Starting phenix.real_space_refine on Mon Jul 6 15:15:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zet_60044/07_2026/8zet_60044.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 10 5.49 5 Mg 146 5.21 5 S 147 5.16 5 C 25935 2.51 5 N 4771 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36577 Number of models: 1 Model: "" Number of chains: 31 Chain: "a" Number of atoms: 5852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5852 Classifications: {'peptide': 743} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 714} Chain: "b" Number of atoms: 5824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5824 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 698} Chain: "c" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 599 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "d" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1040 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 123} Chain: "e" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 503 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "f" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1242 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain: "g" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 981 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 256 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 29} Chain: "j" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 37} Chain: "l" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1095 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "m" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 683 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "B" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1285 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 11, 'TRANS': 153} Chain: "C" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1302 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 160} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1271 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "E" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1413 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "H" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1300 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain: "a" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 3079 Unusual residues: {'BCR': 5, 'CLA': 44, 'LHG': 3, 'LMG': 1, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 55} Link IDs: {None: 54} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'CLA:plan-5': 3, 'SQD:plan-1': 1} Unresolved non-hydrogen planarities: 17 Chain: "b" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 2850 Unusual residues: {'A86': 1, 'BCR': 4, 'CLA': 41, 'DGD': 1, 'LHG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 50} Link IDs: {None: 49} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-5': 4} Unresolved non-hydrogen planarities: 17 Chain: "c" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 255 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 140 Unusual residues: {'BCR': 2, 'CLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Chain: "j" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 207 Unusual residues: {'BCR': 2, 'CLA': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 321 Unusual residues: {'BCR': 2, 'CLA': 3, 'ET4': 1, 'LMG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 6 Chain: "m" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'A86': 1, 'BCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 133 Unusual residues: {'A86': 1, 'BCR': 1, 'CLA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 791 Unusual residues: {'A86': 4, 'CLA': 8, 'DD6': 1, 'KC1': 1, 'LHG': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-5': 2, 'CLA:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 899 Unusual residues: {'A86': 3, 'CLA': 11, 'DD6': 1, 'KC1': 2, 'LMG': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'CLA:plan-5': 7, 'CLA:plan-4': 5} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 850 Unusual residues: {'A86': 3, 'CLA': 11, 'DD6': 1, 'LHG': 1, 'LMG': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'CLA:plan-5': 5, 'CLA:plan-4': 3} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 896 Unusual residues: {'A86': 1, 'BCR': 2, 'CLA': 8, 'DD6': 4, 'LHG': 2, 'LMG': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 854 Unusual residues: {'A86': 3, 'CLA': 10, 'DD6': 1, 'KC1': 1, 'LHG': 1} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10285 SG CYS b 567 69.973 60.271 72.038 1.00 67.92 S ATOM 4515 SG CYS a 584 69.348 62.850 76.752 1.00 67.24 S ATOM 4460 SG CYS a 575 65.572 59.094 76.588 1.00 68.90 S ATOM 10230 SG CYS b 558 65.529 64.092 72.360 1.00 67.37 S ATOM 12043 SG CYS c 51 56.025 62.486 78.738 1.00 70.98 S ATOM 11825 SG CYS c 21 50.523 63.121 79.883 1.00 74.35 S ATOM 12069 SG CYS c 54 53.148 62.410 73.954 1.00 30.00 S ATOM 12026 SG CYS c 48 53.747 67.567 77.254 1.00 77.46 S ATOM 12096 SG CYS c 58 50.040 57.802 67.026 1.00 74.78 S ATOM 11796 SG CYS c 17 46.839 58.989 72.486 1.00 78.03 S ATOM 11774 SG CYS c 14 46.228 54.457 69.650 1.00 78.92 S ATOM 11756 SG CYS c 11 43.844 59.376 67.622 1.00 78.85 S Time building chain proxies: 6.40, per 1000 atoms: 0.17 Number of scatterers: 36577 At special positions: 0 Unit cell: (137.5, 151.8, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 147 16.00 P 10 15.00 Mg 146 11.99 O 5556 8.00 N 4771 7.00 C 25935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS f 32 " - pdb=" SG CYS f 87 " 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=115, symmetry=0 Number of additional bonds: simple=115, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 839.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 b 802 " pdb="FE1 SF4 b 802 " - pdb=" SG CYS b 567 " pdb="FE4 SF4 b 802 " - pdb=" SG CYS b 558 " pdb="FE3 SF4 b 802 " - pdb=" SG CYS a 575 " pdb="FE2 SF4 b 802 " - pdb=" SG CYS a 584 " pdb=" SF4 c 101 " pdb="FE1 SF4 c 101 " - pdb=" SG CYS c 51 " pdb="FE4 SF4 c 101 " - pdb=" SG CYS c 48 " pdb="FE2 SF4 c 101 " - pdb=" SG CYS c 21 " pdb="FE3 SF4 c 101 " - pdb=" SG CYS c 54 " pdb=" SF4 c 102 " pdb="FE3 SF4 c 102 " - pdb=" SG CYS c 14 " pdb="FE4 SF4 c 102 " - pdb=" SG CYS c 11 " pdb="FE2 SF4 c 102 " - pdb=" SG CYS c 17 " pdb="FE1 SF4 c 102 " - pdb=" SG CYS c 58 " Number of angles added : 36 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5842 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 14 sheets defined 63.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'a' and resid 27 through 31 Processing helix chain 'a' and resid 36 through 41 removed outlier: 3.898A pdb=" N LYS a 41 " --> pdb=" O ARG a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 55 removed outlier: 3.583A pdb=" N TRP a 50 " --> pdb=" O THR a 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS a 53 " --> pdb=" O ILE a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 63 Processing helix chain 'a' and resid 65 through 98 Processing helix chain 'a' and resid 100 through 107 Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 143 through 152 Processing helix chain 'a' and resid 156 through 183 Processing helix chain 'a' and resid 187 through 192 Processing helix chain 'a' and resid 193 through 204 Processing helix chain 'a' and resid 206 through 220 Processing helix chain 'a' and resid 220 through 231 Processing helix chain 'a' and resid 233 through 237 Processing helix chain 'a' and resid 239 through 246 removed outlier: 3.649A pdb=" N PHE a 243 " --> pdb=" O LEU a 239 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 254 removed outlier: 3.673A pdb=" N MET a 250 " --> pdb=" O ASN a 246 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU a 253 " --> pdb=" O LEU a 249 " (cutoff:3.500A) Processing helix chain 'a' and resid 256 through 260 Processing helix chain 'a' and resid 261 through 266 Processing helix chain 'a' and resid 268 through 275 removed outlier: 3.674A pdb=" N GLU a 271 " --> pdb=" O ASN a 268 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP a 274 " --> pdb=" O GLU a 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 290 through 309 Processing helix chain 'a' and resid 321 through 329 removed outlier: 3.521A pdb=" N HIS a 329 " --> pdb=" O ILE a 325 " (cutoff:3.500A) Processing helix chain 'a' and resid 340 through 348 Processing helix chain 'a' and resid 348 through 374 removed outlier: 3.698A pdb=" N TYR a 372 " --> pdb=" O ALA a 368 " (cutoff:3.500A) Processing helix chain 'a' and resid 383 through 416 Processing helix chain 'a' and resid 425 through 433 Processing helix chain 'a' and resid 433 through 465 removed outlier: 3.989A pdb=" N TYR a 456 " --> pdb=" O ALA a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 467 through 471 Processing helix chain 'a' and resid 481 through 494 Processing helix chain 'a' and resid 529 through 556 Processing helix chain 'a' and resid 565 through 570 removed outlier: 3.738A pdb=" N LEU a 569 " --> pdb=" O ASP