Starting phenix.real_space_refine on Mon May 19 02:26:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw7_41661/05_2025/8tw7_41661.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 11570 2.51 5 N 3101 2.21 5 O 3569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18337 Number of models: 1 Model: "" Number of chains: 12 Chain: "5" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2606 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "4" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "3" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2655 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "1" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2005 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2003 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2010 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1963 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 245} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.11, per 1000 atoms: 0.55 Number of scatterers: 18337 At special positions: 0 Unit cell: (123.372, 114.264, 147.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 11 15.00 Mg 3 11.99 O 3569 8.00 N 3101 7.00 C 11570 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.55 Conformation dependent library (CDL) restraints added in 2.4 seconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4480 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 53.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain '5' and resid 19 through 32 removed outlier: 4.418A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.516A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.964A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 117 removed outlier: 3.691A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.060A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR 5 161 " --> pdb=" O THR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 209 Processing helix chain '5' and resid 216 through 227 removed outlier: 4.020A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.530A pdb=" N ASN 5 243 " --> pdb=" O SER 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 273 Processing helix chain '5' and resid 275 through 291 removed outlier: 3.655A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.737A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY 5 344 " --> pdb=" O PHE 5 340 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.599A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.071A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.781A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.677A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 232 through 241 Processing helix chain '4' and resid 244 through 255 Processing helix chain '4' and resid 262 through 276 Processing helix chain '4' and resid 281 through 301 Processing helix chain '4' and resid 305 through 321 removed outlier: 3.726A pdb=" N LEU 4 309 " --> pdb=" O THR 4 305 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 13 Processing helix chain '3' and resid 14 through 19 Processing helix chain '3' and resid 23 through 27 removed outlier: 3.734A pdb=" N VAL 3 27 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 44 removed outlier: 3.519A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.513A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.013A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.549A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.379A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 160 removed outlier: 3.552A pdb=" N ARG 3 160 " --> pdb=" O ALA 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 185 Processing helix chain '3' and resid 190 through 200 Processing helix chain '3' and resid 204 through 219 Processing helix chain '3' and resid 228 through 237 removed outlier: 3.555A pdb=" N GLY 3 237 " --> pdb=" O TYR 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.620A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.894A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.635A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN 2 128 " --> pdb=" O HIS 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 145 removed outlier: 3.634A pdb=" N SER 2 144 " --> pdb=" O GLU 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 160 removed outlier: 3.557A pdb=" N LEU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR 2 160 " --> pdb=" O THR 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 176 Processing helix chain '2' and resid 177 through 184 Processing helix chain '2' and resid 193 through 208 removed outlier: 5.161A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.581A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 265 through 277 Processing helix chain '2' and resid 279 through 291 Processing helix chain '2' and resid 296 through 311 Processing helix chain '2' and resid 315 through 334 removed outlier: 3.504A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 352 Processing helix chain '1' and resid 388 through 395 Processing helix chain '1' and resid 398 through 407 Processing helix chain '1' and resid 414 through 430 removed outlier: 3.639A pdb=" N GLY 1 430 " --> pdb=" O VAL 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 443 Processing helix chain '1' and resid 453 through 476 removed outlier: 