Starting phenix.real_space_refine on Sun May 18 12:31:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.map" model { file = "/net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eij_48085/05_2025/9eij_48085.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 86 5.16 5 C 10920 2.51 5 N 2861 2.21 5 O 3094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16970 Number of models: 1 Model: "" Number of chains: 22 Chain: "D" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1029 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Chain: "E" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2146 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain: "F" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2131 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "I" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2184 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 271} Chain: "J" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2184 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 271} Chain: "K" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "N" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 442 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "P" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 326 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "R" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 478 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "T" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 417 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "V" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 350 Classifications: {'peptide': 42} Link IDs: {'TRANS': 41} Chain: "X" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "Z" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "B" Number of atoms: 3411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3411 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 25, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.84, per 1000 atoms: 0.64 Number of scatterers: 16970 At special positions: 0 Unit cell: (177.262, 134.113, 135.279, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 9 15.00 O 3094 8.00 N 2861 7.00 C 10920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS F 47 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 549 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3868 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 36.3% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'D' and resid 6 through 30 removed outlier: 4.494A pdb=" N ALA D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 removed outlier: 4.182A pdb=" N GLY D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 85 through 100 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.522A pdb=" N LEU D 106 " --> pdb=" O GLN D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 3.733A pdb=" N LYS D 125 " --> pdb=" O MET D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 22 through 31 removed outlier: 3.676A pdb=" N ILE E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 158 No H-bonds generated for 'chain 'E' and resid 156 through 158' Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.760A pdb=" N GLY E 282 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 Processing helix chain 'F' and resid 22 through 31 removed outlier: 3.777A pdb=" N ILE F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 278 through 282 removed outlier: 4.202A pdb=" N GLY F 282 " --> pdb=" O ILE F 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 Processing helix chain 'I' and resid 87 through 92 Processing helix chain 'J' and resid 84 through 92 removed outlier: 4.240A pdb=" N ARG J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS J 90 " --> pdb=" O CYS J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'K' and resid 16 through 48 Proline residue: K 42 - end of helix Processing helix chain 'L' and resid 14 through 46 removed outlier: 3.523A pdb=" N TYR L 34 " --> pdb=" O ASN L 30 " (cutoff:3.500A) Proline residue: L 42 - end of helix Processing helix chain 'N' and resid 5 through 39 removed outlier: 3.798A pdb=" N ARG N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN N 14 " --> pdb=" O GLN N 10 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'P' and resid 27 through 36 Processing helix chain 'P' and resid 40 through 62 Processing helix chain 'R' and resid 58 through 64 Processing helix chain 'R' and resid 66 through 96 Processing helix chain 'R' and resid 96 through 114 removed outlier: 3.836A pdb=" N GLU R 102 " --> pdb=" O PRO R 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 96 Processing helix chain 'T' and resid 96 through 116 removed outlier: 3.855A pdb=" N LEU T 114 " --> pdb=" O GLN