Starting phenix.real_space_refine on Mon Jul 6 17:22:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.cif" model { file = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z84_14542/07_2026/7z84_14542.map" } resolution = 2.87 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= 0.004 sd= 0.018 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 Ca 1 9.91 5 Fe 32 7.16 5 P 13 5.49 5 S 267 5.16 5 C 24594 2.51 5 N 6239 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s 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: 37772 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4738 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2544 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 307} Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4629 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 224 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 70.269 60.480 191.525 1.00 12.70 S ATOM 2741 SG CYS F 357 73.673 60.035 196.087 1.00 22.22 S ATOM 3062 SG CYS F 398 67.840 56.764 196.394 1.00 21.57 S ATOM 2697 SG CYS F 351 72.337 54.157 192.920 1.00 14.65 S ATOM 4054 SG CYS E 92 80.559 52.057 212.775 1.00 36.01 S ATOM 4088 SG CYS E 97 80.635 52.886 216.206 1.00 34.35 S ATOM 4366 SG CYS E 133 75.310 51.456 212.367 1.00 47.06 S ATOM 4392 SG CYS E 137 74.503 52.311 215.614 1.00 40.65 S ATOM 5476 SG CYS G 114 81.024 66.621 174.325 1.00 7.04 S ATOM 5416 SG CYS G 105 86.283 70.282 175.941 1.00 7.35 S ATOM 5436 SG CYS G 108 86.951 64.315 173.544 1.00 1.74 S ATOM 5830 SG CYS G 156 75.140 58.831 179.129 1.00 6.41 S ATOM 5811 SG CYS G 153 80.906 57.673 182.204 1.00 3.89 S ATOM 5859 SG CYS G 159 78.175 53.080 178.565 1.00 5.98 S ATOM 6203 SG CYS G 203 80.322 58.302 175.556 1.00 5.88 S ATOM 6428 SG CYS G 230 77.315 49.982 154.306 1.00 15.43 S ATOM 6713 SG CYS G 265 77.106 46.208 159.640 1.00 9.98 S ATOM 6476 SG CYS G 237 71.846 49.626 157.339 1.00 4.70 S ATOM 6452 SG CYS G 233 74.080 44.297 154.329 1.00 18.49 S ATOM 4877 SG CYS G 36 68.783 59.853 181.861 1.00 4.16 S ATOM 4953 SG CYS G 47 70.341 63.183 182.112 1.00 3.85 S ATOM 4979 SG CYS G 50 64.517 64.874 181.919 1.00 11.43 S ATOM 5128 SG CYS G 69 63.989 61.326 181.695 1.00 9.98 S ATOM 17321 SG CYS B 129 91.859 93.860 150.601 1.00 8.44 S ATOM 16818 SG CYS B 64 97.099 97.582 152.343 1.00 15.77 S ATOM 16812 SG CYS B 63 91.569 99.706 154.130 1.00 7.15 S ATOM 17538 SG CYS B 158 93.531 93.758 156.386 1.00 11.15 S ATOM 18869 SG CYS I 102 92.212 87.977 162.405 1.00 2.12 S ATOM 18844 SG CYS I 99 97.671 86.527 158.865 1.00 6.35 S ATOM 18887 SG CYS I 105 96.165 83.229 164.254 1.00 9.95 S ATOM 18602 SG CYS I 70 92.343 82.644 159.000 1.00 7.39 S ATOM 18916 SG CYS I 109 97.040 77.666 170.519 1.00 3.35 S ATOM 18579 SG CYS I 66 95.124 77.030 164.366 1.00 13.84 S ATOM 18539 SG CYS I 60 99.102 72.628 166.711 1.00 7.86 S ATOM 18557 SG CYS I 63 92.828 73.186 169.088 1.00 6.93 S Time building chain proxies: 7.32, per 1000 atoms: 0.19 Number of scatterers: 37772 At special positions: 0 Unit cell: (157.94, 215.18, 243.8, 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 32 26.01 Ca 1 19.99 S 267 16.00 P 13 15.00 O 6626 8.00 N 6239 7.00 C 24594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 0 sheets defined 51.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 419 No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 35 through 47 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 98 Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 158 through 166 Processing helix chain 'G' and resid 196 through 202 removed outlier: 4.868A pdb=" N VAL G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 No H-bonds generated for 'chain 'G' and resid 273 through 276' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 409 removed outlier: 4.422A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 764 through 770 removed outlier: 5.075A pdb=" N ASN G 768 " --> pdb=" O PRO G 764 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS G 769 " --> pdb=" O GLN G 765 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 removed outlier: 4.384A pdb=" N ARG G 829 " --> pdb=" O GLU G 825 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 825 through 829' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.958A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 143 removed outlier: 4.810A pdb=" N TRP C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 9.065A pdb=" N THR C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 10.907A pdb=" N LYS C 187 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ALA C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 399 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.040A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 522 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 38 through 52 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 162 through 177 Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.730A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'H' and resid 6 through 44 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.588A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 4.463A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.961A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 305 through 322 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 66 through 89 Processing helix chain 'A' and resid 97 through 119 Processing helix chain 'L' and resid 4 through 21 removed outlier: 4.527A pdb=" N ILE