Starting phenix.real_space_refine on Sun Jun 15 22:34:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw7_41661/06_2025/8tw7_41661.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw7_41661/06_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_41661/06_2025/8tw7_41661.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw7_41661/06_2025/8tw7_41661.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw7_41661/06_2025/8tw7_41661.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw7_41661/06_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-5710/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: 10.74, per 1000 atoms: 0.59 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: 5.03 Conformation dependent library (CDL) restraints added in 2.3 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: 2.35 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: 6.86 Time building geometry restraints manager: 5.61 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: 0.590 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.140 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- 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 : 2.225 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: 0.3675 time to fit residues: 112.8515 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 : 2.157 ------------------------------------------------------------------------------- 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 = 0.064722 restraints weight = 65136.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.065841 restraints weight = 40238.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.066649 restraints weight = 24582.197| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 2.353 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: 0.8834 (OUTLIER) cc_final: 0.8625 (tp) REVERT: 4 202 MET cc_start: 0.9058 (tpp) cc_final: 0.8200 (tpp) REVERT: 1 420 TYR cc_start: 0.8565 (t80) cc_final: 0.8236 (t80) REVERT: B 45 VAL cc_start: 0.9149 (m) cc_final: 0.8856 (t) REVERT: B 51 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.7324 (tt0) outliers start: 21 outliers final: 8 residues processed: 131 average time/residue: 0.3509 time to fit residues: 69.0655 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 : 2.233 ------------------------------------------------------------------------------- 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: 7.9990 chunk 213 optimal weight: 20.0000 chunk 211 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** 3 148 ASN 2 288 ASN 2 313 ASN ** C 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.061872 restraints weight = 65302.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.063120 restraints weight = 37626.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.063970 restraints weight = 25393.075| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18623 Z= 0.171 Angle : 0.535 7.534 25213 Z= 0.277 Chirality : 0.041 0.221 2961 Planarity : 0.004 0.054 3227 Dihedral : 7.026 124.831 2561 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.34 % Allowed : 9.99 % Favored : 88.67 % 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: 0.38 (0.17), residues: 2324 helix: 1.16 (0.16), residues: 1106 sheet: 0.42 (0.22), residues: 502 loop : -1.26 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 5 259 HIS 0.003 0.001 HIS 5 38 PHE 0.018 0.002 PHE 1 443 TYR 0.017 0.001 TYR A 211 ARG 0.004 0.000 ARG 5 184 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1063) hydrogen bonds : angle 4.68430 ( 3009) covalent geometry : bond 0.00386 (18622) covalent geometry : angle 0.53520 (25213) Misc. bond : bond 0.00270 ( 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 138 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 5 186 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8947 (tt) REVERT: 4 66 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (tp) REVERT: 4 202 MET cc_start: 0.9087 (tpp) cc_final: 0.8175 (tpp) REVERT: 2 71 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7508 (ptpp) REVERT: 1 420 TYR cc_start: 0.8658 (t80) cc_final: 0.8311 (t80) REVERT: A 7 GLU cc_start: 0.9525 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: A 51 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: B 51 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7487 (tt0) outliers start: 27 outliers final: 11 residues processed: 129 average time/residue: 0.3339 time to fit residues: 65.7542 Evaluate side-chains 118 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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 7 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: 5.9990 chunk 108 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 138 optimal weight: 0.0570 chunk 129 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- 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** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 265 HIS C 64 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.060993 restraints weight = 65723.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.062229 restraints weight = 38609.