4.088A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP 1 461 " --> pdb=" O ALA 1 457 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.859A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.873A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.656A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.765A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.675A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.310A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.110A pdb=" N GLN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.107A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.308A pdb=" N PHE C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 141 through 153 removed outlier: 4.107A pdb=" N GLN C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain '5' and resid 69 through 76 removed outlier: 6.876A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE 5 96 " --> pdb=" O ASN 5 141 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 5 136 " --> pdb=" O ARG 5 166 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL 5 138 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL 5 170 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE 5 140 " --> pdb=" O VAL 5 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU 5 40 " --> pdb=" O ILE 5 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '5' and resid 212 through 213 removed outlier: 5.834A pdb=" N GLN 5 212 " --> pdb=" O LEU 5 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '4' and resid 75 through 78 removed outlier: 6.286A pdb=" N LYS 4 109 " --> pdb=" O ARG 4 139 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '4' and resid 185 through 186 removed outlier: 7.488A pdb=" N LYS 4 185 " --> pdb=" O VAL 4 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain '3' and resid 79 through 82 removed outlier: 6.603A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE 3 51 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 92 through 95 removed outlier: 6.221A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 589 through 592 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.522A pdb=" N GLU A 59 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU A 25 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 240 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ARG A 224 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.290A pdb=" N SER A 157 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 59 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 172 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 157 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL B 40 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP B 240 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG B 224 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 177 through 182 removed outlier: 4.662A pdb=" N ASP B 172 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 157 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU C 25 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL C 40 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 244 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP C 240 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG C 224 " --> pdb=" O ASP C 240 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3009 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: 6.08 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 3147 1.26 - 1.43: 4426 1.43 - 1.61: 10919 1.61 - 1.78: 11 1.78 - 1.95: 119 Bond restraints: 18622 Sorted by residual: bond pdb=" C GLU A 258 " pdb=" OXT GLU A 258 " ideal model delta sigma weight residual 1.231 1.090 0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C GLU B 258 " pdb=" OXT GLU B 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C GLU B 258 " pdb=" O GLU B 258 " ideal model delta sigma weight residual 1.231 1.370 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C GLU A 258 " pdb=" O GLU A 258 " ideal model delta sigma weight residual 1.231 1.370 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C4 ADP 5 401 " pdb=" C5 ADP 5 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 18617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 24372 3.06 - 6.12: 757 6.12 - 9.19: 68 9.19 - 12.25: 9 12.25 - 15.31: 7 Bond angle restraints: 25213 Sorted by residual: angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" C GLU B 257 " ideal model delta sigma weight residual 110.41 122.85 -12.44 1.18e+00 7.18e-01 1.11e+02 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 110.41 122.83 -12.42 1.18e+00 7.18e-01 1.11e+02 angle pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" C ASP B 97 " ideal model delta sigma weight residual 113.72 104.56 9.16 1.30e+00 5.92e-01 4.97e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.58 9.14 1.30e+00 5.92e-01 4.94e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.71 9.01 1.30e+00 5.92e-01 4.80e+01 ... (remaining 25208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.35: 10938 26.35 - 52.69: 442 52.69 - 79.04: 65 79.04 - 105.38: 18 105.38 - 131.73: 3 Dihedral angle restraints: 11466 sinusoidal: 4599 harmonic: 6867 Sorted by residual: dihedral pdb=" O1B ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PB ADP 5 401 " pdb=" PA ADP 5 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.27 