L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.155A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.553A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 275 Processing helix chain 'L' and resid 277 through 299 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 548 Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.102A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 584 Proline residue: L 572 - end of helix Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.700A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 491 through 502 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.507A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.191A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 121 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.472A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.412A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 56 through 87 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.062A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 1708 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.52 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 16045 1.42 - 1.64: 22166 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38712 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" O13 3PE J 202 " pdb=" P 3PE J 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O13 3PE J 201 " pdb=" P 3PE J 201 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 ... (remaining 38707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 52100 3.39 - 6.79: 316 6.79 - 10.18: 57 10.18 - 13.58: 10 13.58 - 16.97: 3 Bond angle restraints: 52486 Sorted by residual: angle pdb=" C TYR C 268 " pdb=" N ILE C 269 " pdb=" CA ILE C 269 " ideal model delta sigma weight residual 120.24 124.68 -4.44 6.30e-01 2.52e+00 4.97e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.03 12.78 2.21e+00 2.05e-01 3.34e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 129.67 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" CB LYS L 515 " pdb=" CG LYS L 515 " pdb=" CD LYS L 515 " ideal model delta sigma weight residual 111.30 124.17 -12.87 2.30e+00 1.89e-01 3.13e+01 angle pdb=" CB MET N 255 " pdb=" CG MET N 255 " pdb=" SD MET N 255 " ideal model delta sigma weight residual 112.70 129.36 -16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 52481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 21884 34.21 - 68.41: 775 68.41 - 102.62: 47 102.62 - 136.82: 0 136.82 - 171.03: 1 Dihedral angle restraints: 22707 sinusoidal: 9134 harmonic: 13573 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.31 44.69 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.05 34.95 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.56 171.03 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 22704 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 5813 4.237 - 8.473: 0 8.473 - 12.710: 0 12.710 - 16.947: 0 16.947 - 21.183: 28 Chirality restraints: 5841 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5838 not shown) Planarity restraints: 6553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C VAL N 63 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.028 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 201 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 93 " 0.021 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP J 93 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP J 93 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J 93 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 93 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 93 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 93 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 93 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 6550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5009 2.76 - 3.29: 36241 3.29 - 3.83: 69587 3.83 - 4.36: 83838 4.36 - 4.90: 141055 Nonbonded interactions: 335730 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.221 3.040 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.244 3.040 nonbonded pdb=" O TRP G 668 " pdb=" OG1 THR G 669 " model vdw 2.248 3.040 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.256 3.040 ... (remaining 335725 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: 0.420 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.900 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 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 : 0.005 0.113 38748 Z= 0.210 Angle : 0.780 16.974 52579 Z= 0.388 Chirality : 1.464 21.183 5841 Planarity : 0.006 0.104 6553 Dihedral : 16.294 171.031 14025 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 20.05 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: -0.27 (0.11), residues: 4711 helix: 0.35 (0.09), residues: 2673 sheet: -0.40 (0.27), residues: 323 loop : -0.80 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG L 198 TYR 0.032 0.002 TYR M 435 PHE 0.042 0.002 PHE L 341 TRP 0.060 0.002 TRP J 93 HIS 0.007 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (38712) covalent geometry : angle 0.76466 / 0.39 (52486) hydrogen bonds : bond 0.05372 / 3.63 ( 1708) hydrogen bonds : angle 4.65303 / 3.32 ( 5124) metal coordination : bond 0.05417 / 3.53 ( 36) metal coordination : angle 3.77301 / 2.70 ( 93) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 489 time to evaluate : 1.017 Fit side-chains REVERT: F 80 GLU cc_start: 0.7466 (mp0) cc_final: 0.7064 (pm20) REVERT: F 126 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8036 (p90) REVERT: G 62 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7034 (tpt170) REVERT: L 198 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7958 (mtt180) REVERT: L 258 MET cc_start: 0.8059 (mmm) cc_final: 0.6660 (tmm) REVERT: M 441 HIS cc_start: 0.8170 (m170) cc_final: 0.7792 (m170) REVERT: N 106 TYR cc_start: 0.8626 (m-80) cc_final: 0.8265 (m-80) REVERT: N 135 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8691 (tt) REVERT: N 388 MET cc_start: 0.7978 (mtm) cc_final: 0.7638 (mtp) outliers start: 64 outliers final: 41 residues processed: 547 average time/residue: 0.6360 time to fit residues: 425.1246 Evaluate side-chains 492 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 449 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 497 SER Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 608 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 455 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN F 400 HIS ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN G 765 GLN G 768 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN H 45 ASN L 163 ASN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073760 restraints weight = 51378.036| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.27 r_work: 0.2902 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.260 38748 Z= 0.389 Angle : 2.478 50.567 52579 Z= 1.425 Chirality : 0.444 6.580 5841 Planarity : 0.004 0.071 6553 Dihedral : 7.502 174.904 5654 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.85 % Favored : 98.13 % Rotamer: Outliers : 2.96 % Allowed : 17.99 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.54 (0.12), residues: 4711 helix: 1.09 (0.10), residues: 2678 sheet: -0.13 (0.28), residues: 302 loop : -0.61 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 373 TYR 0.022 0.002 TYR L 428 PHE 0.030 0.001 PHE L 341 TRP 0.028 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.39 (38712) covalent geometry : angle 2.16031 / 1.42 (52486) hydrogen bonds : bond 0.04884 / 3.30 ( 1708) hydrogen bonds : angle 4.16052 / 2.97 ( 5124) metal coordination : bond 0.04845 / 3.28 ( 36) metal coordination : angle 28.96107 / 20.43 ( 93) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 460 time to evaluate : 1.447 Fit side-chains REVERT: F 126 TYR cc_start: 0.8812 (OUTLIER) cc_final: 0.8535 (p90) REVERT: F 307 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8569 (mp) REVERT: F 420 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7843 (mp0) REVERT: G 459 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9034 (tp) REVERT: G 541 MET cc_start: 0.8892 (mmt) cc_final: 0.8460 (mmt) REVERT: G 670 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7712 (tm130) REVERT: B 126 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8546 (ttt) REVERT: B 170 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8393 (mtp) REVERT: L 199 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: L 353 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6592 (mp) REVERT: M 384 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8414 (tt) REVERT: N 379 MET cc_start: 0.9075 (mmt) cc_final: 0.8590 (mmt) REVERT: N 388 MET cc_start: 0.7925 (mtm) cc_final: 0.7408 (mtp) REVERT: N 482 MET cc_start: 0.8255 (tpp) cc_final: 0.7943 (mmm) REVERT: J 122 THR cc_start: 0.9100 (m) cc_final: 0.8595 (p) outliers start: 115 outliers final: 38 residues processed: 533 average time/residue: 0.6428 time to fit residues: 417.5513 Evaluate side-chains 488 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 442 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 249 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 462 optimal weight: 0.9990 chunk 345 optimal weight: 9.9990 chunk 182 optimal weight: 0.6980 chunk 310 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 424 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 313 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 386 GLN E 98 HIS G 299 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 190 GLN H 152 GLN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.074461 restraints weight = 51313.017| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.28 r_work: 0.2918 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38748 Z= 0.383 Angle : 2.476 50.669 52579 Z= 1.424 Chirality : 0.441 6.460 5841 Planarity : 0.004 0.072 6553 Dihedral : 7.052 174.905 5615 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.35 % Allowed : 17.78 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.97 (0.12), residues: 4711 helix: 1.46 (0.10), residues: 2677 sheet: -0.00 (0.29), residues: 303 loop : -0.45 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 198 TYR 0.024 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.025 0.001 TRP J 93 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01121 / 0.38 (38712) covalent geometry : angle 2.15512 / 1.42 (52486) hydrogen bonds : bond 0.04527 / 3.06 ( 1708) hydrogen bonds : angle 4.00916 / 2.87 ( 5124) metal coordination : bond 0.03751 / 2.44 ( 36) metal coordination : angle 29.06642 / 20.64 ( 93) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 472 time to evaluate : 1.469 Fit side-chains REVERT: F 95 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8395 (tp30) REVERT: F 307 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8555 (mp) REVERT: F 373 ARG cc_start: 0.8050 (mpp80) cc_final: 0.7415 (mtm-85) REVERT: F 388 CYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8174 (m) REVERT: E 144 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7894 (tpt) REVERT: G 98 MET cc_start: 0.9102 (mmp) cc_final: 0.8571 (mmp) REVERT: G 459 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9029 (tp) REVERT: G 541 MET cc_start: 0.8882 (mmt) cc_final: 0.8475 (mmt) REVERT: G 670 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7463 (tm130) REVERT: G 833 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: C 190 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8115 (tp40) REVERT: B 126 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8528 (ttt) REVERT: I 126 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8789 (mttp) REVERT: H 140 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7277 (pptt) REVERT: A 81 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7834 (mt-10) REVERT: A 108 PHE cc_start: 0.8678 (t80) cc_final: 0.8438 (t80) REVERT: L 40 LEU cc_start: 0.8814 (mp) cc_final: 0.8560 (mt) REVERT: L 139 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8145 (ttp) REVERT: L 353 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6597 (mp) REVERT: L 360 GLN cc_start: 0.5808 (OUTLIER) cc_final: 0.5369 (mt0) REVERT: L 546 ASP cc_start: 0.8076 (t70) cc_final: 0.7708 (t0) REVERT: M 384 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (tt) REVERT: N 388 MET cc_start: 0.7837 (mtm) cc_final: 0.7305 (mtp) REVERT: N 482 MET cc_start: 0.8211 (tpp) cc_final: 0.7976 (mmm) REVERT: J 122 THR cc_start: 0.9171 (m) cc_final: 0.8783 (p) outliers start: 130 outliers final: 45 residues processed: 563 average time/residue: 0.6802 time to fit residues: 467.4580 Evaluate side-chains 506 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 446 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 833 PHE Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 142 optimal weight: 10.0000 chunk 193 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 387 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 450 optimal weight: 1.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 107 GLN F 386 GLN G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS B 190 GLN H 45 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.069738 restraints weight = 50579.256| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.24 r_work: 0.2833 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38748 Z= 0.434 Angle : 2.496 50.651 52579 Z= 1.433 Chirality : 0.446 6.626 5841 Planarity : 0.005 0.068 6553 Dihedral : 7.427 176.336 5605 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 3.91 % Allowed : 17.40 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.84 (0.12), residues: 4711 helix: 1.34 (0.10), residues: 2686 sheet: -0.14 (0.29), residues: 298 loop : -0.48 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 198 TYR 0.022 0.002 TYR K 52 PHE 0.026 0.002 PHE L 341 TRP 0.022 0.002 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.43 (38712) covalent geometry : angle 2.17978 / 1.43 (52486) hydrogen bonds : bond 0.05825 / 3.96 ( 1708) hydrogen bonds : angle 4.27273 / 3.05 ( 5124) metal coordination : bond 0.05448 / 3.71 ( 36) metal coordination : angle 28.99170 / 20.55 ( 93) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 446 time to evaluate : 1.551 Fit side-chains REVERT: F 417 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: G 98 MET cc_start: 0.9151 (mmp) cc_final: 0.8682 (mmp) REVERT: G 490 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8179 (tp40) REVERT: G 541 MET cc_start: 0.8886 (mmt) cc_final: 0.8393 (mmt) REVERT: C 112 MET cc_start: 0.8801 (ttm) cc_final: 0.8533 (ttm) REVERT: C 190 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (tp40) REVERT: C 219 ASN cc_start: 0.6412 (OUTLIER) cc_final: 0.6059 (t0) REVERT: C 276 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: C 378 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.7937 (ttp-110) REVERT: B 166 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8740 (mtt) REVERT: B 170 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: I 126 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8804 (mttp) REVERT: H 140 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7492 (pptt) REVERT: H 286 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6565 (tmt90) REVERT: A 29 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 108 PHE cc_start: 0.8709 (t80) cc_final: 0.8497 (t80) REVERT: L 40 LEU cc_start: 0.8887 (mp) cc_final: 0.8558 (mt) REVERT: L 139 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8137 (ttp) REVERT: L 199 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: L 258 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.6776 (tmm) REVERT: L 353 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6604 (mp) REVERT: L 360 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5406 (mt0) REVERT: L 578 PHE cc_start: 0.7450 (t80) cc_final: 0.7072 (t80) REVERT: M 291 MET cc_start: 0.8960 (mtp) cc_final: 0.8706 (mtp) REVERT: M 303 TRP cc_start: 0.8865 (OUTLIER) cc_final: 0.6889 (m-10) REVERT: M 384 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8468 (tt) REVERT: N 255 MET cc_start: 0.8586 (tpp) cc_final: 0.8363 (mmm) REVERT: N 379 MET cc_start: 0.9158 (mmt) cc_final: 0.8939 (mmt) REVERT: K 26 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7606 (mtm110) REVERT: J 122 THR cc_start: 0.9106 (m) cc_final: 0.8726 (p) outliers start: 152 outliers final: 67 residues processed: 545 average time/residue: 0.6712 time to fit residues: 444.1794 Evaluate side-chains 516 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 430 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 270 