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.063059 restraints weight = 25623.586| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18623 Z= 0.152 Angle : 0.508 8.578 25213 Z= 0.262 Chirality : 0.040 0.186 2961 Planarity : 0.004 0.053 3227 Dihedral : 6.579 124.537 2561 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 1.44 % Allowed : 11.18 % 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: 0.67 (0.18), residues: 2324 helix: 1.42 (0.16), residues: 1101 sheet: 0.45 (0.22), residues: 507 loop : -1.04 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 5 259 HIS 0.008 0.001 HIS B 64 PHE 0.019 0.001 PHE 1 443 TYR 0.013 0.001 TYR A 211 ARG 0.005 0.000 ARG 3 206 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 1063) hydrogen bonds : angle 4.54952 ( 3009) covalent geometry : bond 0.00341 (18622) covalent geometry : angle 0.50752 (25213) Misc. bond : bond 0.00171 ( 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 139 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 2.080 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.9004 (tpp) cc_final: 0.8091 (tpp) REVERT: 4 307 LEU cc_start: 0.9550 (tp) cc_final: 0.9328 (tp) REVERT: 3 205 MET cc_start: 0.9216 (mmt) cc_final: 0.8583 (mmt) REVERT: 2 71 LYS cc_start: 0.8274 (mtmm) cc_final: 0.7688 (ptpp) REVERT: 1 420 TYR cc_start: 0.8696 (t80) cc_final: 0.8349 (t80) REVERT: A 51 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 51 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.7622 (tt0) outliers start: 29 outliers final: 15 residues processed: 132 average time/residue: 0.3215 time to fit residues: 65.6002 Evaluate side-chains 120 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE 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 131 LEU 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: 7.9990 chunk 94 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 213 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 97 optimal weight: 0.0370 chunk 208 optimal weight: 20.0000 overall best weight: 3.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 19 ASN ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061402 restraints weight = 66230.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.062284 restraints weight = 37527.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.062642 restraints weight = 27564.228| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18623 Z= 0.134 Angle : 0.483 6.844 25213 Z= 0.248 Chirality : 0.040 0.191 2961 Planarity : 0.003 0.053 3227 Dihedral : 6.307 123.282 2561 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.29 % Allowed : 11.88 % Favored : 86.83 % 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: 0.84 (0.18), residues: 2324 helix: 1.60 (0.16), residues: 1091 sheet: 0.49 (0.23), residues: 511 loop : -0.97 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 5 259 HIS 0.010 0.001 HIS B 64 PHE 0.018 0.001 PHE 1 443 TYR 0.011 0.001 TYR A 211 ARG 0.003 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 1063) hydrogen bonds : angle 4.44632 ( 3009) covalent geometry : bond 0.00299 (18622) covalent geometry : angle 0.48273 (25213) Misc. bond : bond 0.00107 ( 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: 26 poor density : 113 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8973 (tpp) cc_final: 0.8048 (tpp) REVERT: 3 299 LEU cc_start: 0.9410 (tp) cc_final: 0.9104 (tt) REVERT: 2 71 LYS cc_start: 0.8344 (mtmm) cc_final: 0.7740 (ptpp) REVERT: 1 420 TYR cc_start: 0.8725 (t80) cc_final: 0.8365 (t80) REVERT: A 7 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: A 51 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: B 51 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: C 7 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8512 (tp30) outliers start: 26 outliers final: 12 residues processed: 132 average time/residue: 0.3126 time to fit residues: 63.8675 Evaluate side-chains 121 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 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 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 C residue 7 GLU 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: 9.9990 chunk 163 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 101 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** 2 124 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.067872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.059622 restraints weight = 67991.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.060452 restraints weight = 37907.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.061206 restraints weight = 27651.940| |-----------------------------------------------------------------------------| r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 18623 Z= 0.226 Angle : 0.559 6.931 25213 Z= 0.287 Chirality : 0.041 0.161 2961 Planarity : 0.004 0.052 3227 Dihedral : 6.246 122.431 2561 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 1.54 % Allowed : 12.03 % Favored : 86.43 % 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: 0.66 (0.18), residues: 2324 helix: 1.38 (0.16), residues: 1099 sheet: 0.47 (0.23), residues: 507 loop : -0.98 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 5 259 HIS 0.012 0.001 HIS B 64 PHE 0.021 0.002 PHE 1 443 TYR 0.012 0.002 TYR A 60 ARG 0.004 0.001 ARG 3 176 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1063) hydrogen bonds : angle 4.63600 ( 3009) covalent geometry : bond 0.00521 (18622) covalent geometry : angle 0.55945 (25213) Misc. bond : bond 0.00162 ( 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 132 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 2.123 Fit side-chains revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8946 (tpp) cc_final: 0.8704 (tpp) REVERT: 2 71 LYS cc_start: 0.8355 (mtmm) cc_final: 0.7789 (ptpp) REVERT: A 7 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: A 51 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7331 (tm-30) REVERT: B 51 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: C 7 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.8576 (tp30) outliers start: 31 outliers final: 17 residues processed: 124 average time/residue: 0.3138 time to fit residues: 60.0684 Evaluate side-chains 121 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain 1 residue 412 HIS Chi-restraints excluded: chain 1 residue 591 ILE Chi-restraints excluded: chain 1 residue 639 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 50 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: 5.9990 chunk 68 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.069298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.060689 restraints weight = 66215.