a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 587 through 618 removed outlier: 3.874A pdb=" N PHE a 597 " --> pdb=" O PHE a 593 " (cutoff:3.500A) Processing helix chain 'a' and resid 635 through 640 Processing helix chain 'a' and resid 642 through 650 Processing helix chain 'a' and resid 650 through 655 Processing helix chain 'a' and resid 655 through 660 Processing helix chain 'a' and resid 666 through 689 removed outlier: 3.657A pdb=" N GLY a 670 " --> pdb=" O SER a 666 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU a 684 " --> pdb=" O TRP a 680 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET a 685 " --> pdb=" O ALA a 681 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE a 686 " --> pdb=" O PHE a 682 " (cutoff:3.500A) Processing helix chain 'a' and resid 690 through 708 removed outlier: 3.841A pdb=" N TRP a 694 " --> pdb=" O GLY a 690 " (cutoff:3.500A) Processing helix chain 'a' and resid 720 through 752 Processing helix chain 'b' and resid 9 through 14 Processing helix chain 'b' and resid 18 through 27 Processing helix chain 'b' and resid 30 through 34 Processing helix chain 'b' and resid 38 through 72 Processing helix chain 'b' and resid 73 through 80 Processing helix chain 'b' and resid 97 through 104 Processing helix chain 'b' and resid 118 through 127 Processing helix chain 'b' and resid 130 through 155 removed outlier: 3.517A pdb=" N LEU b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 163 through 168 Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 182 through 196 Processing helix chain 'b' and resid 196 through 202 Processing helix chain 'b' and resid 221 through 227 Processing helix chain 'b' and resid 228 through 234 Processing helix chain 'b' and resid 268 through 287 Processing helix chain 'b' and resid 299 through 307 removed outlier: 3.601A pdb=" N HIS b 307 " --> pdb=" O ILE b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 320 through 327 Processing helix chain 'b' and resid 328 through 354 removed outlier: 3.547A pdb=" N GLN b 332 " --> pdb=" O SER b 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR b 352 " --> pdb=" O ALA b 348 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA b 353 " --> pdb=" O GLN b 349 " (cutoff:3.500A) Processing helix chain 'b' and resid 363 through 396 Processing helix chain 'b' and resid 405 through 411 removed outlier: 3.561A pdb=" N MET b 410 " --> pdb=" O VAL b 406 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU b 411 " --> pdb=" O LEU b 407 " (cutoff:3.500A) Processing helix chain 'b' and resid 413 through 445 Processing helix chain 'b' and resid 447 through 451 Processing helix chain 'b' and resid 456 through 466 Processing helix chain 'b' and resid 475 through 479 Processing helix chain 'b' and resid 482 through 489 Processing helix chain 'b' and resid 492 through 501 Processing helix chain 'b' and resid 512 through 539 removed outlier: 3.707A pdb=" N LEU b 517 " --> pdb=" O PRO b 513 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL b 518 " --> pdb=" O GLY b 514 " (cutoff:3.500A) Processing helix chain 'b' and resid 548 through 552 Processing helix chain 'b' and resid 570 through 603 removed outlier: 3.833A pdb=" N ALA b 574 " --> pdb=" O SER b 570 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE b 575 " --> pdb=" O ALA b 571 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE b 580 " --> pdb=" O TYR b 576 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP b 581 " --> pdb=" O LEU b 577 " (cutoff:3.500A) Processing helix chain 'b' and resid 605 through 612 Processing helix chain 'b' and resid 614 through 622 removed outlier: 3.959A pdb=" N TRP b 618 " --> pdb=" O TYR b 614 " (cutoff:3.500A) Processing helix chain 'b' and resid 624 through 626 No H-bonds generated for 'chain 'b' and resid 624 through 626' Processing helix chain 'b' and resid 627 through 632 Processing helix chain 'b' and resid 642 through 665 removed outlier: 3.519A pdb=" N PHE b 660 " --> pdb=" O TRP b 656 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET b 661 " --> pdb=" O ALA b 657 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE b 662 " --> pdb=" O THR b 658 " (cutoff:3.500A) Processing helix chain 'b' and resid 666 through 684 removed outlier: 4.152A pdb=" N TRP b 670 " --> pdb=" O TRP b 666 " (cutoff:3.500A) Processing helix chain 'b' and resid 686 through 690 Processing helix chain 'b' and resid 700 through 733 removed outlier: 3.599A pdb=" N THR b 728 " --> pdb=" O VAL b 724 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 48 Processing helix chain 'c' and resid 52 through 58 Processing helix chain 'd' and resid 21 through 26 Processing helix chain 'd' and resid 62 through 76 Processing helix chain 'd' and resid 119 through 123 removed outlier: 3.697A pdb=" N ASN d 123 " --> pdb=" O ILE d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 130 Processing helix chain 'e' and resid 54 through 56 No H-bonds generated for 'chain 'e' and resid 54 through 56' Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 35 through 56 removed outlier: 4.019A pdb=" N GLN f 55 " --> pdb=" O GLN f 51 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR f 56 " --> pdb=" O ARG f 52 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 83 Processing helix chain 'f' and resid 100 through 106 removed outlier: 3.666A pdb=" N HIS f 103 " --> pdb=" O ARG f 100 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA f 105 " --> pdb=" O SER f 102 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 133 removed outlier: 3.527A pdb=" N GLY f 113 " --> pdb=" O LEU f 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 139 through 144 removed outlier: 3.655A pdb=" N ILE f 143 " --> pdb=" O SER f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 146 through 156 removed outlier: 3.507A pdb=" N THR f 156 " --> pdb=" O LYS f 152 " (cutoff:3.500A) Processing helix chain 'f' and resid 159 through 169 Processing helix chain 'g' and resid 100 through 107 removed outlier: 5.288A pdb=" N GLU g 105 " --> pdb=" O TRP g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 113 through 125 removed outlier: 3.530A pdb=" N GLU g 119 " --> pdb=" O GLN g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 139 Processing helix chain 'g' and resid 146 through 157 Processing helix chain 'g' and resid 160 through 165 Processing helix chain 'g' and resid 167 through 175 Processing helix chain 'g' and resid 176 through 177 No H-bonds generated for 'chain 'g' and resid 176 through 177' Processing helix chain 'i' and resid 2 through 5 Processing helix chain 'i' and resid 6 through 16 Proline residue: i 12 - end of helix Processing helix chain 'i' and resid 16 through 31 Processing helix chain 'j' and resid 2 through 9 Processing helix chain 'j' and resid 10 through 33 Processing helix chain 'l' and resid 9 through 11 No H-bonds generated for 'chain 'l' and resid 9 through 11' Processing helix chain 'l' and resid 24 through 34 Processing helix chain 'l' and resid 42 through 66 removed outlier: 3.702A pdb=" N TYR l 56 " --> pdb=" O LEU l 52 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE l 57 " --> pdb=" O ALA l 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU l 58 " --> pdb=" O HIS l 54 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE l 59 " --> pdb=" O GLY l 55 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY l 60 " --> pdb=" O TYR l 56 " (cutoff:3.500A) Proline residue: l 61 - end of helix Processing helix chain 'l' and resid 73 through 102 Processing helix chain 'l' and resid 113 through 141 removed outlier: 4.079A pdb=" N SER l 141 " --> pdb=" O ILE l 137 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 29 Processing helix chain 'r' and resid 60 through 65 Processing helix chain 'r' and resid 67 through 71 Processing helix chain 'r' and resid 72 through 100 Processing helix chain 'r' and resid 104 through 108 Processing helix chain 'r' and resid 111 through 118 Processing helix chain 'r' and resid 119 through 138 removed outlier: 3.582A pdb=" N LEU r 123 " --> pdb=" O LEU r 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 58 through 87 removed outlier: 3.857A pdb=" N VAL B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.533A pdb=" N GLN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 131 removed outlier: 3.646A pdb=" N TRP B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 183 Processing helix chain 'C' and resid 56 through 87 Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.942A pdb=" N VAL C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.788A pdb=" N LEU C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 184 removed outlier: 3.568A pdb=" N LEU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 57 through 88 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.800A pdb=" N VAL D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 133 removed outlier: 3.529A pdb=" N TRP D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 152 through 182 Processing helix chain 