T 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 27 through 36 Processing helix chain 'V' and resid 40 through 62 Processing helix chain 'X' and resid 6 through 39 removed outlier: 5.364A pdb=" N ILE X 28 " --> pdb=" O ARG X 24 " (cutoff:3.500A) Proline residue: X 29 - end of helix Processing helix chain 'X' and resid 48 through 52 removed outlier: 3.518A pdb=" N LEU X 52 " --> pdb=" O VAL X 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 46 Proline residue: Z 42 - end of helix Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.557A pdb=" N SER B 73 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 75 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 107 through 136 removed outlier: 4.387A pdb=" N GLN B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.468A pdb=" N CYS B 387 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 433 through 447 removed outlier: 3.571A pdb=" N TRP B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 460 removed outlier: 4.138A pdb=" N ALA B 459 " --> pdb=" O GLN B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.639A pdb=" N ARG B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 499 through 513 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 523 through 545 removed outlier: 4.091A pdb=" N ARG B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 removed outlier: 3.584A pdb=" N LYS B 553 " --> pdb=" O CYS B 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 removed outlier: 3.826A pdb=" N CYS B 568 " --> pdb=" O CYS B 564 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 45 removed outlier: 3.666A pdb=" N LEU E 92 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP E 100 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU E 106 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE E 125 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL E 140 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER E 127 " --> pdb=" O CYS E 138 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY E 151 " --> pdb=" O MET E 166 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 153 " --> pdb=" O TYR E 164 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 162 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 200 " --> pdb=" O ASN E 196 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP E 221 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU E 253 " --> pdb=" O ASN E 249 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU E 37 " --> pdb=" O VAL E 286 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 37 through 45 removed outlier: 3.647A pdb=" N THR F 44 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 52 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE F 82 " --> pdb=" O TYR F 73 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 94 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU F 108 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE F 125 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL F 140 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP F 169 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 175 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA F 242 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU F 37 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU F 290 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS F 39 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LEU F 292 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASP F 41 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 100 through 110 removed outlier: 3.658A pdb=" N LEU I 109 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS I 139 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA I 146 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N PHE I 147 " --> pdb=" O GLN I 167 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLN I 167 " --> pdb=" O PHE I 147 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN I 181 " --> pdb=" O PHE I 185 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU I 229 " --> pdb=" O ILE I 225 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY I 100 " --> pdb=" O PHE I 356 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU I 358 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS I 102 " --> pdb=" O LEU I 358 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE I 360 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR I 104 " --> pdb=" O ILE I 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 100 through 110 removed outlier: 6.219A pdb=" N PHE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS J 139 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA J 146 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE J 147 " --> pdb=" O GLN