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.061904 restraints weight = 38367.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.062709 restraints weight = 25851.463| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18623 Z= 0.119 Angle : 0.476 6.463 25213 Z= 0.245 Chirality : 0.039 0.177 2961 Planarity : 0.003 0.052 3227 Dihedral : 6.167 123.067 2561 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 1.04 % Allowed : 13.17 % Favored : 85.79 % 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: 0.85 (0.18), residues: 2324 helix: 1.58 (0.16), residues: 1101 sheet: 0.45 (0.23), residues: 507 loop : -0.89 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 5 259 HIS 0.011 0.001 HIS B 64 PHE 0.017 0.001 PHE 1 443 TYR 0.010 0.001 TYR B 211 ARG 0.008 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1063) hydrogen bonds : angle 4.46230 ( 3009) covalent geometry : bond 0.00263 (18622) covalent geometry : angle 0.47597 (25213) Misc. bond : bond 0.00087 ( 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: 21 poor density : 109 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8917 (tpp) cc_final: 0.8683 (tpp) REVERT: 3 205 MET cc_start: 0.9278 (mmt) cc_final: 0.8691 (mmt) REVERT: 3 299 LEU cc_start: 0.9395 (tp) cc_final: 0.9109 (tt) REVERT: 2 71 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7722 (ptpp) REVERT: 2 88 MET cc_start: 0.8610 (tpp) cc_final: 0.7704 (tpt) REVERT: 2 172 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: 1 420 TYR cc_start: 0.8600 (t80) cc_final: 0.8314 (t80) REVERT: A 7 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: A 51 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7153 (tm-30) REVERT: B 51 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: B 199 MET cc_start: 0.6476 (ttp) cc_final: 0.6175 (ttm) REVERT: C 7 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.8565 (tp30) outliers start: 21 outliers final: 10 residues processed: 124 average time/residue: 0.3240 time to fit residues: 61.6107 Evaluate side-chains 119 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 4 residue 12 VAL 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 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 232 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 0.0470 chunk 123 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 overall best weight: 2.9682 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.069603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.061726 restraints weight = 65638.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062811 restraints weight = 35320.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062856 restraints weight = 23345.551| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18623 Z= 0.116 Angle : 0.470 7.132 25213 Z= 0.241 Chirality : 0.039 0.157 2961 Planarity : 0.003 0.051 3227 Dihedral : 6.009 122.215 2561 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.21 % Rotamer: Outliers : 0.99 % Allowed : 13.32 % Favored : 85.69 % 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: 0.95 (0.18), residues: 2324 helix: 1.72 (0.16), residues: 1095 sheet: 0.32 (0.23), residues: 515 loop : -0.79 (0.24), residues: 714 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 0.017 0.001 PHE 1 443 TYR 0.010 0.001 TYR B 211 ARG 0.006 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 1063) hydrogen bonds : angle 4.38100 ( 3009) covalent geometry : bond 0.00257 (18622) covalent geometry : angle 0.47042 (25213) Misc. bond : bond 0.00081 ( 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 127 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8898 (tpp) cc_final: 0.8675 (tpp) REVERT: 4 307 LEU cc_start: 0.9564 (tp) cc_final: 0.9359 (tp) REVERT: 3 299 LEU cc_start: 0.9412 (tp) cc_final: 0.9129 (tt) REVERT: 2 71 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7767 (ptpp) REVERT: 2 172 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: 1 420 TYR cc_start: 0.8601 (t80) cc_final: 0.8323 (t80) REVERT: A 7 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: A 51 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: C 7 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8568 (tp30) outliers start: 20 outliers final: 13 residues processed: 121 average time/residue: 0.3361 time to fit residues: 62.2600 Evaluate side-chains 122 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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 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 2 residue 305 HIS Chi-restraints excluded: chain 1 residue 412 HIS 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 121 ILE Chi-restraints excluded: chain C residue 7 GLU 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: 20.0000 chunk 214 optimal weight: 0.6980 chunk 188 optimal weight: 0.2980 chunk 209 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 221 optimal weight: 30.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.2922 r_free = 0.2922 target = 0.070090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.061445 restraints weight = 66311.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.062681 restraints weight = 38116.