'E' and resid 39 through 50 Processing helix chain 'E' and resid 50 through 56 removed outlier: 4.099A pdb=" N TRP E 56 " --> pdb=" O GLN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 88 removed outlier: 3.780A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 116 through 139 Processing helix chain 'E' and resid 155 through 165 Processing helix chain 'E' and resid 179 through 204 Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'H' and resid 67 through 93 Processing helix chain 'H' and resid 106 through 115 removed outlier: 4.141A pdb=" N ILE H 111 " --> pdb=" O PRO H 107 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER H 112 " --> pdb=" O TRP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 133 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 157 through 189 Processing sheet with id=AA1, first strand: chain 'a' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'a' and resid 114 through 116 removed outlier: 4.079A pdb=" N GLN a 116 " --> pdb=" O ILE a 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 515 through 517 removed outlier: 6.817A pdb=" N ILE a 515 " --> pdb=" O ALA a 522 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS a 520 " --> pdb=" O VAL a 517 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 620 through 622 Processing sheet with id=AA5, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.669A pdb=" N ASN b 113 " --> pdb=" O ALA b 88 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 634 through 635 Processing sheet with id=AA7, first strand: chain 'c' and resid 65 through 68 removed outlier: 7.696A pdb=" N ARG d 116 " --> pdb=" O VAL c 5 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE c 7 " --> pdb=" O ARG d 116 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 27 through 30 Processing sheet with id=AA9, first strand: chain 'd' and resid 55 through 60 removed outlier: 6.677A pdb=" N ILE d 83 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'e' and resid 50 through 53 removed outlier: 6.678A pdb=" N VAL e 37 " --> pdb=" O ALA e 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 30 through 31 removed outlier: 4.068A pdb=" N LEU f 86 " --> pdb=" O HIS f 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'l' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'E' and resid 108 through 110 removed outlier: 6.860A pdb=" N ASN E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) 1483 hydrogen bonds defined for protein. 4239 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: 5.68 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.39: 13938 1.39 - 1.61: 23767 1.61 - 1.84: 248 1.84 - 2.06: 300 2.06 - 2.28: 320 Bond restraints: 38573 Sorted by residual: bond pdb=" C6 SQD a 849 " pdb=" S SQD a 849 " ideal model delta sigma weight residual 1.840 1.593 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2 LMG E 318 " pdb=" O2 LMG E 318 " ideal model delta sigma weight residual 1.405 1.172 0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C7 SQD a 849 " pdb=" O49 SQD a 849 " ideal model delta sigma weight residual 1.190 1.399 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C2 LMG D 202 " pdb=" O2 LMG D 202 " ideal model delta sigma weight residual 1.405 1.205 0.200 2.00e-02 2.50e+03 9.98e+01 bond pdb=" C25 LHG D 201 " pdb=" C26 LHG D 201 " ideal model delta sigma weight residual 1.527 1.338 0.189 2.00e-02 2.50e+03 8.91e+01 ... (remaining 38568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.85: 54494 9.85 - 19.70: 180 19.70 - 29.55: 8 29.55 - 39.40: 0 39.40 - 49.25: 3 Bond angle restraints: 54685 Sorted by residual: angle pdb=" C1 LMG j 103 " pdb=" C2 LMG j 103 " pdb=" O2 LMG j 103 " ideal model delta sigma weight residual 107.53 58.28 49.25 3.00e+00 1.11e-01 2.70e+02 angle pdb=" C1 LMG a 851 " pdb=" C2 LMG a 851 " pdb=" O2 LMG a 851 " ideal model delta sigma weight residual 107.53 64.35 43.18 3.00e+00 1.11e-01 2.07e+02 angle pdb=" C1 LMG C 301 " pdb=" C2 LMG C 301 " pdb=" O2 LMG C 301 " ideal model delta sigma weight residual 107.53 147.09 -39.56 3.00e+00 1.11e-01 1.74e+02 angle pdb=" C15 DD6 E 304 " pdb=" C20 DD6 E 304 " pdb=" C21 DD6 E 304 " ideal model delta sigma weight residual 121.84 95.14 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C31 BCR b 833 " pdb=" C1 BCR b 833 " pdb=" C32 BCR b 833 " ideal model delta sigma weight residual 108.53 82.06 26.47 3.00e+00 1.11e-01 7.79e+01 ... (remaining 54680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 17925 35.92 - 71.84: 1057 71.84 - 107.76: 228 107.76 - 143.67: 38 143.67 - 179.59: 4 Dihedral angle restraints: 19252 sinusoidal: 10088 harmonic: 9164 Sorted by residual: dihedral pdb=" CA HIS d 96 " pdb=" C HIS d 96 " pdb=" N PRO d 97 " pdb=" CA PRO d 97 " ideal model delta harmonic sigma weight residual 0.00 -37.46 37.46 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" C34 A86 r 203 " pdb=" C38 A86 r 203 " pdb=" O4 A86 r 203 " pdb=" C39 A86 r 203 " ideal model delta sinusoidal sigma weight residual 182.73 3.14 179.59 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 ET4 l 206 " pdb=" C23 ET4 l 206 " pdb=" C32 ET4 l 206 " pdb=" C33 ET4 l 206 " ideal model delta sinusoidal sigma weight residual 170.20 12.88 157.32 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 19249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 4572 0.309 - 0.618: 10 0.618 - 0.927: 12 0.927 - 1.235: 25 1.235 - 1.544: 2 Chirality restraints: 4621 Sorted by residual: chirality pdb=" C2 LMG C 301 " pdb=" C1 LMG C 301 " pdb=" C3 LMG C 301 " pdb=" O2 LMG C 301 " both_signs ideal model delta sigma weight residual False -2.53 -0.99 -1.54 2.00e-01 2.50e+01 5.96e+01 chirality pdb=" C20 DD6 E 304 " pdb=" C15 DD6 E 304 " pdb=" C19 DD6 E 304 " pdb=" C21 DD6 E 304 " both_signs ideal model delta sigma weight residual True 1.03 2.53 -1.49 2.00e-01 2.50e+01 5.58e+01 chirality pdb=" C15 A86 D 206 " pdb=" C14 A86 D 206 " pdb=" C16 A86 D 206 " pdb=" C20 A86 D 206 " both_signs ideal model delta sigma weight residual True 1.20 0.06 1.14 2.00e-01 2.50e+01 3.25e+01 ... (remaining 4618 not shown) Planarity restraints: 7058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND CLA a 801 " 0.072 2.00e-02 2.50e+03 6.02e-02 5.43e+01 pdb=" C1A CLA a 801 " -0.053 2.00e-02 2.50e+03 pdb=" C3D CLA a 801 " -0.085 2.00e-02 2.50e+03 pdb=" C4D CLA a 801 " -0.006 2.00e-02 2.50e+03 pdb=" CBD CLA a 801 " 0.080 2.00e-02 2.50e+03 pdb=" CHA CLA a 801 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D CLA a 801 " -0.025 2.00e-02 2.50e+03 3.79e-02 2.15e+01 pdb=" C2D CLA a 801 " -0.002 2.00e-02 2.50e+03 pdb=" C3D CLA a 801 " 0.077 2.00e-02 2.50e+03 pdb=" C4D CLA a 801 " -0.002 2.00e-02 2.50e+03 pdb=" CAD CLA a 801 " -0.045 2.00e-02 2.50e+03 pdb=" CMD CLA a 801 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND CLA a 854 " 0.035 2.00e-02 2.50e+03 3.66e-02 2.01e+01 pdb=" C1A CLA a 854 " -0.040 2.00e-02 2.50e+03 pdb=" C3D CLA a 854 " -0.056 2.00e-02 2.50e+03 pdb=" C4D CLA a 854 " 0.012 2.00e-02 2.50e+03 pdb=" CBD CLA a 854 " 0.043 2.00e-02 2.50e+03 pdb=" CHA CLA a 854 " 0.007 2.00e-02 2.50e+03 ... (remaining 7055 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1177 2.68 - 3.24: 33851 3.24 - 3.79: 63164 3.79 - 4.35: 83970 4.35 - 4.90: 136706 Nonbonded interactions: 318868 Sorted by model distance: nonbonded pdb=" O1 LMG a 851 " pdb=" O2 LMG a 851 " model vdw 2.129 2.432 nonbonded pdb=" O1 LMG j 103 " pdb=" O2 LMG j 103 " model vdw 2.134 2.432 nonbonded pdb=" OH TYR f 80 " pdb=" O ASP j 35 " model vdw 2.243 3.040 nonbonded pdb=" C18 A86 r 203 " pdb=" O1 A86 r 203 " model vdw 2.267 2.776 nonbonded pdb=" C1 A86 H 302 " pdb=" CMD CLA H 309 " model vdw 2.275 3.690 ... (remaining 318863 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 33.480 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 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 : 0.021 0.795 38701 Z= 1.248 Angle : 1.651 61.263 54723 Z= 0.710 Chirality : 0.104 1.544 4621 Planarity : 0.005 0.060 7058 Dihedral : 22.140 179.592 13407 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.09 % Rotamer: Outliers : 1.61 % Allowed : 3.72 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.14), residues: 3195 helix: 1.54 (0.11), residues: 1809 sheet: -0.92 (0.50), residues: 92 loop : -1.10 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 572 TYR 0.015 0.001 TYR b 634 PHE 0.017 0.001 PHE j 25 TRP 0.014 0.001 TRP b 656 HIS 0.006 0.001 HIS r 128 Details of bonding type rmsd/Z covalent geometry : bond 0.01110 / 0.64 (38573) covalent geometry : angle 1.57245 / 0.71 (54685) SS BOND : bond 0.00258 / 0.14 ( 1) SS BOND : angle 0.13901 / 0.08 ( 2) hydrogen bonds : bond 0.19864 / 13.25 ( 1483) hydrogen bonds : angle 6.40174 / 4.66 ( 4239) metal coordination : bond 0.35629 / 20.87 ( 12) metal coordination : angle 19.68448 / 13.68 ( 36) Misc. bond : bond 0.29924 / 20.18 ( 115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 509 time to evaluate : 0.800 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: a 107 