131.73 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O2A ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PA ADP 5 401 " pdb=" PB ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.68 -120.68 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta harmonic sigma weight residual 122.80 134.80 -12.00 0 2.50e+00 1.60e-01 2.30e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2571 0.119 - 0.238: 310 0.238 - 0.357: 63 0.357 - 0.476: 12 0.476 - 0.595: 5 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.60 2.00e-01 2.50e+01 8.86e+00 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CA CYS C 22 " pdb=" N CYS C 22 " pdb=" C CYS C 22 " pdb=" CB CYS C 22 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 2958 not shown) Planarity restraints: 3227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 258 " 0.037 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C GLU A 258 " -0.141 2.00e-02 2.50e+03 pdb=" O GLU A 258 " 0.042 2.00e-02 2.50e+03 pdb=" OXT GLU A 258 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 258 " -0.037 2.00e-02 2.50e+03 8.16e-02 6.66e+01 pdb=" C GLU B 258 " 0.141 2.00e-02 2.50e+03 pdb=" O GLU B 258 " -0.042 2.00e-02 2.50e+03 pdb=" OXT GLU B 258 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 563 " -0.087 2.00e-02 2.50e+03 5.82e-02 5.92e+01 pdb=" CG PHE 1 563 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3224 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 20 2.33 - 2.97: 8745 2.97 - 3.61: 26477 3.61 - 4.26: 41430 4.26 - 4.90: 69770 Nonbonded interactions: 146442 Sorted by model distance: nonbonded pdb=" CD1 LEU 5 242 " pdb=" CG MET 1 558 " model vdw 1.684 3.860 nonbonded pdb=" O ASP A 109 " pdb=" O ILE B 181 " model vdw 1.772 3.040 nonbonded pdb=" CB ALA 2 297 " pdb=" OE1 GLU 2 339 " model vdw 2.094 3.460 nonbonded pdb=" O3G AGS 3 401 " pdb="MG MG 3 402 " model vdw 2.104 2.170 nonbonded pdb=" OD1 ASP 3 229 " pdb=" OD1 ASP 3 230 " model vdw 2.122 3.040 ... (remaining 146437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 96 or ( \ resid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 th \ rough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 or (resid 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 through 125 or (resid 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 254)) selection = (chain 'B' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 43 or (resid 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 through 96 or (resid 97 and (name N or name CA or name C or name O or n \ ame CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C \ or name O or name CB )) or resid 111 through 125 or (resid 126 and (name N or n \ ame CA or name C or name O or name CB )) or resid 127 through 173 or (resid 174 \ and (name N or name CA or name C or name O or name CB )) or resid 175 through 23 \ 5 or (resid 236 and (name N or name CA or name C or name O or name CB )) or resi \ d 237 through 254)) selection = (chain 'C' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 or (resid 72 and (name N or name CA or na \ me C or name O or name CB )) or resid 73 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 through 11 \ 8 or (resid 119 and (name N or name CA or name C or name O or name CB )) or resi \ d 120 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.100 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.009 0.336 18623 Z= 0.571 Angle : 1.207 15.312 25213 Z= 0.783 Chirality : 0.088 0.595 2961 Planarity : 0.009 0.184 3227 Dihedral : 14.636 131.731 6986 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.95 % Allowed : 3.53 % Favored : 95.52 % Rotamer: Outliers : 0.55 % Allowed : 6.66 % Favored : 92.79 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2324 helix: -0.45 (0.14), residues: 1099 sheet: 0.11 (0.22), residues: 505 loop : -1.87 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP 1 399 HIS 0.045 0.002 HIS 4 232 PHE 0.087 0.010 PHE 1 563 TYR 0.078 0.007 TYR A 133 ARG 0.028 0.002 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.15447 ( 1063) hydrogen bonds : angle 6.40307 ( 3009) covalent geometry : bond 0.00875 (18622) covalent geometry : angle 1.20721 (25213) Misc. bond : bond 0.33567 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 96 ILE cc_start: 0.9412 (mp) cc_final: 0.9171 (mt) REVERT: 4 45 MET cc_start: 0.8985 (ptp) cc_final: 0.8783 (ptp) REVERT: 4 202 MET cc_start: 0.8928 (tpp) cc_final: 0.8303 (tpp) REVERT: 2 291 MET cc_start: 0.8918 (mmm) cc_final: 0.8718 (mmm) REVERT: 2 345 ASN cc_start: 0.8747 (t0) cc_final: 0.8382 (t0) REVERT: 1 420 TYR cc_start: 0.8481 (t80) cc_final: 0.8155 (t80) REVERT: B 45 VAL cc_start: 0.9434 (m) cc_final: 0.9135 (t) outliers start: 11 outliers final: 1 residues processed: 211 average time/residue: 0.3444 time to fit residues: 105.4426 Evaluate side-chains 119 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN 5 104 ASN 5 244 ASN 5 341 HIS 4 18 GLN ** 4 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 92 GLN 4 177 GLN 4 232 HIS 4 244 ASN 4 320 ASN 3 180 ASN 3 317 GLN 2 236 GLN ** 2 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 352 GLN 1 534 GLN 1 620 HIS A 159 ASN B 159 ASN ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 159 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.072892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.064718 restraints weight = 65136.