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 374 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 834 GLN G 839 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 190 GLN H 296 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.070075 restraints weight = 50604.146| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.23 r_work: 0.2840 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38748 Z= 0.414 Angle : 2.490 50.662 52579 Z= 1.430 Chirality : 0.444 6.565 5841 Planarity : 0.005 0.069 6553 Dihedral : 7.419 176.837 5603 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 3.78 % Allowed : 17.65 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.89 (0.12), residues: 4711 helix: 1.39 (0.10), residues: 2688 sheet: -0.06 (0.29), residues: 294 loop : -0.48 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 198 TYR 0.021 0.002 TYR L 428 PHE 0.027 0.002 PHE L 341 TRP 0.024 0.001 TRP J 93 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.41 (38712) covalent geometry : angle 2.17297 / 1.43 (52486) hydrogen bonds : bond 0.05544 / 3.76 ( 1708) hydrogen bonds : angle 4.24775 / 3.03 ( 5124) metal coordination : bond 0.04730 / 3.19 ( 36) metal coordination : angle 29.00421 / 20.57 ( 93) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 439 time to evaluate : 1.610 Fit side-chains REVERT: F 417 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8011 (pp20) REVERT: G 98 MET cc_start: 0.9132 (mmp) cc_final: 0.8618 (mmp) REVERT: G 541 MET cc_start: 0.8865 (mmt) cc_final: 0.8386 (mmt) REVERT: C 127 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8835 (t80) REVERT: C 190 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8109 (tp40) REVERT: B 166 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8536 (mtt) REVERT: I 126 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8785 (mttp) REVERT: H 47 TYR cc_start: 0.8752 (m-80) cc_final: 0.8541 (m-80) REVERT: H 140 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7532 (pptt) REVERT: H 286 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.6674 (tmt90) REVERT: A 29 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8417 (mm) REVERT: L 40 LEU cc_start: 0.8925 (mp) cc_final: 0.8569 (mt) REVERT: L 139 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8146 (ttp) REVERT: L 199 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: L 258 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.6725 (tmm) REVERT: L 318 TYR cc_start: 0.8305 (m-80) cc_final: 0.7292 (t80) REVERT: L 353 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6529 (mp) REVERT: L 360 GLN cc_start: 0.5794 (OUTLIER) cc_final: 0.5374 (mt0) REVERT: L 546 ASP cc_start: 0.8103 (t70) cc_final: 0.7836 (t0) REVERT: L 578 PHE cc_start: 0.7489 (t80) cc_final: 0.7129 (t80) REVERT: M 291 MET cc_start: 0.8964 (mtp) cc_final: 0.8676 (mtp) REVERT: M 303 TRP cc_start: 0.8884 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: M 384 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8499 (tt) REVERT: M 447 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7124 (mtpt) REVERT: N 379 MET cc_start: 0.9162 (mmt) cc_final: 0.8611 (mmt) REVERT: N 388 MET cc_start: 0.8044 (mtm) cc_final: 0.7595 (mtp) REVERT: K 26 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7626 (mtm110) REVERT: J 122 THR cc_start: 0.9113 (m) cc_final: 0.8759 (p) outliers start: 147 outliers final: 69 residues processed: 539 average time/residue: 0.6929 time to fit residues: 454.8533 Evaluate side-chains 517 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 431 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 880 THR Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 175 optimal weight: 1.9990 chunk 312 optimal weight: 9.9990 chunk 462 optimal weight: 0.9990 chunk 411 optimal weight: 9.9990 chunk 388 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 357 optimal weight: 20.0000 chunk 203 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 839 GLN G 901 HIS C 228 HIS C 400 GLN B 190 GLN H 312 ASN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 124 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072618 restraints weight = 50964.562| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.26 r_work: 0.2876 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38748 Z= 0.386 Angle : 2.481 50.697 52579 Z= 1.425 Chirality : 0.441 6.462 5841 Planarity : 0.004 0.072 6553 Dihedral : 7.131 176.144 5601 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.11 % Allowed : 18.71 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.14 (0.12), residues: 4711 helix: 1.60 (0.10), residues: 2682 sheet: -0.01 (0.30), residues: 297 loop : -0.38 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 198 TYR 0.024 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.026 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.38 (38712) covalent geometry : angle 2.15939 / 1.42 (52486) hydrogen bonds : bond 0.04817 / 3.26 ( 1708) hydrogen bonds : angle 4.07963 / 2.91 ( 5124) metal coordination : bond 0.03312 / 2.18 ( 36) metal coordination : angle 29.13776 / 20.74 ( 93) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 460 time to evaluate : 1.585 Fit side-chains REVERT: F 80 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7257 (pm20) REVERT: F 417 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7956 (pp20) REVERT: G 541 MET cc_start: 0.8861 (mmt) cc_final: 0.8392 (mmt) REVERT: I 126 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8799 (mttp) REVERT: H 47 TYR cc_start: 0.8791 (m-80) cc_final: 