J 167 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN J 167 " --> pdb=" O PHE J 147 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN J 181 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 225 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU J 229 " --> pdb=" O ILE J 225 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE J 323 " --> pdb=" O ASP J 319 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY J 100 " --> pdb=" O PHE J 356 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU J 358 " --> pdb=" O GLY J 100 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS J 102 " --> pdb=" O LEU J 358 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE J 360 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR J 104 " --> pdb=" O ILE J 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 164 removed outlier: 5.665A pdb=" N ILE B 158 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR B 174 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLN B 160 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 170 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 164 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 314 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 279 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 323 through 324 removed outlier: 3.981A pdb=" N CYS B 323 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 399 1098 hydrogen bonds defined for protein. 3114 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: 6.01 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3108 1.33 - 1.45: 4231 1.45 - 1.58: 9806 1.58 - 1.70: 18 1.70 - 1.83: 130 Bond restraints: 17293 Sorted by residual: bond pdb=" CB TRP E 221 " pdb=" CG TRP E 221 " ideal model delta sigma weight residual 1.498 1.522 -0.024 3.10e-02 1.04e+03 5.99e-01 bond pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.29e-02 6.01e+03 5.89e-01 bond pdb=" CB ARG T 79 " pdb=" CG ARG T 79 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.84e-01 bond pdb=" N PRO I 333 " pdb=" CA PRO I 333 " ideal model delta sigma weight residual 1.465 1.480 -0.015 2.03e-02 2.43e+03 5.21e-01 bond pdb=" CB ARG E 263 " pdb=" CG ARG E 263 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.05e-01 ... (remaining 17288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 22823 1.92 - 3.84: 369 3.84 - 5.76: 67 5.76 - 7.68: 17 7.68 - 9.60: 4 Bond angle restraints: 23280 Sorted by residual: angle pdb=" N LYS E 74 " pdb=" CA LYS E 74 " pdb=" C LYS E 74 " ideal model delta sigma weight residual 110.80 117.71 -6.91 2.13e+00 2.20e-01 1.05e+01 angle pdb=" C ALA B 383 " pdb=" N ASP B 384 " pdb=" CA ASP B 384 " ideal model delta sigma weight residual 122.20 114.77 7.43 2.32e+00 1.86e-01 1.03e+01 angle pdb=" N PRO I 333 " pdb=" CA PRO I 333 " pdb=" C PRO I 333 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.44e+00 angle pdb=" N PRO J 333 " pdb=" CA PRO J 333 " pdb=" C PRO J 333 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.44e+00 angle pdb=" C3 PC1 R 202 " pdb=" O31 PC1 R 202 " pdb=" C31 PC1 R 202 " ideal model delta sigma weight residual 118.27 126.86 -8.59 3.00e+00 1.11e-01 8.19e+00 ... (remaining 23275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9697 17.91 - 35.83: 578 35.83 - 53.74: 142 53.74 - 71.65: 35 71.65 - 89.57: 25 Dihedral angle restraints: 10477 sinusoidal: 4447 harmonic: 6030 Sorted by residual: dihedral pdb=" CA GLU B 563 " pdb=" C GLU B 563 " pdb=" N CYS B 564 " pdb=" CA CYS B 564 " ideal model delta harmonic sigma weight residual 180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE B 382 " pdb=" C ILE B 382 " pdb=" N ALA B 383 " pdb=" CA ALA B 383 " ideal model delta harmonic sigma weight residual -180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA SER I 320 " pdb=" C SER I 320 " pdb=" N ASN I 321 " pdb=" CA ASN I 321 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 10474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1582 0.030 - 0.059: 644 0.059 - 0.089: 173 0.089 - 0.119: 105 0.119 - 0.148: 55 Chirality restraints: 2559 Sorted by residual: chirality pdb=" CA ILE V 65 " pdb=" N ILE V 65 " pdb=" C ILE V 65 " pdb=" CB ILE V 65 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" C2 PC1 P 101 " pdb=" C1 PC1 P 101 " pdb=" C3 PC1 P 101 " pdb=" O21 PC1 P 101 " both_signs ideal model delta sigma weight residual False -2.49 -2.35 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA LYS E 74 " pdb=" N LYS E 74 " pdb=" C LYS E 74 " pdb=" CB LYS E 74 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 2556 not shown) Planarity restraints: 2928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 PC1 I 401 " -0.050 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C22 PC1 I 401 " 0.015 