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.065834 restraints weight = 40255.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066910 restraints weight = 24635.992| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18623 Z= 0.174 Angle : 0.591 8.925 25213 Z= 0.307 Chirality : 0.042 0.237 2961 Planarity : 0.004 0.054 3227 Dihedral : 7.608 129.862 2564 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.04 % Allowed : 8.95 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2324 helix: 0.84 (0.15), residues: 1114 sheet: 0.56 (0.22), residues: 498 loop : -1.40 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 399 HIS 0.007 0.001 HIS B 64 PHE 0.019 0.002 PHE 1 443 TYR 0.025 0.002 TYR A 211 ARG 0.004 0.001 ARG 4 285 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 1063) hydrogen bonds : angle 4.94575 ( 3009) covalent geometry : bond 0.00385 (18622) covalent geometry : angle 0.59077 (25213) Misc. bond : bond 0.00475 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 96 ILE cc_start: 0.9232 (mp) cc_final: 0.8916 (mt) REVERT: 4 66 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8623 (tp) REVERT: 4 202 MET cc_start: 0.9054 (tpp) cc_final: 0.8197 (tpp) REVERT: 1 420 TYR cc_start: 0.8559 (t80) cc_final: 0.8231 (t80) REVERT: B 45 VAL cc_start: 0.9158 (m) cc_final: 0.8842 (t) REVERT: B 51 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7311 (tt0) outliers start: 21 outliers final: 8 residues processed: 131 average time/residue: 0.3297 time to fit residues: 64.4579 Evaluate side-chains 114 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 104 ASN Chi-restraints excluded: chain 4 residue 66 LEU Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 224 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 170 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 overall best weight: 5.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 104 ASN ** 4 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 GLN 4 208 ASN 3 148 ASN 2 265 HIS 2 288 ASN 2 313 ASN ** C 64 HIS ** 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 = 0.2907 r_free = 0.2907 target = 0.069880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.061844 restraints weight = 65598.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.062872 restraints weight = 41421.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.063744 restraints weight = 25421.384| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18623 Z= 0.190 Angle : 0.558 7.379 25213 Z= 0.288 Chirality : 0.041 0.216 2961 Planarity : 0.004 0.053 3227 Dihedral : 6.966 123.900 2561 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 1.39 % Allowed : 10.29 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2324 helix: 1.09 (0.16), residues: 1104 sheet: 0.39 (0.22), residues: 503 loop : -1.27 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 5 259 HIS 0.004 0.001 HIS 4 102 PHE 0.019 0.002 PHE 1 443 TYR 0.017 0.002 TYR A 211 ARG 0.005 0.001 ARG 5 184 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1063) hydrogen bonds : angle 4.72354 ( 3009) covalent geometry : bond 0.00435 (18622) covalent geometry : angle 0.55792 (25213) Misc. bond : bond 0.00340 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 2.074 Fit side-chains revert: symmetry clash REVERT: 5 186 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8913 (tt) REVERT: 4 66 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8694 (tp) REVERT: 4 202 MET cc_start: 0.9056 (tpp) cc_final: 0.8188 (tpp) REVERT: 2 71 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7589 (ptpp) REVERT: 1 420 TYR cc_start: 0.8622 (t80) cc_final: 0.8271 (t80) REVERT: A 7 GLU cc_start: 0.9558 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: A 51 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: B 51 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.7652 (tt0) outliers start: 28 outliers final: 10 residues processed: 134 average time/residue: 0.3232 time to fit residues: 65.4127 Evaluate side-chains 121 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 186 LEU Chi-restraints excluded: chain 4 residue 66 LEU Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain 1 residue 600 VAL Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 210 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 138 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 223 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 overall best weight: 2.4482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.070823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.062430 restraints weight = 65286.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.063245 restraints weight = 36173.