0.8516 (m-80) REVERT: H 140 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (pptt) REVERT: A 31 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (mp) REVERT: A 108 PHE cc_start: 0.8734 (t80) cc_final: 0.8504 (t80) REVERT: L 40 LEU cc_start: 0.8885 (mp) cc_final: 0.8531 (mt) REVERT: L 199 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: L 318 TYR cc_start: 0.8206 (m-80) cc_final: 0.7241 (t80) REVERT: L 546 ASP cc_start: 0.8086 (t70) cc_final: 0.7601 (t0) REVERT: M 90 MET cc_start: 0.8405 (mmt) cc_final: 0.8155 (mmt) REVERT: M 291 MET cc_start: 0.8930 (mtp) cc_final: 0.8703 (mtp) REVERT: M 303 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.6892 (m-10) REVERT: M 384 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8477 (tt) REVERT: M 447 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7111 (mtpt) REVERT: N 379 MET cc_start: 0.9074 (mmt) cc_final: 0.8806 (mmt) REVERT: N 388 MET cc_start: 0.7941 (mtm) cc_final: 0.7493 (mtp) REVERT: K 98 MET cc_start: 0.8669 (mtm) cc_final: 0.8460 (mtp) REVERT: J 122 THR cc_start: 0.9094 (m) cc_final: 0.8759 (p) outliers start: 121 outliers final: 56 residues processed: 543 average time/residue: 0.7213 time to fit residues: 476.8548 Evaluate side-chains 500 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 436 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 171 LYS Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 140 LYS Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 199 GLU Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 52 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 381 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 834 GLN G 839 GLN ** G 901 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.070797 restraints weight = 50738.177| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.23 r_work: 0.2855 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38748 Z= 0.402 Angle : 2.487 50.658 52579 Z= 1.429 Chirality : 0.443 6.526 5841 Planarity : 0.005 0.132 6553 Dihedral : 7.256 176.058 5600 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.42 % Favored : 97.56 % Rotamer: Outliers : 3.06 % Allowed : 19.22 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.09 (0.12), residues: 4711 helix: 1.54 (0.10), residues: 2694 sheet: -0.00 (0.29), residues: 298 loop : -0.38 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 198 TYR 0.025 0.002 TYR K 52 PHE 0.026 0.002 PHE L 341 TRP 0.026 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.40 (38712) covalent geometry : angle 2.16879 / 1.43 (52486) hydrogen bonds : bond 0.05228 / 3.55 ( 1708) hydrogen bonds : angle 4.15767 / 2.97 ( 5124) metal coordination : bond 0.04184 / 2.81 ( 36) metal coordination : angle 29.02600 / 20.63 ( 93) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 444 time to evaluate : 1.464 Fit side-chains REVERT: F 373 ARG cc_start: 0.8071 (mpp80) cc_final: 0.7487 (mtm-85) REVERT: F 417 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: G 490 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8224 (tp40) REVERT: G 541 MET cc_start: 0.8864 (mmt) cc_final: 0.8388 (mmt) REVERT: C 276 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 84 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8051 (pp20) REVERT: B 126 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8586 (ttt) REVERT: I 126 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8809 (mttp) REVERT: H 47 TYR cc_start: 0.8844 (m-80) cc_final: 0.8586 (m-80) REVERT: H 286 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.6662 (tmt90) REVERT: A 31 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 108 PHE cc_start: 0.8735 (t80) cc_final: 0.8530 (t80) REVERT: L 40 LEU cc_start: 0.8914 (mp) cc_final: 0.8604 (mt) REVERT: L 258 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.6734 (tmm) REVERT: L 546 ASP cc_start: 0.8098 (t70) cc_final: 0.7609 (t0) REVERT: M 291 MET cc_start: 0.8962 (mtp) cc_final: 0.8692 (mtp) REVERT: M 303 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.6900 (m-10) REVERT: M 384 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8503 (tt) REVERT: M 447 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7121 (mtpt) REVERT: N 388 MET cc_start: 0.8014 (mtm) cc_final: 0.7499 (mtt) REVERT: J 72 MET cc_start: 0.8322 (mpt) cc_final: 0.8031 (mpt) REVERT: J 122 THR cc_start: 0.9101 (m) cc_final: 0.8766 (p) outliers start: 119 outliers final: 66 residues processed: 533 average time/residue: 0.6629 time to fit residues: 430.0357 Evaluate side-chains 512 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 434 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 446 optimal weight: 5.9990 chunk 410 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 424 optimal weight: 0.7980 chunk 355 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 839 GLN G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070149 restraints weight = 50327.554| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.22 r_work: 0.2834 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38748 Z= 0.415 Angle : 2.493 50.674 52579 Z= 1.432 Chirality : 0.444 6.571 5841 Planarity : 0.005 0.099 6553 Dihedral : 7.489 176.815 5600 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.41 % Rotamer: Outliers : 3.06 % Allowed : 19.43 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.01 (0.12), residues: 4711 helix: 1.48 (0.10), residues: 2688 sheet: -0.06 (0.29), residues: 298 loop : -0.41 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 198 TYR 0.024 0.002 TYR