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.063405 restraints weight = 25550.390| |-----------------------------------------------------------------------------| r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18623 Z= 0.102 Angle : 0.459 6.965 25213 Z= 0.235 Chirality : 0.039 0.158 2961 Planarity : 0.003 0.049 3227 Dihedral : 5.940 122.025 2561 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 0.99 % Allowed : 13.37 % Favored : 85.64 % 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: 1.75 (0.16), residues: 1103 sheet: 0.38 (0.23), residues: 515 loop : -0.72 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 399 HIS 0.011 0.001 HIS B 64 PHE 0.017 0.001 PHE 1 443 TYR 0.013 0.001 TYR 5 42 ARG 0.005 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 1063) hydrogen bonds : angle 4.30920 ( 3009) covalent geometry : bond 0.00223 (18622) covalent geometry : angle 0.45929 (25213) Misc. bond : bond 0.00072 ( 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: 20 poor density : 104 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8878 (tpp) cc_final: 0.8667 (tpp) REVERT: 3 299 LEU cc_start: 0.9384 (tp) cc_final: 0.9116 (tt) REVERT: 2 71 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7786 (ptpp) REVERT: 2 88 MET cc_start: 0.8467 (tpp) cc_final: 0.7693 (tpt) REVERT: 2 172 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: 1 420 TYR cc_start: 0.8576 (t80) cc_final: 0.8342 (t80) REVERT: A 7 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: A 51 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: C 7 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.8549 (tp30) outliers start: 20 outliers final: 13 residues processed: 119 average time/residue: 0.3168 time to fit residues: 57.9812 Evaluate side-chains 117 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 2.075 ------------------------------------------------------------------------------- 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 305 HIS 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 68 LEU 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: 6.9990 chunk 195 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 171 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.2905 r_free = 0.2905 target = 0.069363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.061637 restraints weight = 66411.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.062441 restraints weight = 35506.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.062796 restraints weight = 24762.992| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18623 Z= 0.140 Angle : 0.483 6.872 25213 Z= 0.247 Chirality : 0.040 0.175 2961 Planarity : 0.003 0.049 3227 Dihedral : 5.902 121.702 2561 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 1.04 % Allowed : 13.32 % Favored : 85.64 % 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: 1.01 (0.18), residues: 2324 helix: 1.72 (0.16), residues: 1102 sheet: 0.39 (0.23), residues: 515 loop : -0.74 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.006 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 1063) hydrogen bonds : angle 4.36803 ( 3009) covalent geometry : bond 0.00317 (18622) covalent geometry : angle 0.48281 (25213) Misc. bond : bond 0.00095 ( 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 119 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 202 MET cc_start: 0.8872 (tpp) cc_final: 0.8663 (tpp) REVERT: 3 299 LEU cc_start: 0.9417 (tp) cc_final: 0.9140 (tt) REVERT: 2 71 LYS cc_start: 0.8293 (mtmm) cc_final: 0.7822 (ptpp) REVERT: 2 172 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: 1 420 TYR cc_start: 0.8582 (t80) cc_final: 0.8323 (t80) REVERT: A 7 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: A 51 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: C 7 GLU cc_start: 0.9305 (OUTLIER) cc_final: 0.8536 (tp30) outliers start: 21 outliers final: 15 residues processed: 115 average time/residue: 0.3116 time to fit residues: 55.5576 Evaluate side-chains 115 residues out of total 2102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 2.236 ------------------------------------------------------------------------------- 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 305 HIS 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 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: 0.7980 chunk 168 optimal weight: 0.0010 chunk 148 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.9768 ------------------------------------------------------------------------------- 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 = 0.2945 r_free = 0.2945 target = 0.071019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.062404 restraints weight = 65557.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.063656 restraints weight = 37846.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.064372 restraints weight = 25108.291| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3630 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= 0.084 Angle : 0.453 7.322 25213 Z= 0.232 Chirality : 0.039 0.167 2961 Planarity : 0.003 0.048 3227 Dihedral : 5.871 121.831 2561 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 0.89 % Allowed : 13.57 % Favored : 85.54 % 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: 1.16 (0.18), residues: 2324 helix: 1.84 (0.16), residues: 1104 sheet: 0.46 (0.23), residues: 517 loop : -0.64 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 399 HIS 0.012 0.001 HIS B 64 PHE 0.016 0.001 PHE 1 443 TYR 0.009 0.001 TYR B 211 ARG 0.005 0.000 ARG 4 69 Details of bonding type rmsd hydrogen bonds : bond 0.02859 ( 1063) hydrogen bonds : angle 4.24063 ( 3009) covalent geometry : bond 0.00170 (18622) covalent geometry : angle 0.45321 (25213) Misc. bond : bond 0.00042 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.73 seconds wall clock time: 80 minutes 55.05 seconds (4855.05 seconds total)