2.00e-02 2.50e+03 pdb=" O21 PC1 I 401 " 0.016 2.00e-02 2.50e+03 pdb=" O22 PC1 I 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 60 " 0.196 9.50e-02 1.11e+02 8.85e-02 5.77e+00 pdb=" NE ARG P 60 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG P 60 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG P 60 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG P 60 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 80 " 0.177 9.50e-02 1.11e+02 7.99e-02 4.97e+00 pdb=" NE ARG B 80 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 80 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 80 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 80 " 0.000 2.00e-02 2.50e+03 ... (remaining 2925 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2720 2.77 - 3.30: 16061 3.30 - 3.83: 26154 3.83 - 4.37: 30734 4.37 - 4.90: 55485 Nonbonded interactions: 131154 Sorted by model distance: nonbonded pdb=" OE1 GLN E 165 " pdb=" ND2 ASN E 179 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASP D 91 " pdb=" NZ LYS D 125 " model vdw 2.255 3.120 nonbonded pdb=" OG SER I 197 " pdb=" O12 PC1 F 301 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP D 31 " pdb=" NH2 ARG D 37 " model vdw 2.293 3.120 nonbonded pdb=" OE1 GLU R 104 " pdb=" NE2 GLN R 107 " model vdw 2.302 3.120 ... (remaining 131149 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 'E' and resid 13 through 294) selection = (chain 'F' and resid 13 through 294) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'Z' } ncs_group { reference = (chain 'N' and resid 5 through 55) selection = chain 'X' } ncs_group { reference = (chain 'P' and resid 26 through 64) selection = (chain 'V' and resid 26 through 64) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.990 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.890 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.002 0.024 17297 Z= 0.105 Angle : 0.648 9.597 23288 Z= 0.325 Chirality : 0.042 0.148 2559 Planarity : 0.006 0.088 2928 Dihedral : 13.603 89.567 6597 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 3.96 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 0.53 (0.18), residues: 2085 helix: -0.02 (0.19), residues: 647 sheet: 1.28 (0.18), residues: 794 loop : -0.28 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.005 0.001 HIS I 220 PHE 0.015 0.001 PHE B 70 TYR 0.014 0.002 TYR I 129 ARG 0.018 0.003 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.20552 ( 1098) hydrogen bonds : angle 7.92067 ( 3114) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.32496 ( 8) covalent geometry : bond 0.00222 (17293) covalent geometry : angle 0.64770 (23280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 497 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 59 ASP cc_start: 0.8452 (t0) cc_final: 0.8181 (t0) REVERT: D 113 THR cc_start: 0.8835 (p) cc_final: 0.8599 (t) REVERT: E 164 TYR cc_start: 0.7571 (t80) cc_final: 0.7256 (t80) REVERT: F 30 ASN cc_start: 0.8796 (m-40) cc_final: 0.8463 (p0) REVERT: F 193 THR cc_start: 0.8711 (m) cc_final: 0.8471 (p) REVERT: I 109 LEU cc_start: 0.8643 (mt) cc_final: 0.8429 (mp) REVERT: I 135 TYR cc_start: 0.8672 (t80) cc_final: 0.8111 (t80) REVERT: I 236 VAL cc_start: 0.9623 (t) cc_final: 0.9421 (p) REVERT: K 30 ASN cc_start: 0.8450 (m-40) cc_final: 0.8074 (t0) REVERT: L 10 LYS cc_start: 0.8708 (tppt) cc_final: 0.8427 (tptt) REVERT: L 12 ASP cc_start: 0.8594 (t0) cc_final: 0.7892 (t0) REVERT: L 15 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8693 (tm-30) REVERT: L 18 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8552 (ttp-110) REVERT: N 13 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8051 (tm-30) REVERT: P 37 ASP cc_start: 0.8218 (t0) cc_final: 0.7788 (t0) REVERT: V 29 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.7123 (tpp-160) REVERT: X 50 LEU cc_start: 0.8903 (mt) cc_final: 0.8497 (pp) REVERT: Z 21 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8421 (mmm160) REVERT: Z 41 THR cc_start: 0.8484 (m) cc_final: 0.8174 (m) REVERT: B 71 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7767 (ttp80) REVERT: B 74 VAL cc_start: 0.8308 (p) cc_final: 0.8082 (t) REVERT: B 160 GLN cc_start: 0.8795 (mt0) cc_final: 0.8592 (mm-40) REVERT: B 379 TRP cc_start: 0.8048 (t60) cc_final: 0.7821 (t60) REVERT: B 538 THR cc_start: 0.9389 (m) cc_final: 0.9094 (p) REVERT: B 539 LEU cc_start: 0.9516 (mt) cc_final: 0.9313 (mt) outliers start: 17 outliers final: 5 residues processed: 507 average time/residue: 0.3865 time to fit residues: 272.5873 Evaluate side-chains 287 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 282 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain I residue 142 SER Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 