 235 average time/residue: 0.3289 time to fit residues: 118.1240 Evaluate side-chains 172 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 74 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 GLN a 338 HIS ** b 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 HIS g 139 GLN g 210 HIS ** n 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 51 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.160989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.152963 restraints weight = 34775.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.152121 restraints weight = 46090.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.151346 restraints weight = 38532.857| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 19919 Z= 0.370 Angle : 0.898 13.161 27083 Z= 0.459 Chirality : 0.053 0.296 3182 Planarity : 0.006 0.058 3422 Dihedral : 8.281 51.309 3145 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.75 % Allowed : 6.53 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2436 helix: 0.78 (0.19), residues: 771 sheet: -0.57 (0.28), residues: 307 loop : -1.69 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 509 HIS 0.015 0.002 HIS b 103 PHE 0.033 0.003 PHE d 138 TYR 0.033 0.002 TYR g 37 ARG 0.013 0.001 ARG n 169 Details of bonding type rmsd link_NAG-ASN : bond 0.01090 ( 10) link_NAG-ASN : angle 2.57734 ( 30) link_BETA1-4 : bond 0.00589 ( 15) link_BETA1-4 : angle 2.54713 ( 45) hydrogen bonds : bond 0.05348 ( 797) hydrogen bonds : angle 5.81309 ( 2247) SS BOND : bond 0.00395 ( 13) SS BOND : angle 0.87105 ( 26) covalent geometry : bond 0.00822 (19881) covalent geometry : angle 0.88893 (26982) *********************** 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 212 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 2.021 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 202 MET cc_start: 0.0042 (mtm) cc_final: -0.0164 (mtm) REVERT: A 238 MET cc_start: 0.0213 (mtt) cc_final: -0.2386 (pmm) REVERT: a 124 ILE cc_start: 0.5426 (mt) cc_final: 0.5201 (mt) REVERT: b 116 MET cc_start: 0.8250 (mmm) cc_final: 0.7604 (mtp) REVERT: d 37 PHE cc_start: 0.7962 (m-80) cc_final: 0.7680 (m-10) REVERT: d 66 MET cc_start: 0.8735 (mpp) cc_final: 0.8257 (mpp) REVERT: d 84 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: g 106 GLN cc_start: 0.8857 (pt0) cc_final: 0.8350 (pp30) REVERT: n 99 MET cc_start: 0.5546 (ttt) cc_final: 0.5154 (ttp) REVERT: V 1 MET cc_start: 0.1881 (tpt) cc_final: 0.0665 (mpp) outliers start: 16 outliers final: 10 residues processed: 212 average time/residue: 0.3202 time to fit residues: 104.2553 Evaluate side-chains 162 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 91 optimal weight: 0.2980 chunk 150 optimal weight: 0.5980 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS D3043 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 219 HIS ** b 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN ** g 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.166664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.158001 restraints weight = 33936.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.156792 restraints weight = 44244.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.156154 restraints weight = 40130.899| |-----------------------------------------------------------------------------| r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19919 Z= 0.165 Angle : 0.682 11.191 27083 Z= 0.336 Chirality : 0.046 0.295 3182 Planarity : 0.005 0.055 3422 Dihedral : 6.902 47.859 3145 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2436 helix: 1.06 (0.19), residues: 769 sheet: -0.42 (0.28), residues: 315 loop : -1.58 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 62 HIS 0.005 0.001 HIS b 103 PHE 0.026 0.002 PHE n 114 TYR 0.028 0.001 TYR g 37 ARG 0.008 0.000 ARG D3100 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 10) link_NAG-ASN : angle 1.95879 ( 30) link_BETA1-4 : bond 0.00571 ( 15) link_BETA1-4 : angle 2.12059 ( 45) hydrogen bonds : bond 0.03939 ( 797) hydrogen bonds : angle 5.35312 ( 2247) SS BOND : bond 0.00207 ( 13) SS BOND : angle 0.96209 ( 26) covalent geometry : bond 0.00365 (19881) covalent geometry : angle 0.67357 (26982) *********************** 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 210 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 2.176 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: A 202 MET cc_start: -0.0163 (mtm) cc_final: -0.0411 (mtm) REVERT: A 238 MET cc_start: 0.0107 (mtt) cc_final: -0.2472 (pmm) REVERT: b 116 MET cc_start: 0.8056 (mmm) cc_final: 0.7575 (mmm) REVERT: d 37 PHE cc_start: 0.7801 (m-80) cc_final: 0.7588 (m-10) REVERT: n 94 TYR cc_start: 0.4352 (t80) cc_final: 0.3871 (t80) REVERT: n 116 MET cc_start: 0.4606 (ptt) cc_final: 0.4099 (ptt) REVERT: V 1 MET cc_start: 0.1373 (tpt) cc_final: 0.0171 (mpp) REVERT: V 145 MET cc_start: 0.4900 (mmp) cc_final: 0.4048 (mmt) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3085 time to fit residues: 100.9965 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 : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 142 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 221 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.163349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.155181 restraints weight = 34517.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.153495 restraints weight = 43764.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.153341 restraints weight = 42874.666| |-----------------------------------------------------------------------------| r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19919 Z= 0.237 Angle : 0.728 10.791 27083 Z= 0.368 Chirality : 0.047 0.300 3182 Planarity : 0.005 0.064 3422 Dihedral : 6.576 47.449 3145 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2436 helix: 0.98 (0.19), residues: 772 sheet: -0.61 (0.27), residues: 312 loop : -1.68 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 62 HIS 0.010 0.001 HIS A 212 PHE 0.025 0.002 PHE b 146 TYR 0.026 0.002 TYR g 37 ARG 0.013 0.001 ARG D3056 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 10) link_NAG-ASN : angle 1.96798 ( 30) link_BETA1-4 : bond 0.00550 ( 15) link_BETA1-4 : angle 2.10399 ( 45) hydrogen bonds : bond 0.04208 ( 797) hydrogen bonds : angle 5.36605 ( 2247) SS BOND : bond 0.00192 ( 13) SS BOND : angle 0.81117 ( 26) covalent geometry : bond 0.00538 (19881) covalent geometry : angle 0.72038 (26982) *********************** 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 201 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 2.069 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 202 MET cc_start: -0.0538 (mtm) cc_final: -0.0843 (mtm) REVERT: A 238 MET cc_start: -0.0360 (mtt) cc_final: -0.2767 (pmm) REVERT: a 124 ILE cc_start: 0.5462 (mt) cc_final: 0.5084 (mt) REVERT: b 116 MET cc_start: 0.8105 (mmm) cc_final: 0.7243 (mtp) REVERT: d 66 MET cc_start: 0.8684 (mpp) cc_final: 0.8389 (mpp) REVERT: g 106 GLN cc_start: 0.8597 (pt0) cc_final: 0.7906 (pp30) REVERT: n 94 TYR cc_start: 0.4714 (t80) cc_final: 0.3627 (t80) REVERT: n 116 MET cc_start: 0.4906 (ptt) cc_final: 0.4427 (ptt) REVERT: V 1 MET cc_start: 0.1148 (tpt) cc_final: -0.0097 (mpp) outliers start: 2 outliers final: 2 residues processed: 201 average time/residue: 0.3194 time to fit residues: 98.8567 Evaluate side-chains 157 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 228 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 chunk 145 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.158178 restraints weight = 34034.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.156933 restraints weight = 44259.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.155480 restraints weight = 42389.275| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19919 Z= 0.160 Angle : 0.663 11.696 27083 Z= 0.329 Chirality : 0.045 0.292 3182 Planarity : 0.005 0.056 3422 Dihedral : 6.026 45.316 3145 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2436 helix: 1.09 (0.19), residues: 771 sheet: -0.46 (0.28), residues: 317 loop : -1.58 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP g 62 HIS 0.006 0.001 HIS A 212 PHE 0.038 0.002 PHE d 149 TYR 0.030 0.001 TYR D3347 ARG 0.007 0.000 ARG d 221 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 10) link_NAG-ASN : angle 1.77423 ( 30) link_BETA1-4 : bond 0.00572 ( 15) link_BETA1-4 : angle 1.85317 ( 