ASP cc_start: 0.8029 (t0) cc_final: 0.7506 (t0) REVERT: a 147 MET cc_start: 0.9150 (ttp) cc_final: 0.8790 (ttt) REVERT: a 413 MET cc_start: 0.8816 (mmm) cc_final: 0.8528 (mmm) REVERT: a 599 MET cc_start: 0.8643 (tmm) cc_final: 0.8401 (tmm) REVERT: d 50 ILE cc_start: 0.9140 (mt) cc_final: 0.8936 (tp) REVERT: l 105 LYS cc_start: 0.7261 (ptmm) cc_final: 0.6560 (mmmt) REVERT: C 61 ASP cc_start: 0.8599 (m-30) cc_final: 0.7695 (m-30) REVERT: C 68 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8598 (tt) REVERT: C 81 TYR cc_start: 0.8113 (t80) cc_final: 0.7843 (t80) REVERT: C 156 ILE cc_start: 0.8191 (mp) cc_final: 0.7742 (mp) REVERT: C 157 ASP cc_start: 0.8481 (t0) cc_final: 0.8204 (t0) REVERT: D 63 TYR cc_start: 0.8790 (t80) cc_final: 0.8180 (t80) REVERT: E 155 MET cc_start: 0.8277 (mmt) cc_final: 0.7969 (mmt) REVERT: E 175 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8233 (mppt) REVERT: H 38 PHE cc_start: 0.8304 (p90) cc_final: 0.6757 (t80) REVERT: H 154 SER cc_start: 0.8538 (m) cc_final: 0.8114 (t) outliers start: 42 outliers final: 4 residues processed: 541 average time/residue: 0.2157 time to fit residues: 191.0505 Evaluate side-chains 309 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 304 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 658 VAL Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain c residue 65 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 14 GLN a 134 ASN a 321 ASN a 421 ASN a 478 GLN a 489 ASN a 501 ASN b 10 GLN b 14 GLN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 451 GLN b 472 GLN b 474 ASN b 626 ASN b 688 ASN d 53 ASN d 65 GLN d 114 ASN f 94 HIS f 166 GLN f 171 ASN l 9 ASN r 93 GLN r 137 ASN B 69 ASN B 181 HIS ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 165 ASN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 ASN H 185 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.086881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.070971 restraints weight = 95672.348| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.17 r_work: 0.3032 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 2.324 38701 Z= 1.196 Angle : 0.928 36.883 54723 Z= 0.351 Chirality : 0.060 0.908 4621 Planarity : 0.005 0.054 7058 Dihedral : 20.837 156.157 7861 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.84 % Allowed : 7.71 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 3195 helix: 2.08 (0.12), residues: 1832 sheet: -0.56 (0.53), residues: 92 loop : -0.70 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG f 76 TYR 0.017 0.001 TYR b 716 PHE 0.026 0.002 PHE j 25 TRP 0.017 0.001 TRP r 125 HIS 0.011 0.002 HIS b 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (38573) covalent geometry : angle 0.87089 / 0.35 (54685) SS BOND : bond 0.02117 / 1.11 ( 1) SS BOND : angle 1.74192 / 1.01 ( 2) hydrogen bonds : bond 0.05759 / 3.83 ( 1483) hydrogen bonds : angle 4.48893 / 3.30 ( 4239) metal coordination : bond 0.01451 / 0.86 ( 12) metal coordination : angle 12.52663 / 9.31 ( 36) Misc. bond : bond 0.31082 / 20.17 ( 115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 344 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8293 (t0) cc_final: 0.7649 (t0) REVERT: a 460 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8675 (t0) REVERT: c 46 GLU cc_start: 0.8905 (pm20) cc_final: 0.8324 (pm20) REVERT: d 53 ASN cc_start: 0.8437 (t0) cc_final: 0.8083 (t0) REVERT: d 55 GLU cc_start: 0.8876 (mp0) cc_final: 0.8481 (mt-10) REVERT: d 138 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8424 (mt-10) REVERT: e 4 ARG cc_start: 0.8577 (mtp85) cc_final: 0.8137 (mtp-110) REVERT: f 172 ASP cc_start: 0.8827 (t0) cc_final: 0.8550 (t0) REVERT: g 107 ILE cc_start: 0.8629 (mm) cc_final: 0.8413 (mt) REVERT: g 113 ASP cc_start: 0.7474 (t0) cc_final: 0.6775 (t0) REVERT: g 135 GLU cc_start: 0.6231 (tt0) cc_final: 0.6014 (tt0) REVERT: g 166 MET cc_start: 0.7042 (mtp) cc_final: 0.6388 (mmp) REVERT: l 71 SER cc_start: 0.8340 (m) cc_final: 0.7849 (t) REVERT: l 105 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.5863 (mmmt) REVERT: r 64 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7752 (tp) REVERT: r 125 TRP cc_start: 0.7490 (t60) cc_final: 0.7006 (t60) REVERT: B 159 MET cc_start: 0.9055 (mmm) cc_final: 0.8776 (mmm) REVERT: C 57 GLN cc_start: 0.7676 (tm-30) cc_final: 0.6872 (tm-30) REVERT: C 61 ASP cc_start: 0.8729 (m-30) cc_final: 0.8322 (m-30) REVERT: C 68 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8733 (tt) REVERT: C 152 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 156 ILE cc_start: 0.8413 (mp) cc_final: 0.7864 (mp) REVERT: C 171 MET cc_start: 0.8367 (tpp) cc_final: 0.8105 (tpp) REVERT: C 191 ASP cc_start: 0.8475 (p0) cc_final: 0.8195 (p0) REVERT: D 61 MET cc_start: 0.9448 (mmm) cc_final: 0.9146 (mmm) REVERT: D 63 TYR cc_start: 0.9106 (t80) cc_final: 0.8264 (t80) REVERT: D 66 GLU cc_start: 0.8751 (tp30) cc_final: 0.8200 (tp30) REVERT: D 94 ASN cc_start: 0.8993 (m110) cc_final: 0.8681 (m110) REVERT: D 152 ASP cc_start: 0.8470 (t0) cc_final: 0.8214 (t0) REVERT: D 170 MET cc_start: 0.8436 (mtm) cc_final: 0.8173 (mtm) REVERT: D 189 MET cc_start: 0.8398 (mtm) cc_final: 0.8150 (mtm) REVERT: E 41 ASP cc_start: 0.7707 (p0) cc_final: 0.7506 (p0) REVERT: E 45 ASP cc_start: 0.8652 (m-30) cc_final: 0.8439 (m-30) REVERT: E 48 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8637 (pt0) REVERT: E 86 LYS cc_start: 0.8349 (tppp) cc_final: 0.7985 (tppp) REVERT: E 175 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8155 (mppt) REVERT: H 106 ASP cc_start: 0.7960 (t0) cc_final: 0.7576 (t0) REVERT: H 109 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7800 (mm-30) REVERT: H 149 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.7953 (m) REVERT: H 152 GLN cc_start: 0.7173 (mm-40) cc_final: 0.5830 (mm-40) REVERT: H 154 SER cc_start: 0.8855 (m) cc_final: 0.8035 (t) outliers start: 48 outliers final: 23 residues processed: 368 average time/residue: 0.2073 time to fit residues: 127.6319 Evaluate side-chains 326 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 460 ASP Chi-restraints excluded: chain a residue 658 VAL Chi-restraints excluded: chain b residue 345 SER Chi-restraints excluded: chain b residue 511 ILE Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 174 THR Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 2 ASN Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain r residue 64 LEU Chi-restraints excluded: chain r residue 68 MET Chi-restraints excluded: chain r residue 73 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 162 optimal weight: 4.9990 chunk 287 optimal weight: 4.9990 chunk 236 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 286 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 314 optimal weight: 1.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 GLN ** b 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 330 HIS b 597 HIS b 607 GLN f 103 HIS m 6 GLN ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN E 63 GLN ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.076147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.061538 restraints weight = 97489.346| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.03 r_work: 0.2852 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 1.009 38701 Z= 0.300 Angle : 0.956 15.992 54723 Z= 0.382 Chirality : 0.062 0.867 4621 Planarity : 0.006 0.050 7058 Dihedral : 19.888 131.692 7859 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.26 % Allowed : 9.09 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3195 helix: 1.76 (0.12), residues: 1834 sheet: 0.03 (0.65), residues: 80 loop : -0.69 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 76 TYR 0.021 0.002 TYR b 716 PHE 0.030 0.002 PHE b 649 TRP 0.021 0.002 TRP g 102 HIS 0.017 0.002 HIS b 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (38573) covalent geometry : angle 0.93450 / 0.38 (54685) SS BOND : bond 0.00166 / 0.09 ( 1) SS BOND : angle 3.24810 / 1.90 ( 2) hydrogen bonds : bond 0.06919 / 4.64 ( 1483) hydrogen bonds : angle 4.59404 / 3.38 ( 4239) metal coordination : bond 0.02361 / 1.42 ( 12) metal coordination : angle 7.89192 / 4.99 ( 36) Misc. bond : bond 0.18490 / 12.94 ( 115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 296 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8751 (t0) cc_final: 0.8112 (t0) REVERT: b 648 MET cc_start: 0.8979 (ttm) cc_final: 0.8776 (ttp) REVERT: c 46 GLU cc_start: 0.9087 (pm20) cc_final: 0.8427 (pm20) REVERT: d 52 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7675 (mtm110) REVERT: d 55 GLU cc_start: 0.8924 (mp0) cc_final: 0.8719 (mt-10) REVERT: d 138 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8715 (mt-10) REVERT: g 107 ILE cc_start: 0.8524 (mm) cc_final: 0.8297 (mt) REVERT: g 135 GLU cc_start: 0.6446 (tt0) cc_final: 0.5987 (tt0) REVERT: g 162 LYS cc_start: 0.7797 (tptt) cc_final: 0.7556 (tptt) REVERT: g 166 MET cc_start: 0.7191 (mtp) cc_final: 0.6727 (mmp) REVERT: g 167 SER cc_start: 0.6286 (p) cc_final: 0.6055 (p) REVERT: l 105 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.5966 (mmmt) REVERT: r 64 LEU cc_start: 0.8261 (tp) cc_final: 0.8056 (tp) REVERT: r 105 GLU cc_start: 0.7019 (tp30) cc_final: 0.6447 (tp30) REVERT: B 30 TYR cc_start: 0.7242 (p90) cc_final: 0.6615 (p90) REVERT: B 33 GLU cc_start: 0.8931 (mp0) cc_final: 0.8684 (mp0) REVERT: B 38 THR cc_start: 0.8802 (m) cc_final: 0.8537 (m) REVERT: C 68 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8828 (tt) REVERT: C 152 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7981 (tm-30) REVERT: C 154 ASP cc_start: 0.8557 (m-30) cc_final: 0.8325 (m-30) REVERT: C 156 ILE cc_start: 0.8526 (mp) cc_final: 0.8021 (mp) REVERT: C 191 ASP cc_start: 0.8560 (p0) cc_final: 0.8226 (p0) REVERT: D 61 MET cc_start: 0.9537 (mmm) cc_final: 0.9185 (mmp) REVERT: D 66 GLU cc_start: 0.8827 (tp30) cc_final: 0.8317 (tp30) REVERT: D 152 ASP cc_start: 0.8645 (t0) cc_final: 0.8103 (t0) REVERT: E 45 ASP cc_start: 0.8615 (m-30) cc_final: 0.8353 (m-30) REVERT: E 48 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8429 (pt0) REVERT: E 86 LYS cc_start: 0.8370 (tppp) cc_final: 0.7819 (tppp) REVERT: H 106 ASP cc_start: 0.8107 (t0) cc_final: 0.7789 (t0) REVERT: H 109 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7783 (mm-30) REVERT: H 152 GLN cc_start: 0.7674 (mm-40) cc_final: 0.6714 (mm-40) REVERT: H 154 SER cc_start: 0.8671 (m) cc_final: 0.8406 (p) outliers start: 59 outliers final: 36 residues processed: 335 average time/residue: 0.1948 time to fit residues: 110.0303 Evaluate side-chains 318 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 345 SER Chi-restraints excluded: chain b residue 684 THR Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 86 ILE Chi-restraints excluded: chain d residue 119 SER Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 139 SER Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain r residue 123 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 183 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 146 optimal weight: 0.3980 chunk 229 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 206 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 261 optimal weight: 50.0000 chunk 253 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 6 GLN B 166 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 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 = 0.3337 r_free = 0.3337 target = 0.079200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.065042 restraints weight = 95025.384| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.98 r_work: 0.2920 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.777 38701 Z= 0.142 Angle : 0.793 15.052 54723 Z= 0.312 Chirality : 0.058 0.924 4621 Planarity : 0.004 0.052 7058 Dihedral : 18.988 134.202 7858 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.77 % Allowed : 10.17 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3195 helix: 2.02 (0.12), residues: 1834 sheet: -0.09 (0.65), residues: 78 loop : -0.61 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG r 99 TYR 0.017 0.001 TYR b 716 PHE 0.023 0.001 PHE g 131 TRP 0.019 0.001 TRP r 125 HIS 0.009 0.001 HIS r 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (38573) covalent geometry : angle 0.77720 / 0.31 (54685) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 3.68796 / 2.16 ( 2) hydrogen bonds : bond 0.05300 / 3.53 ( 1483) hydrogen bonds : angle 4.17022 / 3.06 ( 4239) metal coordination : bond 0.01073 / 0.63 ( 12) metal coordination : angle 6.18047 / 3.87 ( 36) Misc. bond : bond 0.13719 / 8.59 ( 115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8462 (t0) cc_final: 0.7822 (t0) REVERT: a 198 MET cc_start: 0.9011 (mmm) cc_final: 0.8424 (tpt) REVERT: b 382 MET cc_start: 0.9051 (mmt) cc_final: 0.8638 (mmt) REVERT: c 24 ASP cc_start: 0.8878 (t0) cc_final: 0.8640 (t0) REVERT: c 46 GLU cc_start: 0.9078 (pm20) cc_final: 0.8491 (pm20) REVERT: d 52 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7621 (mtm110) REVERT: d 55 GLU cc_start: 0.8995 (mp0) cc_final: 0.8728 (tt0) REVERT: d 84 TYR cc_start: 0.8813 (m-80) cc_final: 0.8457 (m-80) REVERT: d 132 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.9175 (p) REVERT: d 138 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8724 (mt-10) REVERT: f 172 ASP cc_start: 0.8737 (t0) cc_final: 0.8533 (t0) REVERT: g 55 ASN cc_start: 0.7468 (p0) cc_final: 0.7217 (p0) REVERT: g 107 ILE cc_start: 0.8574 (mm) cc_final: 0.8343 (mt) REVERT: g 115 GLN cc_start: 0.8161 (mp10) cc_final: 0.7805 (mp10) REVERT: g 135 GLU cc_start: 0.6717 (tt0) cc_final: 0.6237 (tt0) REVERT: g 166 MET cc_start: 0.7052 (mtp) cc_final: 0.6355 (mtp) REVERT: g 172 MET cc_start: 0.7103 (tpp) cc_final: 0.6841 (mmm) REVERT: l 105 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.5693 (mmmt) REVERT: B 30 TYR cc_start: 0.7213 (p90) cc_final: 0.6614 (p90) REVERT: B 33 GLU cc_start: 0.8912 (mp0) cc_final: 0.8661 (mp0) REVERT: B 38 THR cc_start: 0.8765 (m) cc_final: 0.8476 (m) REVERT: B 143 VAL cc_start: 0.9127 (t) cc_final: 0.8835 (p) REVERT: C 68 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8784 (tt) REVERT: C 152 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7756 (tm-30) REVERT: C 154 ASP cc_start: 0.8559 (m-30) cc_final: 0.8340 (m-30) REVERT: C 156 ILE cc_start: 0.8480 (mp) cc_final: 0.7941 (mp) REVERT: C 191 ASP cc_start: 0.8485 (p0) cc_final: 0.8100 (p0) REVERT: D 61 MET cc_start: 0.9523 (mmm) cc_final: 0.9064 (mmp) REVERT: E 45 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: E 48 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8437 (pt0) REVERT: H 32 MET cc_start: 0.7404 (mmm) cc_final: 0.7085 (mmm) REVERT: H 38 PHE cc_start: 0.8717 (p90) cc_final: 0.7014 (t80) REVERT: H 106 ASP cc_start: 0.8117 (t0) cc_final: 0.7732 (t0) REVERT: H 109 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7883 (mm-30) REVERT: H 152 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6595 (mm-40) REVERT: H 154 SER cc_start: 0.8662 (m) cc_final: 0.8332 (t) outliers start: 46 outliers final: 24 residues processed: 331 average time/residue: 0.2205 time to fit residues: 122.2295 Evaluate side-chains 315 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 575 PHE Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 2 ASN Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 123 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 122 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 206 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 34 HIS ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 6 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061534 restraints weight = 96996.233| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.98 r_work: 0.2852 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.804 38701 Z= 0.249 Angle : 0.872 15.506 54723 Z= 0.344 Chirality : 0.060 0.898 4621 Planarity : 0.005 0.048 7058 Dihedral : 18.918 133.053 7858 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.46 % Allowed : 9.82 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3195 helix: 1.87 (0.12), residues: 1831 sheet: 0.30 (0.66), residues: 73 loop : -0.62 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 52 TYR 0.019 0.002 TYR b 716 PHE 0.022 0.002 PHE b 649 TRP 0.019 0.001 TRP r 125 HIS 0.012 0.002 HIS b 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.24 (38573) covalent geometry : angle 0.85220 / 0.34 (54685) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 4.43947 / 2.61 ( 2) hydrogen bonds : bond 0.06072 / 4.06 ( 1483) hydrogen bonds : angle 4.32412 / 3.17 ( 4239) metal coordination : bond 0.02071 / 1.22 ( 12) metal coordination : angle 7.11542 / 4.19 ( 36) Misc. bond : bond 0.13397 / 8.40 ( 115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8743 (t0) cc_final: 0.8130 (t0) REVERT: a 685 MET cc_start: 0.8918 (ttp) cc_final: 0.8709 (ttm) REVERT: c 46 GLU cc_start: 0.9122 (pm20) cc_final: 0.8464 (pm20) REVERT: d 52 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7591 (mtm110) REVERT: d 55 GLU cc_start: 0.9034 (mp0) cc_final: 0.8771 (tt0) REVERT: d 132 SER cc_start: 0.9390 (OUTLIER) cc_final: 0.9187 (p) REVERT: d 138 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8754 (mt-10) REVERT: f 172 ASP cc_start: 0.8735 (t0) cc_final: 0.8495 (t0) REVERT: g 107 ILE cc_start: 0.8550 (mm) cc_final: 0.8315 (mt) REVERT: g 135 GLU cc_start: 0.6600 (tt0) cc_final: 0.6154 (tt0) REVERT: g 162 LYS cc_start: 0.8119 (tptt) cc_final: 0.7866 (tptt) REVERT: g 166 MET cc_start: 0.6862 (mtp) cc_final: 0.6321 (mtp) REVERT: g 172 MET cc_start: 0.7225 (tpp) cc_final: 0.6891 (mmm) REVERT: l 105 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.5786 (mmmt) REVERT: r 125 TRP cc_start: 0.7733 (t60) cc_final: 0.7268 (t60) REVERT: B 33 GLU cc_start: 0.8920 (mp0) cc_final: 0.8647 (mp0) REVERT: B 38 THR cc_start: 0.8850 (m) cc_final: 0.8554 (m) REVERT: B 143 VAL cc_start: 0.9165 (t) cc_final: 0.8909 (p) REVERT: C 68 