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.064097 restraints weight = 26337.021| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18623 Z= 0.107 Angle : 0.476 7.095 25213 Z= 0.246 Chirality : 0.039 0.183 2961 Planarity : 0.003 0.053 3227 Dihedral : 6.680 124.757 2561 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 1.14 % Allowed : 11.03 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2324 helix: 1.39 (0.16), residues: 1113 sheet: 0.40 (0.23), residues: 509 loop : -1.06 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 5 259 HIS 0.009 0.001 HIS B 64 PHE 0.017 0.001 PHE 1 443 TYR 0.012 0.001 TYR A 211 ARG 0.004 0.000 ARG 5 184 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 1063) hydrogen bonds : angle 4.49729 ( 3009) covalent geometry : bond 0.00228 (18622) covalent geometry : angle 0.47618 (25213) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 2.207 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.9007 (tpp) cc_final: 0.8103 (tpp) REVERT: 3 205 MET cc_start: 0.9280 (mmt) cc_final: 0.8709 (mmt) REVERT: 3 299 LEU cc_start: 0.9428 (tp) cc_final: 0.9114 (tt) REVERT: 2 71 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7418 (ptpp) REVERT: 1 420 TYR cc_start: 0.8695 (t80) cc_final: 0.8360 (t80) REVERT: A 51 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8450 (tm-30) REVERT: C 7 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8425 (tp30) outliers start: 23 outliers final: 9 residues processed: 134 average time/residue: 0.3161 time to fit residues: 64.8904 Evaluate side-chains 118 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 150 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 197 optimal weight: 30.0000 chunk 213 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 208 optimal weight: 30.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.070943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.062577 restraints weight = 65951.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.063384 restraints weight = 36458.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.064272 restraints weight = 26403.356| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18623 Z= 0.103 Angle : 0.464 7.354 25213 Z= 0.238 Chirality : 0.039 0.196 2961 Planarity : 0.003 0.053 3227 Dihedral : 6.370 123.442 2561 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.34 % Allowed : 11.28 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2324 helix: 1.59 (0.16), residues: 1109 sheet: 0.49 (0.23), residues: 509 loop : -0.92 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 5 259 HIS 0.010 0.001 HIS B 64 PHE 0.018 0.001 PHE 1 443 TYR 0.010 0.001 TYR B 211 ARG 0.003 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 1063) hydrogen bonds : angle 4.37642 ( 3009) covalent geometry : bond 0.00224 (18622) covalent geometry : angle 0.46448 (25213) Misc. bond : bond 0.00081 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8961 (tpp) cc_final: 0.8073 (tpp) REVERT: 3 205 MET cc_start: 0.9258 (mmt) cc_final: 0.8664 (mmt) REVERT: 3 299 LEU cc_start: 0.9436 (tp) cc_final: 0.9137 (tt) REVERT: 2 71 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7448 (ptpp) REVERT: 1 420 TYR cc_start: 0.8688 (t80) cc_final: 0.8373 (t80) REVERT: A 7 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 14 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8533 (mtp180) REVERT: A 51 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8463 (tm-30) REVERT: B 51 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 7 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8441 (tp30) outliers start: 27 outliers final: 15 residues processed: 134 average time/residue: 0.3214 time to fit residues: 66.2776 Evaluate side-chains 124 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 0.0470 chunk 36 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 116 optimal weight: 0.0060 chunk 93 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 2.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.070920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.063108 restraints weight = 66094.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.063891 restraints weight = 34718.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.064281 restraints weight = 24119.809| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18623 Z= 0.103 Angle : 0.458 6.367 25213 Z= 0.236 Chirality : 0.039 0.181 2961 Planarity : 0.003 0.052 3227 Dihedral : 6.159 122.658 2561 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 1.59 % Allowed : 11.03 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2324 helix: 1.69 (0.16), residues: 1112 sheet: 0.56 (0.23), residues: 491 loop : -0.87 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 259 HIS 0.010 0.001 HIS B 64 PHE 0.018 0.001 PHE 1 443 TYR 0.010 0.001 TYR 2 83 ARG 0.003 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.02961 ( 1063) hydrogen bonds : angle 4.28747 ( 3009) covalent geometry : bond 0.00224 (18622) covalent geometry : angle 0.45833 (25213) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8943 (tpp) cc_final: 0.8053 (tpp) REVERT: 3 205 MET cc_start: 0.9215 (mmt) cc_final: 0.8701 (mmt) REVERT: 3 299 LEU cc_start: 0.9412 (tp) cc_final: 0.9128 (tt) REVERT: 2 71 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7699 (ptpp) REVERT: 1 420 TYR cc_start: 0.8659 (t80) cc_final: 0.8335 (t80) REVERT: 1 577 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 7 GLU cc_start: 0.9322 (OUTLIER) cc_final: 0.7260 (tp30) REVERT: A 14 ARG cc_start: 0.9064 (mtp85) cc_final: 0.8532 (mtp180) REVERT: A 51 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7097 (tm-30) REVERT: B 51 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: C 7 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8445 (tp30) outliers start: 32 outliers final: 17 residues processed: 138 average time/residue: 0.2883 time to fit residues: 62.9046 Evaluate side-chains 129 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 19 ASN 2 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.060815 restraints weight = 66629.