45) hydrogen bonds : bond 0.03730 ( 797) hydrogen bonds : angle 5.14895 ( 2247) SS BOND : bond 0.00206 ( 13) SS BOND : angle 0.94843 ( 26) covalent geometry : bond 0.00357 (19881) covalent geometry : angle 0.65612 (26982) *********************** 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 196 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.061 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 202 MET cc_start: -0.0518 (mtm) cc_final: -0.0792 (mtm) REVERT: A 238 MET cc_start: 0.0166 (mtt) cc_final: -0.2479 (pmm) REVERT: b 116 MET cc_start: 0.7970 (mmm) cc_final: 0.7176 (mtp) REVERT: g 106 GLN cc_start: 0.8545 (pt0) cc_final: 0.8030 (tm-30) REVERT: n 94 TYR cc_start: 0.4262 (t80) cc_final: 0.3864 (t80) REVERT: n 116 MET cc_start: 0.4546 (ptt) cc_final: 0.4255 (ptt) REVERT: V 1 MET cc_start: 0.1440 (tpt) cc_final: 0.0277 (mpp) REVERT: V 251 MET cc_start: 0.6297 (mpp) cc_final: 0.2756 (tmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2970 time to fit residues: 91.1288 Evaluate side-chains 155 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 215 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 151 optimal weight: 0.0770 chunk 160 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 249 GLN ** n 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.165816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.157361 restraints weight = 34054.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.156294 restraints weight = 43993.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.155260 restraints weight = 41202.932| |-----------------------------------------------------------------------------| r_work (final): 0.4749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19919 Z= 0.171 Angle : 0.671 11.948 27083 Z= 0.333 Chirality : 0.046 0.407 3182 Planarity : 0.005 0.087 3422 Dihedral : 5.799 44.329 3145 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2436 helix: 1.06 (0.19), residues: 777 sheet: -0.44 (0.27), residues: 322 loop : -1.57 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D3287 HIS 0.005 0.001 HIS A 212 PHE 0.036 0.002 PHE d 37 TYR 0.027 0.002 TYR V 90 ARG 0.014 0.000 ARG g 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 10) link_NAG-ASN : angle 2.21721 ( 30) link_BETA1-4 : bond 0.00546 ( 15) link_BETA1-4 : angle 1.79990 ( 45) hydrogen bonds : bond 0.03752 ( 797) hydrogen bonds : angle 5.12480 ( 2247) SS BOND : bond 0.00219 ( 13) SS BOND : angle 0.90006 ( 26) covalent geometry : bond 0.00385 (19881) covalent geometry : angle 0.66389 (26982) *********************** 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 195 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.174 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 202 MET cc_start: -0.0467 (mtm) cc_final: -0.0880 (mtm) REVERT: A 238 MET cc_start: 0.0602 (mtt) cc_final: -0.2241 (pmm) REVERT: b 116 MET cc_start: 0.8026 (mmm) cc_final: 0.7273 (mtp) REVERT: d 37 PHE cc_start: 0.7607 (m-80) cc_final: 0.7349 (m-10) REVERT: g 106 GLN cc_start: 0.8766 (pt0) cc_final: 0.8044 (tm-30) REVERT: n 94 TYR cc_start: 0.4433 (t80) cc_final: 0.4042 (t80) REVERT: n 116 MET cc_start: 0.4515 (ptt) cc_final: 0.4198 (ptt) REVERT: V 1 MET cc_start: 0.1456 (tpt) cc_final: 0.0441 (mpp) REVERT: V 251 MET cc_start: 0.6254 (mpp) cc_final: 0.2745 (tmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3087 time to fit residues: 94.5291 Evaluate side-chains 153 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 65 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS A 648 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 158 GLN V 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.166621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.158285 restraints weight = 33939.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.157006 restraints weight = 43181.