K 52 PHE 0.026 0.002 PHE L 341 TRP 0.028 0.001 TRP J 93 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01176 / 0.41 (38712) covalent geometry : angle 2.17663 / 1.43 (52486) hydrogen bonds : bond 0.05556 / 3.77 ( 1708) hydrogen bonds : angle 4.25136 / 3.03 ( 5124) metal coordination : bond 0.04761 / 3.26 ( 36) metal coordination : angle 28.99523 / 20.55 ( 93) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 437 time to evaluate : 1.421 Fit side-chains REVERT: F 302 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: F 373 ARG cc_start: 0.8115 (mpp80) cc_final: 0.7543 (mtm-85) REVERT: F 417 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7993 (pp20) REVERT: G 490 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8204 (tp40) REVERT: G 541 MET cc_start: 0.8872 (mmt) cc_final: 0.8381 (mmt) REVERT: C 276 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: C 469 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8713 (mt) REVERT: B 84 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8185 (pp20) REVERT: I 126 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8816 (mttp) REVERT: H 47 TYR cc_start: 0.8875 (m-80) cc_final: 0.8583 (m-80) REVERT: H 286 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.6651 (tmt90) REVERT: A 31 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8818 (mp) REVERT: L 40 LEU cc_start: 0.8921 (mp) cc_final: 0.8602 (mt) REVERT: L 578 PHE cc_start: 0.7519 (t80) cc_final: 0.7157 (t80) REVERT: M 291 MET cc_start: 0.8958 (mtp) cc_final: 0.8707 (mtp) REVERT: M 303 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: M 384 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8495 (tt) REVERT: M 447 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7116 (mtpt) REVERT: N 255 MET cc_start: 0.8656 (tpp) cc_final: 0.8177 (mmm) REVERT: N 294 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8500 (tp) REVERT: N 323 MET cc_start: 0.8274 (mmt) cc_final: 0.7911 (mpt) REVERT: N 379 MET cc_start: 0.9072 (mmt) cc_final: 0.8450 (mmt) REVERT: J 72 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8022 (mpt) REVERT: J 122 THR cc_start: 0.9104 (m) cc_final: 0.8764 (p) outliers start: 119 outliers final: 69 residues processed: 527 average time/residue: 0.6683 time to fit residues: 427.6749 Evaluate side-chains 507 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 424 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain M residue 455 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 463 optimal weight: 8.9990 chunk 454 optimal weight: 5.9990 chunk 424 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 146 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 403 optimal weight: 3.9990 chunk 364 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 834 GLN G 839 GLN G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 190 GLN H 312 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN N 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.070677 restraints weight = 50826.941| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.25 r_work: 0.2842 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 38748 Z= 0.412 Angle : 2.493 50.668 52579 Z= 1.431 Chirality : 0.444 6.558 5841 Planarity : 0.005 0.094 6553 Dihedral : 7.591 176.696 5600 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 2.80 % Allowed : 19.84 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.99 (0.12), residues: 4711 helix: 1.46 (0.10), residues: 2688 sheet: -0.10 (0.29), residues: 300 loop : -0.40 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 198 TYR 0.025 0.002 TYR K 52 PHE 0.026 0.002 PHE L 341 TRP 0.033 0.001 TRP J 93 HIS 0.009 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01172 / 0.41 (38712) covalent geometry : angle 2.17658 / 1.43 (52486) hydrogen bonds : bond 0.05508 / 3.74 ( 1708) hydrogen bonds : angle 4.25937 / 3.04 ( 5124) metal coordination : bond 0.04681 / 3.21 ( 36) metal coordination : angle 28.99075 / 20.54 ( 93) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 434 time to evaluate : 1.354 Fit side-chains REVERT: F 417 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8040 (pp20) REVERT: G 490 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8209 (tp40) REVERT: G 541 MET cc_start: 0.8869 (mmt) cc_final: 0.8416 (mmt) REVERT: C 276 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: C 378 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.8009 (ttp-110) REVERT: C 469 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8708 (mt) REVERT: C 475 ARG cc_start: 0.8875 (mtt90) cc_final: 0.8510 (mtt90) REVERT: B 84 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8176 (pp20) REVERT: I 126 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8812 (mttp) REVERT: H 47 TYR cc_start: 0.8867 (m-80) cc_final: 0.8558 (m-80) REVERT: H 286 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.6658 (tmt90) REVERT: A 31 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8867 (mp) REVERT: L 40 LEU cc_start: 0.8927 (mp) cc_final: 0.8604 (mt) REVERT: L 318 TYR cc_start: 0.8290 (m-80) cc_final: 0.7280 (t80) REVERT: L 546 ASP cc_start: 0.8122 (t70) cc_final: 0.7644 (t0) REVERT: L 578 PHE cc_start: 0.7492 (t80) cc_final: 0.7145 (t80) REVERT: M 90 MET cc_start: 0.8354 (mmt) cc_final: 0.7995 (mmt) REVERT: M 291 MET cc_start: 0.8946 (mtp) cc_final: 0.8692 (mtp) REVERT: M 303 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: M 345 MET cc_start: 0.8312 (ptp) cc_final: 0.8088 (ptm) REVERT: M 384 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8496 (tt) REVERT: M 447 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7110 (mtpt) REVERT: N 255 MET cc_start: 0.8628 (tpp) cc_final: 0.8391 (mmm) REVERT: N 294 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (tp) REVERT: N 379 MET cc_start: 0.9064 (mmt) cc_final: 0.8494 (mmt) REVERT: J 72 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8053 (mpt) REVERT: J 109 TYR cc_start: 0.8343 (t80) cc_final: 0.8081 (t80) REVERT: J 122 THR cc_start: 0.9102 (m) cc_final: 0.8727 (p) outliers start: 109 outliers final: 73 residues processed: 520 average time/residue: 0.7511 time to fit residues: 473.2229 Evaluate side-chains 510 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 294 ILE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 93 optimal weight: 0.9990 chunk 428 optimal weight: 8.9990 chunk 267 optimal weight: 0.9980 chunk 364 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 132 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 283 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 834 GLN G 839 GLN G 901 HIS C 135 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.072367 restraints weight = 50805.990| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.24 r_work: 0.2884 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38748 Z= 0.386 Angle : 2.487 50.677 52579 Z= 1.428 Chirality : 0.441 6.458 5841 Planarity : 0.004 0.074 6553 Dihedral : 7.282 175.893 5600 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.14 % Allowed : 20.61 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.18 (0.12), residues: 4711 helix: 1.61 (0.10), residues: 2683 sheet: 0.03 (0.30), residues: 299 loop : -0.32 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 198 TYR 0.025 0.002 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.037 0.001 TRP J 93 HIS 0.007 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01126 / 0.39 (38712) covalent geometry : angle 2.16615 / 1.43 (52486) hydrogen bonds : bond 0.04805 / 3.25 ( 1708) hydrogen bonds : angle 4.11726 / 2.94 ( 5124) metal coordination : bond 0.03272 / 2.16 ( 36) metal coordination : angle 29.11911 / 20.71 ( 93) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 448 time to evaluate : 1.849 Fit side-chains REVERT: F 417 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7964 (pp20) REVERT: G 541 MET cc_start: 0.8843 (mmt) cc_final: 0.8401 (mmt) REVERT: C 475 ARG cc_start: 0.8723 (mtt90) cc_final: 0.8447 (mtt90) REVERT: B 126 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8545 (ttt) REVERT: I 126 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8817 (mttp) REVERT: H 47 TYR cc_start: 0.8804 (m-80) cc_final: 0.8556 (m-80) REVERT: H 286 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.6653 (tmt90) REVERT: L 40 LEU cc_start: 0.8899 (mp) cc_final: 0.8576 (mt) REVERT: L 546 ASP cc_start: 0.8107 (t70) cc_final: 0.7610 (t0) REVERT: M 291 MET cc_start: 0.8903 (mtp) cc_final: 0.8688 (mtp) REVERT: M 303 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.7035 (m-10) REVERT: M 345 MET cc_start: 0.8171 (ptp) cc_final: 0.7966 (ptp) REVERT: M 384 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8496 (tt) REVERT: M 414 SER cc_start: 0.8553 (t) cc_final: 0.8238 (p) REVERT: M 447 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7187 (mtpt) REVERT: N 255 MET cc_start: 0.8589 (tpp) cc_final: 0.8269 (mmm) REVERT: N 379 MET cc_start: 0.8952 (mmt) cc_final: 0.8386 (mmt) REVERT: J 72 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (mpt) REVERT: J 122 THR cc_start: 0.9107 (m) cc_final: 0.8775 (p) outliers start: 83 outliers final: 50 residues processed: 507 average time/residue: 0.7372 time to fit residues: 454.0754 Evaluate side-chains 492 residues out of total 3887 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 434 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 417 GLU Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 126 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 310 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 461 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 404 optimal weight: 0.9990 chunk 346 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 302 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 834 GLN G 839 GLN G 901 HIS C 228 HIS C 400 GLN B 190 GLN H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.093547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.073675 restraints weight = 51066.360| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.24 r_work: 0.2916 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38748 Z= 0.383 Angle : 2.485 50.657 52579 Z= 1.427 Chirality : 0.440 6.424 5841 Planarity : 0.004 0.077 6553 Dihedral : 7.041 174.971 5596 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 20.84 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.29 (0.12), residues: 4711 helix: 1.70 (0.10), residues: 2683 sheet: 0.14 (0.30), residues: 306 loop : -0.29 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 198 TYR 0.026 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.039 0.001 TRP J 93 HIS 0.006 0.001 HIS G 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.38 (38712) covalent geometry : angle 2.16383 / 1.42 (52486) hydrogen bonds : bond 0.04551 / 3.08 ( 1708) hydrogen bonds : angle 4.03044 / 2.87 ( 5124) metal coordination : bond 0.02886 / 1.89 ( 36) metal coordination : angle 29.15101 / 20.83 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15384.87 seconds wall clock time: 262 minutes 0.61 seconds (15720.61 seconds total)