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8820 (tt) REVERT: C 152 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8038 (tm-30) REVERT: C 156 ILE cc_start: 0.8491 (mp) cc_final: 0.7915 (mp) REVERT: C 191 ASP cc_start: 0.8584 (p0) cc_final: 0.8252 (p0) REVERT: D 61 MET cc_start: 0.9539 (mmm) cc_final: 0.9161 (mmp) REVERT: D 152 ASP cc_start: 0.8465 (t0) cc_final: 0.8120 (t0) REVERT: E 45 ASP cc_start: 0.8633 (m-30) cc_final: 0.8355 (m-30) REVERT: E 48 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8429 (pt0) REVERT: E 86 LYS cc_start: 0.8135 (tppp) cc_final: 0.7669 (tppp) REVERT: H 32 MET cc_start: 0.7610 (mmm) cc_final: 0.7211 (mmm) REVERT: H 106 ASP cc_start: 0.8182 (t0) cc_final: 0.7807 (t0) REVERT: H 109 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7873 (mm-30) REVERT: H 149 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8564 (m) REVERT: H 152 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7202 (mp10) REVERT: H 153 LEU cc_start: 0.8317 (tp) cc_final: 0.7806 (tp) outliers start: 64 outliers final: 39 residues processed: 328 average time/residue: 0.2219 time to fit residues: 122.5051 Evaluate side-chains 322 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 364 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain b residue 511 ILE Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 139 SER Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 130 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 211 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 GLN ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 6 GLN r 106 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 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 = 0.3323 r_free = 0.3323 target = 0.078320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.063761 restraints weight = 94045.446| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.01 r_work: 0.2903 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.749 38701 Z= 0.131 Angle : 0.773 14.694 54723 Z= 0.302 Chirality : 0.058 0.925 4621 Planarity : 0.004 0.047 7058 Dihedral : 18.396 134.760 7858 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.15 % Allowed : 10.44 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3195 helix: 2.09 (0.12), residues: 1836 sheet: 0.38 (0.66), residues: 73 loop : -0.56 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 52 TYR 0.016 0.001 TYR b 716 PHE 0.019 0.001 PHE g 131 TRP 0.020 0.001 TRP g 175 HIS 0.007 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (38573) covalent geometry : angle 0.75582 / 0.30 (54685) SS BOND : bond 0.00030 / 0.02 ( 1) SS BOND : angle 4.27082 / 2.51 ( 2) hydrogen bonds : bond 0.05124 / 3.41 ( 1483) hydrogen bonds : angle 4.06161 / 2.97 ( 4239) metal coordination : bond 0.00843 / 0.49 ( 12) metal coordination : angle 6.28401 / 3.73 ( 36) Misc. bond : bond 0.12430 / 7.55 ( 115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 293 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8439 (t0) cc_final: 0.7749 (t0) REVERT: a 198 MET cc_start: 0.8923 (mmm) cc_final: 0.8204 (tpt) REVERT: a 250 MET cc_start: 0.8514 (mmm) cc_final: 0.8104 (mmm) REVERT: a 371 MET cc_start: 0.8534 (ttm) cc_final: 0.8286 (mtt) REVERT: b 382 MET cc_start: 0.9077 (mmt) cc_final: 0.8664 (mmt) REVERT: c 46 GLU cc_start: 0.9112 (pm20) cc_final: 0.8517 (pm20) REVERT: c 76 SER cc_start: 0.9275 (m) cc_final: 0.8997 (t) REVERT: d 52 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7606 (mtm110) REVERT: d 55 GLU cc_start: 0.9022 (mp0) cc_final: 0.8687 (tt0) REVERT: d 84 TYR cc_start: 0.8834 (m-80) cc_final: 0.8421 (m-80) REVERT: d 132 SER cc_start: 0.9314 (OUTLIER) cc_final: 0.9093 (p) REVERT: d 138 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8731 (mt-10) REVERT: f 51 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: f 172 ASP cc_start: 0.8670 (t0) cc_final: 0.8420 (t0) REVERT: g 55 ASN cc_start: 0.7172 (p0) cc_final: 0.6941 (p0) REVERT: g 107 ILE cc_start: 0.8357 (mm) cc_final: 0.8146 (mt) REVERT: g 135 GLU cc_start: 0.6449 (tt0) cc_final: 0.6130 (tt0) REVERT: g 162 LYS cc_start: 0.7904 (tptt) cc_final: 0.7654 (tptt) REVERT: g 166 MET cc_start: 0.6848 (mtp) cc_final: 0.6226 (mtp) REVERT: g 172 MET cc_start: 0.7175 (tpp) cc_final: 0.6905 (mmm) REVERT: g 175 TRP cc_start: 0.6784 (t-100) cc_final: 0.6090 (t-100) REVERT: l 105 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.5514 (mmmt) REVERT: B 33 GLU cc_start: 0.8942 (mp0) cc_final: 0.8651 (mp0) REVERT: B 38 THR cc_start: 0.8791 (m) cc_final: 0.8501 (m) REVERT: B 131 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8289 (tt0) REVERT: B 143 VAL cc_start: 0.9095 (t) cc_final: 0.8827 (p) REVERT: C 68 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 152 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7811 (tm-30) REVERT: C 156 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7906 (mp) REVERT: C 191 ASP cc_start: 0.8617 (p0) cc_final: 0.8292 (p0) REVERT: D 61 MET cc_start: 0.9495 (mmm) cc_final: 0.9029 (mmp) REVERT: E 45 ASP cc_start: 0.8636 (m-30) cc_final: 0.8321 (m-30) REVERT: E 48 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8678 (pp20) REVERT: H 32 MET cc_start: 0.7597 (mmm) cc_final: 0.7149 (mmm) REVERT: H 106 ASP cc_start: 0.8208 (t0) cc_final: 0.7764 (t0) REVERT: H 109 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7882 (mm-30) REVERT: H 149 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8572 (m) REVERT: H 152 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7273 (mp10) REVERT: H 153 LEU cc_start: 0.8360 (tp) cc_final: 0.7959 (tp) outliers start: 56 outliers final: 32 residues processed: 328 average time/residue: 0.2035 time to fit residues: 113.1695 Evaluate side-chains 316 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain b residue 575 PHE Chi-restraints excluded: chain b residue 663 LEU Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 86 ILE Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 132 VAL Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 123 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 83 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 715 GLN ** a 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 ASN m 6 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 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 = 0.3246 r_free = 0.3246 target = 0.074308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059686 restraints weight = 96679.663| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.07 r_work: 0.2804 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.823 38701 Z= 0.313 Angle : 0.930 16.523 54723 Z= 0.371 Chirality : 0.061 0.885 4621 Planarity : 0.005 0.048 7058 Dihedral : 18.787 131.836 7858 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.46 % Allowed : 10.71 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3195 helix: 1.72 (0.11), residues: 1832 sheet: -0.14 (0.59), residues: 83 loop : -0.66 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG d 52 TYR 0.020 0.002 TYR b 716 PHE 0.025 0.002 PHE b 649 TRP 0.017 0.002 TRP r 125 HIS 0.013 0.002 HIS b 413 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.31 (38573) covalent geometry : angle 0.90971 / 0.37 (54685) SS BOND : bond 0.01789 / 0.94 ( 1) SS BOND : angle 2.24286 / 1.20 ( 2) hydrogen bonds : bond 0.06487 / 4.35 ( 1483) hydrogen bonds : angle 4.43121 / 3.25 ( 4239) metal coordination : bond 0.02456 / 1.46 ( 12) metal coordination : angle 7.66041 / 4.50 ( 36) Misc. bond : bond 0.13882 / 8.86 ( 115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8706 (t0) cc_final: 0.8100 (t0) REVERT: c 46 GLU cc_start: 0.9147 (pm20) cc_final: 0.8532 (pm20) REVERT: d 52 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7543 (mtm110) REVERT: d 55 GLU cc_start: 0.9087 (mp0) cc_final: 0.8710 (tt0) REVERT: d 132 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.9099 (p) REVERT: d 138 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8745 (mt-10) REVERT: e 62 LYS cc_start: 0.8357 (pptt) cc_final: 0.8155 (mtpp) REVERT: f 51 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: f 172 ASP cc_start: 0.8636 (t0) cc_final: 0.8394 (t0) REVERT: g 107 ILE cc_start: 0.8325 (mm) cc_final: 0.8115 (mt) REVERT: g 111 SER cc_start: 0.8915 (p) cc_final: 0.8594 (p) REVERT: g 135 GLU cc_start: 0.6466 (tt0) cc_final: 0.6122 (tt0) REVERT: g 166 MET cc_start: 0.6837 (mtp) cc_final: 0.6076 (mtm) REVERT: g 172 MET cc_start: 0.7258 (tpp) cc_final: 0.7057 (tpp) REVERT: g 175 TRP cc_start: 0.6713 (t-100) cc_final: 0.6101 (t-100) REVERT: j 2 ASN cc_start: 0.8657 (m110) cc_final: 0.8060 (t0) REVERT: l 105 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7093 (ptmm) REVERT: B 33 GLU cc_start: 0.8950 (mp0) cc_final: 0.8647 (mp0) REVERT: B 38 THR cc_start: 0.8911 (m) cc_final: 0.8624 (m) REVERT: B 131 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8337 (tt0) REVERT: C 68 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8730 (tt) REVERT: C 108 THR cc_start: 