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.155848 restraints weight = 40312.641| |-----------------------------------------------------------------------------| r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5242 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19919 Z= 0.153 Angle : 0.646 7.805 27083 Z= 0.321 Chirality : 0.045 0.326 3182 Planarity : 0.004 0.056 3422 Dihedral : 5.567 43.099 3145 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.17), residues: 2436 helix: 1.15 (0.19), residues: 771 sheet: -0.37 (0.28), residues: 315 loop : -1.51 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D3287 HIS 0.004 0.001 HIS A 212 PHE 0.025 0.002 PHE d 149 TYR 0.025 0.001 TYR g 37 ARG 0.005 0.000 ARG g 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 10) link_NAG-ASN : angle 2.01781 ( 30) link_BETA1-4 : bond 0.00544 ( 15) link_BETA1-4 : angle 1.70853 ( 45) hydrogen bonds : bond 0.03623 ( 797) hydrogen bonds : angle 5.04348 ( 2247) SS BOND : bond 0.00184 ( 13) SS BOND : angle 0.82659 ( 26) covalent geometry : bond 0.00342 (19881) covalent geometry : angle 0.63969 (26982) *********************** 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 195 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 2.080 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: 0.0623 (mtt) cc_final: -0.2235 (pmm) REVERT: b 116 MET cc_start: 0.7925 (mmm) cc_final: 0.7140 (mtp) REVERT: b 225 ILE cc_start: 0.8918 (mp) cc_final: 0.8679 (mt) REVERT: d 37 PHE cc_start: 0.7653 (m-80) cc_final: 0.7245 (m-10) REVERT: g 106 GLN cc_start: 0.8751 (pt0) cc_final: 0.7967 (tm-30) REVERT: n 94 TYR cc_start: 0.4326 (t80) cc_final: 0.3920 (t80) REVERT: n 99 MET cc_start: 0.5586 (ttp) cc_final: 0.5255 (ttt) REVERT: n 116 MET cc_start: 0.4813 (ptt) cc_final: 0.4382 (ptt) REVERT: V 1 MET cc_start: 0.0888 (tpt) cc_final: 0.0089 (mpp) REVERT: V 251 MET cc_start: 0.6181 (mpp) cc_final: 0.2724 (tmm) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2874 time to fit residues: 88.3190 Evaluate side-chains 157 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 233 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 13 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 303 GLN ** g 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 103 HIS V 229 HIS ** V 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.155629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.148006 restraints weight = 36170.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.146923 restraints weight = 51118.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.146579 restraints weight = 49078.403| |-----------------------------------------------------------------------------| r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.167 19919 Z= 0.509 Angle : 1.119 17.445 27083 Z= 0.573 Chirality : 0.060 0.342 3182 Planarity : 0.007 0.073 3422 Dihedral : 7.482 49.132 3145 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.10 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.16), residues: 2436 helix: 0.20 (0.18), residues: 773 sheet: -1.26 (0.29), residues: 300 loop : -2.07 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP g 56 HIS 0.017 0.003 HIS b 120 PHE 0.066 0.005 PHE b 102 TYR 0.027 0.003 TYR D3347 ARG 0.008 0.001 ARG d 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01598 ( 10) link_NAG-ASN : angle 3.41738 ( 30) link_BETA1-4 : bond 0.00738 ( 15) link_BETA1-4 : angle 2.47818 ( 45) hydrogen bonds : bond 0.06416 ( 797) hydrogen bonds : angle 6.13016 ( 2247) SS BOND : bond 0.00508 ( 13) SS BOND : angle 1.27264 ( 26) covalent geometry : bond 0.01147 (19881) covalent geometry : angle 1.11001 (26982) *********************** 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 182 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 2.091 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 89 LEU cc_start: 0.7292 (mp) cc_final: 0.6998 (mp) REVERT: d 37 PHE cc_start: 0.7899 (m-80) cc_final: 0.7571 (m-10) REVERT: d 66 MET cc_start: 0.8945 (mpp) cc_final: 0.8678 (mpp) REVERT: g 106 GLN cc_start: 0.9049 (pt0) cc_final: 0.8274 (tm-30) REVERT: n 94 TYR cc_start: 0.4356 (t80) cc_final: 0.3161 (t80) REVERT: n 99 MET cc_start: 0.5718 (ttp) cc_final: 0.5501 (ttt) REVERT: n 116 MET cc_start: 0.4808 (ptt) cc_final: 0.4467 (ptt) REVERT: V 1 MET cc_start: 0.1362 (tpt) cc_final: 0.0266 (mpp) REVERT: V 251 MET cc_start: 0.6496 (mpp) cc_final: 0.2886 (tmm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2932 time to fit residues: 84.9030 Evaluate side-chains 150 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 181 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 HIS A 648 GLN ** D3302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** b 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 284 ASN g 96 HIS ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.166486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.157995 restraints weight = 33751.