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.061746 restraints weight = 36651.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.062052 restraints weight = 24687.522| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18623 Z= 0.190 Angle : 0.530 7.274 25213 Z= 0.272 Chirality : 0.041 0.168 2961 Planarity : 0.004 0.051 3227 Dihedral : 6.101 121.861 2561 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 1.34 % Allowed : 12.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 2324 helix: 1.57 (0.16), residues: 1100 sheet: 0.56 (0.23), residues: 503 loop : -0.90 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 5 259 HIS 0.010 0.001 HIS B 64 PHE 0.021 0.002 PHE 1 443 TYR 0.013 0.001 TYR 2 286 ARG 0.003 0.000 ARG 3 176 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 1063) hydrogen bonds : angle 4.49800 ( 3009) covalent geometry : bond 0.00438 (18622) covalent geometry : angle 0.52976 (25213) Misc. bond : bond 0.00129 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 2.322 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8947 (tpp) cc_final: 0.8711 (tpp) REVERT: 3 205 MET cc_start: 0.9249 (mmt) cc_final: 0.8715 (mmt) REVERT: 2 71 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7764 (ptpp) REVERT: 2 172 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: 1 420 TYR cc_start: 0.8748 (t80) cc_final: 0.8404 (t80) REVERT: A 7 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: A 51 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 119 MET cc_start: 0.8825 (mtp) cc_final: 0.8609 (mtp) REVERT: B 51 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: C 7 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8533 (tp30) outliers start: 27 outliers final: 17 residues processed: 123 average time/residue: 0.3008 time to fit residues: 58.1477 Evaluate side-chains 123 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 240 MET Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 125 GLN 2 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.069187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.061310 restraints weight = 65901.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.062233 restraints weight = 35964.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062709 restraints weight = 24263.239| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18623 Z= 0.147 Angle : 0.493 9.017 25213 Z= 0.253 Chirality : 0.040 0.191 2961 Planarity : 0.003 0.050 3227 Dihedral : 6.067 122.946 2561 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 1.04 % Allowed : 12.57 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2324 helix: 1.60 (0.16), residues: 1103 sheet: 0.40 (0.23), residues: 501 loop : -0.84 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 5 259 HIS 0.011 0.001 HIS B 64 PHE 0.019 0.001 PHE 1 443 TYR 0.010 0.001 TYR 2 286 ARG 0.008 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 1063) hydrogen bonds : angle 4.44853 ( 3009) covalent geometry : bond 0.00333 (18622) covalent geometry : angle 0.49337 (25213) Misc. bond : bond 0.00106 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8913 (tpp) cc_final: 0.8695 (tpp) REVERT: 3 205 MET cc_start: 0.9226 (mmt) cc_final: 0.8757 (mmt) REVERT: 3 299 LEU cc_start: 0.9410 (tp) cc_final: 0.9119 (tt) REVERT: 2 71 LYS cc_start: 0.8316 (mtmm) cc_final: 0.7751 (ptpp) REVERT: 2 172 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: 1 420 TYR cc_start: 0.8714 (t80) cc_final: 0.8387 (t80) REVERT: 1 577 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7980 (mp0) REVERT: A 7 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: A 51 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: A 119 MET cc_start: 0.8823 (mtp) cc_final: 0.8600 (mtp) REVERT: B 51 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: C 7 GLU cc_start: 0.9297 (OUTLIER) cc_final: 0.8550 (tp30) outliers start: 21 outliers final: 13 residues processed: 122 average time/residue: 0.3191 time to fit residues: 60.7493 Evaluate side-chains 120 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 61 MET Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 104 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 188 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 213 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 0.0050 chunk 41 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 216 HIS 2 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.061017 restraints weight = 66862.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.061946 restraints weight = 36262.