0.8561 (p) cc_final: 0.8321 (t) REVERT: C 152 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 156 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 191 ASP cc_start: 0.8685 (p0) cc_final: 0.8367 (p0) REVERT: D 61 MET cc_start: 0.9500 (mmm) cc_final: 0.9135 (mmp) REVERT: D 96 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 152 ASP cc_start: 0.8348 (t0) cc_final: 0.8042 (t0) REVERT: E 45 ASP cc_start: 0.8613 (m-30) cc_final: 0.8275 (m-30) REVERT: E 48 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8634 (pp20) REVERT: H 32 MET cc_start: 0.7682 (mmm) cc_final: 0.7170 (mmm) REVERT: H 106 ASP cc_start: 0.8280 (t0) cc_final: 0.7857 (t0) REVERT: H 109 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7792 (mm-30) REVERT: H 149 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8633 (m) REVERT: H 152 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7349 (mp10) REVERT: H 153 LEU cc_start: 0.8513 (tp) cc_final: 0.8138 (tp) outliers start: 64 outliers final: 39 residues processed: 313 average time/residue: 0.2205 time to fit residues: 116.4880 Evaluate side-chains 318 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain d residue 39 GLN Chi-restraints excluded: chain d residue 43 MET Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 121 ILE Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 167 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 12 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 276 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 ASN d 53 ASN m 6 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 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 = 0.3301 r_free = 0.3301 target = 0.077128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062545 restraints weight = 94628.038| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.06 r_work: 0.2872 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.761 38701 Z= 0.143 Angle : 0.785 14.678 54723 Z= 0.308 Chirality : 0.058 0.922 4621 Planarity : 0.004 0.048 7058 Dihedral : 18.307 133.348 7858 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.73 % Allowed : 11.59 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3195 helix: 1.99 (0.12), residues: 1835 sheet: 0.30 (0.65), residues: 73 loop : -0.57 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 39 TYR 0.016 0.001 TYR b 716 PHE 0.021 0.001 PHE g 131 TRP 0.021 0.001 TRP r 125 HIS 0.010 0.001 HIS b 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (38573) covalent geometry : angle 0.76693 / 0.31 (54685) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.83896 / 0.45 ( 2) hydrogen bonds : bond 0.05397 / 3.59 ( 1483) hydrogen bonds : angle 4.11554 / 3.01 ( 4239) metal coordination : bond 0.00981 / 0.59 ( 12) metal coordination : angle 6.53625 / 3.88 ( 36) Misc. bond : bond 0.12656 / 7.75 ( 115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8492 (t0) cc_final: 0.7947 (t0) REVERT: a 198 MET cc_start: 0.8899 (mmm) cc_final: 0.8192 (tpt) REVERT: a 371 MET cc_start: 0.8506 (ttm) cc_final: 0.8234 (mtt) REVERT: b 115 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7981 (t) REVERT: c 46 GLU cc_start: 0.9121 (pm20) cc_final: 0.8539 (pm20) REVERT: c 76 SER cc_start: 0.9286 (m) cc_final: 0.8992 (t) REVERT: d 52 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7647 (mtm110) REVERT: d 55 GLU cc_start: 0.9064 (mp0) cc_final: 0.8697 (tt0) REVERT: d 74 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: d 84 TYR cc_start: 0.8874 (m-80) cc_final: 0.8461 (m-80) REVERT: d 132 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.9077 (p) REVERT: d 138 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8724 (mt-10) REVERT: e 3 ASP cc_start: 0.8576 (m-30) cc_final: 0.8322 (m-30) REVERT: e 62 LYS cc_start: 0.8390 (pptt) cc_final: 0.8142 (mtpp) REVERT: f 51 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: f 172 ASP cc_start: 0.8632 (t0) cc_final: 0.8383 (t0) REVERT: g 88 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7430 (pt0) REVERT: g 135 GLU cc_start: 0.6445 (tt0) cc_final: 0.6010 (tt0) REVERT: g 175 TRP cc_start: 0.6761 (t-100) cc_final: 0.6206 (t-100) REVERT: j 2 ASN cc_start: 0.8623 (m110) cc_final: 0.8018 (t0) REVERT: l 105 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.5646 (mmmt) REVERT: B 33 GLU cc_start: 0.8953 (mp0) cc_final: 0.8650 (mp0) REVERT: B 38 THR cc_start: 0.8869 (m) cc_final: 0.8557 (m) REVERT: B 131 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8340 (tt0) REVERT: B 143 VAL cc_start: 0.9112 (t) cc_final: 0.8824 (p) REVERT: C 68 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 109 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9035 (pm20) REVERT: C 152 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7810 (tm-30) REVERT: C 156 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7893 (mp) REVERT: C 191 ASP cc_start: 0.8635 (p0) cc_final: 0.8306 (p0) REVERT: D 61 MET cc_start: 0.9498 (mmm) cc_final: 0.9054 (mmp) REVERT: D 66 GLU cc_start: 0.8583 (tp30) cc_final: 0.8201 (tp30) REVERT: D 96 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 45 ASP cc_start: 0.8674 (m-30) cc_final: 0.8372 (m-30) REVERT: E 48 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8623 (pp20) REVERT: H 32 MET cc_start: 0.7720 (mmm) cc_final: 0.7156 (mmm) REVERT: H 106 ASP cc_start: 0.8256 (t0) cc_final: 0.7800 (t0) REVERT: H 109 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7793 (mm-30) REVERT: H 149 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8614 (m) REVERT: H 152 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7320 (mp10) REVERT: H 153 LEU cc_start: 0.8372 (tp) cc_final: 0.8062 (tp) outliers start: 45 outliers final: 31 residues processed: 317 average time/residue: 0.2357 time to fit residues: 124.7837 Evaluate side-chains 322 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 282 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain b residue 575 PHE Chi-restraints excluded: chain c residue 65 VAL Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 265 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 ASN d 53 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062160 restraints weight = 95335.027| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.00 r_work: 0.2866 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.769 38701 Z= 0.192 Angle : 0.804 14.680 54723 Z= 0.317 Chirality : 0.058 0.910 4621 Planarity : 0.004 0.048 7058 Dihedral : 18.274 133.887 7858 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.03 % Allowed : 11.67 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3195 helix: 2.00 (0.12), residues: 1836 sheet: 0.28 (0.65), residues: 73 loop : -0.57 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 39 TYR 0.018 0.001 TYR b 716 PHE 0.020 0.001 PHE g 131 TRP 0.021 0.001 TRP r 125 HIS 0.008 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (38573) covalent geometry : angle 0.78678 / 0.32 (54685) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 0.85213 / 0.46 ( 2) hydrogen bonds : bond 0.05396 / 3.59 ( 1483) hydrogen bonds : angle 4.12806 / 3.02 ( 4239) metal coordination : bond 0.01550 / 0.92 ( 12) metal coordination : angle 6.57794 / 3.92 ( 36) Misc. bond : bond 0.12728 / 7.83 ( 115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 283 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8548 (t0) cc_final: 0.8010 (t0) REVERT: a 198 MET cc_start: 0.8918 (mmm) cc_final: 0.8213 (tpt) REVERT: a 371 MET cc_start: 0.8609 (ttm) cc_final: 0.8363 (mtt) REVERT: b 115 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8041 (t) REVERT: c 46 GLU cc_start: 0.9129 (pm20) cc_final: 0.8546 (pm20) REVERT: c 76 SER cc_start: 0.9294 (m) cc_final: 0.9021 (t) REVERT: d 52 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7655 (mtm110) REVERT: d 55 GLU cc_start: 0.9055 (mp0) cc_final: 0.8723 (tt0) REVERT: d 74 ARG cc_start: 0.8227 (mmm-85) cc_final: 0.7916 (mmm-85) REVERT: d 84 TYR cc_start: 0.8880 (m-80) cc_final: 0.8424 (m-80) REVERT: d 132 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.9089 (p) REVERT: d 138 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8737 (mt-10) REVERT: e 3 ASP cc_start: 0.8645 (m-30) cc_final: 0.8356 (m-30) REVERT: e 62 LYS cc_start: 0.8380 (pptt) cc_final: 0.8137 (mtpp) REVERT: f 51 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: f 172 ASP cc_start: 0.8635 (t0) cc_final: 0.8394 (t0) REVERT: g 88 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7445 (pt0) REVERT: g 135 GLU cc_start: 0.6515 (tt0) cc_final: 0.6083 (tt0) REVERT: g 172 MET cc_start: 0.6831 (tpp) cc_final: 0.6449 (mmm) REVERT: g 175 TRP cc_start: 0.6699 (t-100) cc_final: 0.6222 (t-100) REVERT: j 2 ASN cc_start: 0.8636 (m110) cc_final: 0.8041 (t0) REVERT: j 30 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8920 (m-40) REVERT: l 105 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.5646 (mmmt) REVERT: B 33 GLU cc_start: 0.8947 (mp0) cc_final: 0.8638 (mp0) REVERT: B 38 THR cc_start: 0.8918 (m) cc_final: 