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.156624 restraints weight = 43032.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.155623 restraints weight = 38114.629| |-----------------------------------------------------------------------------| r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5275 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19919 Z= 0.152 Angle : 0.738 12.453 27083 Z= 0.369 Chirality : 0.048 0.367 3182 Planarity : 0.005 0.105 3422 Dihedral : 6.182 44.002 3145 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2436 helix: 0.70 (0.18), residues: 779 sheet: -0.92 (0.27), residues: 340 loop : -1.67 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D3287 HIS 0.029 0.001 HIS b 318 PHE 0.032 0.002 PHE d 36 TYR 0.021 0.002 TYR g 37 ARG 0.006 0.001 ARG g 145 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 10) link_NAG-ASN : angle 2.24446 ( 30) link_BETA1-4 : bond 0.00636 ( 15) link_BETA1-4 : angle 1.75184 ( 45) hydrogen bonds : bond 0.03995 ( 797) hydrogen bonds : angle 5.37752 ( 2247) SS BOND : bond 0.00381 ( 13) SS BOND : angle 0.97141 ( 26) covalent geometry : bond 0.00328 (19881) covalent geometry : angle 0.73154 (26982) ********************** 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 198 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 2.075 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: B 741 PRO cc_start: 0.7046 (Cg_exo) cc_final: 0.6838 (Cg_endo) REVERT: b 225 ILE cc_start: 0.9010 (mp) cc_final: 0.8744 (mm) REVERT: d 37 PHE cc_start: 0.7773 (m-80) cc_final: 0.7429 (m-10) REVERT: g 106 GLN cc_start: 0.8583 (pt0) cc_final: 0.8017 (tm-30) REVERT: n 94 TYR cc_start: 0.4190 (t80) cc_final: 0.3756 (t80) REVERT: n 99 MET cc_start: 0.5317 (ttp) cc_final: 0.5041 (ttt) REVERT: n 116 MET cc_start: 0.5279 (ptt) cc_final: 0.4686 (ptt) REVERT: V 1 MET cc_start: 0.0609 (tpt) cc_final: -0.0086 (mpp) REVERT: V 251 MET cc_start: 0.6732 (mpp) cc_final: 0.3398 (tmm) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.3013 time to fit residues: 96.0006 Evaluate side-chains 157 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 132 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 185 optimal weight: 0.0980 chunk 49 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 140 ASN ** b 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 HIS V 169 GLN V 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176506 restraints weight = 34779.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176503 restraints weight = 53534.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.176500 restraints weight = 42251.845| |-----------------------------------------------------------------------------| r_work (final): 0.4873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4894 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19919 Z= 0.124 Angle : 0.650 9.364 27083 Z= 0.322 Chirality : 0.045 0.261 3182 Planarity : 0.005 0.090 3422 Dihedral : 5.464 40.688 3145 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2436 helix: 0.97 (0.19), residues: 775 sheet: -0.35 (0.28), residues: 316 loop : -1.47 (0.17), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D3287 HIS 0.016 0.001 HIS b 318 PHE 0.023 0.002 PHE n 114 TYR 0.018 0.001 TYR A 562 ARG 0.003 0.000 ARG d 225 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 10) link_NAG-ASN : angle 1.88021 ( 30) link_BETA1-4 : bond 0.00584 ( 15) link_BETA1-4 : angle 1.67163 ( 45) hydrogen bonds : bond 0.03508 ( 797) hydrogen bonds : angle 5.08495 ( 2247) SS BOND : bond 0.00161 ( 13) SS BOND : angle 0.91396 ( 26) covalent geometry : bond 0.00279 (19881) covalent geometry : angle 0.64364 (26982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4899.12 seconds wall clock time: 87 minutes 11.08 seconds (5231.08 seconds total)