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.062395 restraints weight = 24540.453| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18623 Z= 0.159 Angle : 0.503 8.035 25213 Z= 0.258 Chirality : 0.040 0.175 2961 Planarity : 0.003 0.051 3227 Dihedral : 6.016 122.145 2561 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 1.29 % Allowed : 12.43 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2324 helix: 1.64 (0.16), residues: 1094 sheet: 0.36 (0.23), residues: 501 loop : -0.86 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 5 259 HIS 0.011 0.001 HIS B 64 PHE 0.019 0.001 PHE 1 443 TYR 0.011 0.001 TYR 2 286 ARG 0.007 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 1063) hydrogen bonds : angle 4.46983 ( 3009) covalent geometry : bond 0.00363 (18622) covalent geometry : angle 0.50267 (25213) Misc. bond : bond 0.00114 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8902 (tpp) cc_final: 0.8671 (tpp) REVERT: 3 205 MET cc_start: 0.9233 (mmt) cc_final: 0.8794 (mmt) REVERT: 3 299 LEU cc_start: 0.9423 (tp) cc_final: 0.9137 (tt) REVERT: 2 71 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7798 (ptpp) REVERT: 2 172 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: 1 420 TYR cc_start: 0.8735 (t80) cc_final: 0.8406 (t80) REVERT: 1 577 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: A 7 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: A 51 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7279 (tm-30) REVERT: B 51 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: C 7 GLU cc_start: 0.9311 (OUTLIER) cc_final: 0.8550 (tp30) outliers start: 26 outliers final: 15 residues processed: 117 average time/residue: 0.2886 time to fit residues: 53.2779 Evaluate side-chains 117 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 34 ILE Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 2 residue 259 LEU Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 172 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 34 optimal weight: 0.0770 chunk 50 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 0.3980 chunk 171 optimal weight: 9.9990 overall best weight: 2.6944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.069968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.061297 restraints weight = 66011.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.062532 restraints weight = 38145.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.063365 restraints weight = 25584.175| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18623 Z= 0.109 Angle : 0.471 7.605 25213 Z= 0.240 Chirality : 0.039 0.176 2961 Planarity : 0.003 0.048 3227 Dihedral : 5.968 122.570 2561 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 0.99 % Allowed : 12.87 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2324 helix: 1.74 (0.16), residues: 1101 sheet: 0.41 (0.23), residues: 503 loop : -0.72 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 259 HIS 0.012 0.001 HIS B 64 PHE 0.017 0.001 PHE 1 443 TYR 0.009 0.001 TYR B 211 ARG 0.007 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 1063) hydrogen bonds : angle 4.36976 ( 3009) covalent geometry : bond 0.00240 (18622) covalent geometry : angle 0.47051 (25213) Misc. bond : bond 0.00078 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8894 (tpp) cc_final: 0.8674 (tpp) REVERT: 3 205 MET cc_start: 0.9177 (mmt) cc_final: 0.8809 (mmt) REVERT: 3 299 LEU cc_start: 0.9395 (tp) cc_final: 0.9129 (tt) REVERT: 2 71 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7776 (ptpp) REVERT: 2 172 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: 1 420 TYR cc_start: 0.8731 (t80) cc_final: 0.8419 (t80) REVERT: 1 577 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: A 7 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: A 51 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.6978 (tm-30) REVERT: B 51 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: C 7 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8531 (tp30) outliers start: 20 outliers final: 12 residues processed: 120 average time/residue: 0.3248 time to fit residues: 59.7317 Evaluate side-chains 116 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 5 VAL Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL Chi-restraints excluded: chain 4 residue 289 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 256 TRP Chi-restraints excluded: chain 3 residue 309 SER Chi-restraints excluded: chain 2 residue 172 TYR Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 577 GLU Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 232 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 60 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 171 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 94 optimal weight: 0.0370 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.061541 restraints weight = 66095.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062772 restraints weight = 38096.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.063513 restraints weight = 25587.288| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18623 Z= 0.104 Angle : 0.469 7.827 25213 Z= 0.239 Chirality : 0.039 0.181 2961 Planarity : 0.003 0.049 3227 Dihedral : 5.894 121.993 2561 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Rotamer: Outliers : 0.99 % Allowed : 13.02 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.18), residues: 2324 helix: 1.77 (0.16), residues: 1103 sheet: 0.42 (0.23), residues: 503 loop : -0.69 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 5 259 HIS 0.012 0.001 HIS B 64 PHE 0.017 0.001 PHE 1 443 TYR 0.009 0.001 TYR 2 286 ARG 0.007 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 1063) hydrogen bonds : angle 4.32549 ( 3009) covalent geometry : bond 0.00229 (18622) covalent geometry : angle 0.46904 (25213) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.98 seconds wall clock time: 76 minutes 7.08 seconds (4567.08 seconds total)