0.8645 (m) REVERT: B 131 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8360 (tt0) REVERT: B 143 VAL cc_start: 0.9128 (t) cc_final: 0.8844 (p) REVERT: C 68 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8700 (tt) REVERT: C 152 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7835 (tm-30) REVERT: C 156 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 191 ASP cc_start: 0.8626 (p0) cc_final: 0.8302 (p0) REVERT: D 61 MET cc_start: 0.9511 (mmm) cc_final: 0.9053 (mmp) REVERT: D 152 ASP cc_start: 0.8350 (t0) cc_final: 0.7996 (t0) REVERT: E 45 ASP cc_start: 0.8683 (m-30) cc_final: 0.8387 (m-30) REVERT: E 48 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8637 (pp20) REVERT: H 32 MET cc_start: 0.7676 (mmm) cc_final: 0.7139 (mmm) REVERT: H 106 ASP cc_start: 0.8368 (t0) cc_final: 0.7893 (t0) REVERT: H 109 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7808 (mm-30) REVERT: H 149 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8655 (m) REVERT: H 152 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7363 (mp10) REVERT: H 153 LEU cc_start: 0.8332 (tp) cc_final: 0.8048 (tp) outliers start: 53 outliers final: 40 residues processed: 314 average time/residue: 0.2220 time to fit residues: 116.3370 Evaluate side-chains 329 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain a residue 471 MET Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain b residue 575 PHE Chi-restraints excluded: chain c residue 65 VAL Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 86 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 121 ILE Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 30 ASN Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 123 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 2 optimal weight: 1.9990 chunk 273 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 227 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062157 restraints weight = 95197.470| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.01 r_work: 0.2865 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.769 38701 Z= 0.191 Angle : 0.804 14.679 54723 Z= 0.317 Chirality : 0.058 0.910 4621 Planarity : 0.004 0.048 7058 Dihedral : 18.280 133.887 7858 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.92 % Allowed : 11.78 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3195 helix: 2.00 (0.12), residues: 1836 sheet: 0.28 (0.65), residues: 73 loop : -0.57 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 39 TYR 0.018 0.001 TYR b 716 PHE 0.020 0.001 PHE g 131 TRP 0.021 0.001 TRP r 125 HIS 0.008 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (38573) covalent geometry : angle 0.78670 / 0.32 (54685) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.85186 / 0.46 ( 2) hydrogen bonds : bond 0.05395 / 3.59 ( 1483) hydrogen bonds : angle 4.12806 / 3.02 ( 4239) metal coordination : bond 0.01550 / 0.92 ( 12) metal coordination : angle 6.57798 / 3.92 ( 36) Misc. bond : bond 0.12728 / 7.83 ( 115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6390 Ramachandran restraints generated. 3195 Oldfield, 0 Emsley, 3195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 107 ASP cc_start: 0.8547 (t0) cc_final: 0.8009 (t0) REVERT: a 198 MET cc_start: 0.8918 (mmm) cc_final: 0.8211 (tpt) REVERT: a 371 MET cc_start: 0.8609 (ttm) cc_final: 0.8362 (mtt) REVERT: b 115 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8039 (t) REVERT: c 46 GLU cc_start: 0.9131 (pm20) cc_final: 0.8548 (pm20) REVERT: c 76 SER cc_start: 0.9297 (m) cc_final: 0.9026 (t) REVERT: d 52 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7651 (mtm110) REVERT: d 55 GLU cc_start: 0.9055 (mp0) cc_final: 0.8724 (tt0) REVERT: d 74 ARG cc_start: 0.8226 (mmm-85) cc_final: 0.7913 (mmm-85) REVERT: d 84 TYR cc_start: 0.8879 (m-80) cc_final: 0.8423 (m-80) REVERT: d 132 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.9087 (p) REVERT: d 138 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8735 (mt-10) REVERT: e 3 ASP cc_start: 0.8635 (m-30) cc_final: 0.8348 (m-30) REVERT: e 62 LYS cc_start: 0.8386 (pptt) cc_final: 0.8138 (mtpp) REVERT: f 51 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: f 172 ASP cc_start: 0.8633 (t0) cc_final: 0.8394 (t0) REVERT: g 88 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7441 (pt0) REVERT: g 135 GLU cc_start: 0.6470 (tt0) cc_final: 0.6045 (tt0) REVERT: g 172 MET cc_start: 0.6788 (tpp) cc_final: 0.6416 (mmm) REVERT: g 175 TRP cc_start: 0.6653 (t-100) cc_final: 0.6188 (t-100) REVERT: j 2 ASN cc_start: 0.8636 (m110) cc_final: 0.8040 (t0) REVERT: j 30 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8925 (m-40) REVERT: l 105 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.5641 (mmmt) REVERT: B 33 GLU cc_start: 0.8951 (mp0) cc_final: 0.8640 (mp0) REVERT: B 38 THR cc_start: 0.8918 (m) cc_final: 0.8638 (m) REVERT: B 131 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8362 (tt0) REVERT: B 143 VAL cc_start: 0.9129 (t) cc_final: 0.8846 (p) REVERT: C 68 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 152 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7838 (tm-30) REVERT: C 156 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.7914 (mp) REVERT: C 191 ASP cc_start: 0.8630 (p0) cc_final: 0.8305 (p0) REVERT: D 61 MET cc_start: 0.9510 (mmm) cc_final: 0.9052 (mmp) REVERT: E 45 ASP cc_start: 0.8681 (m-30) cc_final: 0.8381 (m-30) REVERT: E 48 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8634 (pp20) REVERT: H 32 MET cc_start: 0.7672 (mmm) cc_final: 0.7134 (mmm) REVERT: H 106 ASP cc_start: 0.8366 (t0) cc_final: 0.7890 (t0) REVERT: H 109 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7804 (mm-30) REVERT: H 149 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8646 (m) REVERT: H 152 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7359 (mp10) REVERT: H 153 LEU cc_start: 0.8335 (tp) cc_final: 0.8048 (tp) outliers start: 50 outliers final: 40 residues processed: 307 average time/residue: 0.2120 time to fit residues: 108.5727 Evaluate side-chains 329 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 97 TYR Chi-restraints excluded: chain a residue 118 VAL Chi-restraints excluded: chain a residue 348 SER Chi-restraints excluded: chain a residue 372 TYR Chi-restraints excluded: chain a residue 471 MET Chi-restraints excluded: chain b residue 115 THR Chi-restraints excluded: chain b residue 245 THR Chi-restraints excluded: chain b residue 281 VAL Chi-restraints excluded: chain b residue 575 PHE Chi-restraints excluded: chain c residue 65 VAL Chi-restraints excluded: chain d residue 52 ARG Chi-restraints excluded: chain d residue 86 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 132 SER Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 51 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 87 CYS Chi-restraints excluded: chain f residue 121 ILE Chi-restraints excluded: chain f residue 176 VAL Chi-restraints excluded: chain g residue 56 SER Chi-restraints excluded: chain g residue 74 SER Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 33 ASP Chi-restraints excluded: chain j residue 3 ASP Chi-restraints excluded: chain j residue 16 THR Chi-restraints excluded: chain j residue 25 PHE Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 30 ASN Chi-restraints excluded: chain l residue 10 ASP Chi-restraints excluded: chain l residue 105 LYS Chi-restraints excluded: chain m residue 22 ILE Chi-restraints excluded: chain r residue 63 VAL Chi-restraints excluded: chain r residue 123 LEU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 11 optimal weight: 0.0670 chunk 107 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 291 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 53 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062185 restraints weight = 94716.223| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.99 r_work: 0.2867 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.769 38701 Z= 0.191 Angle : 0.804 14.679 54723 Z= 0.317 Chirality : 0.058 0.910 4621 Planarity : 0.004 0.048 7058 Dihedral : 18.271 133.887 7858 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.92 % Allowed : 11.78 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3195 helix: 2.00 (0.12), residues: 1836 sheet: 0.28 (0.65), residues: 73 loop : -0.57 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 39 TYR 0.018 0.001 TYR b 716 PHE 0.020 0.001 PHE g 131 TRP 0.021 0.001 TRP r 125 HIS 0.008 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (38573) covalent geometry : angle 0.78668 / 0.32 (54685) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.85181 / 0.46 ( 2) hydrogen bonds : bond 0.05395 / 3.59 ( 1483) hydrogen bonds : angle 4.12806 / 3.02 ( 4239) metal coordination : bond 0.01550 / 0.92 ( 12) metal coordination : angle 6.57801 / 3.92 ( 36) Misc. bond : bond 0.12728 / 7.83 ( 115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8653.39 seconds wall clock time: 149 minutes 26.19 seconds (8966.19 seconds total)