297 THR Chi-restraints excluded: chain P residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 161 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.0000 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.0170 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 HIS I 114 GLN J 353 GLN ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.109959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.074859 restraints weight = 46383.022| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.13 r_work: 0.3136 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17297 Z= 0.154 Angle : 0.704 10.210 23288 Z= 0.367 Chirality : 0.045 0.293 2559 Planarity : 0.005 0.087 2928 Dihedral : 10.474 85.588 2709 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.81 % Allowed : 11.98 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.50 (0.18), residues: 2085 helix: 1.58 (0.19), residues: 655 sheet: 1.27 (0.18), residues: 809 loop : 0.07 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 221 HIS 0.005 0.001 HIS B 360 PHE 0.027 0.002 PHE D 119 TYR 0.020 0.002 TYR F 206 ARG 0.008 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1098) hydrogen bonds : angle 5.52742 ( 3114) SS BOND : bond 0.00573 ( 4) SS BOND : angle 3.03457 ( 8) covalent geometry : bond 0.00313 (17293) covalent geometry : angle 0.70191 (23280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 319 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 SER cc_start: 0.7357 (t) cc_final: 0.7062 (m) REVERT: D 64 GLU cc_start: 0.8941 (pp20) cc_final: 0.8636 (pp20) REVERT: D 68 LYS cc_start: 0.9518 (pttp) cc_final: 0.9210 (pttp) REVERT: D 69 PHE cc_start: 0.9152 (t80) cc_final: 0.8624 (t80) REVERT: D 72 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8933 (pt0) REVERT: D 73 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8166 (mm-30) REVERT: D 88 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8851 (ptpp) REVERT: E 293 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7981 (tp30) REVERT: F 30 ASN cc_start: 0.9268 (m-40) cc_final: 0.8734 (p0) REVERT: F 193 THR cc_start: 0.8858 (m) cc_final: 0.8484 (p) REVERT: F 291 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6784 (tm-30) REVERT: I 184 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8218 (tmtt) REVERT: J 154 MET cc_start: 0.8608 (ttp) cc_final: 0.7862 (tpp) REVERT: K 20 MET cc_start: 0.8389 (mtm) cc_final: 0.7871 (ttt) REVERT: K 30 ASN cc_start: 0.8401 (m-40) cc_final: 0.7947 (t0) REVERT: L 10 LYS cc_start: 0.8715 (tppt) cc_final: 0.8417 (tptt) REVERT: L 46 LYS cc_start: 0.9115 (mttt) cc_final: 0.8588 (mptt) REVERT: P 37 ASP cc_start: 0.8322 (t0) cc_final: 0.7876 (t0) REVERT: R 112 GLN cc_start: 0.8614 (pp30) cc_final: 0.8279 (pp30) REVERT: T 112 GLN cc_start: 0.9221 (tt0) cc_final: 0.8887 (tm-30) REVERT: V 29 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6978 (tpp-160) REVERT: X 50 LEU cc_start: 0.8880 (mt) cc_final: 0.8416 (pp) REVERT: Z 21 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8215 (mmm160) REVERT: Z 41 THR cc_start: 0.8539 (m) cc_final: 0.8253 (m) REVERT: B 71 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.8056 (tpp80) REVERT: B 214 PHE cc_start: 0.8844 (m-80) cc_final: 0.8274 (m-80) REVERT: B 379 TRP cc_start: 0.8148 (t60) cc_final: 0.7938 (t60) REVERT: B 476 GLU cc_start: 0.8923 (pm20) cc_final: 0.8539 (tp30) outliers start: 32 outliers final: 15 residues processed: 337 average time/residue: 0.2903 time to fit residues: 143.6993 Evaluate side-chains 284 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 206 TYR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 138 CYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 184 LYS Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 189 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 HIS D 95 ASN ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.109120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073683 restraints weight = 46493.615| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.13 r_work: 0.3117 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 17297 Z= 0.145 Angle : 0.655 9.229 23288 Z= 0.339 Chirality : 0.044 0.205 2559 Planarity : 0.005 0.052 2928 Dihedral : 10.273 88.356 2703 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.04 % Allowed : 13.51 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.65 (0.19), residues: 2085 helix: 1.92 (0.20), residues: 656 sheet: 1.25 (0.18), residues: 821 loop : 0.04 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 86 HIS 0.008 0.001 HIS E 284 PHE 0.021 0.001 PHE B 70 TYR 0.024 0.001 TYR E 164 ARG 0.007 0.000 ARG R 60 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 1098) hydrogen bonds : angle 5.06317 ( 3114) SS BOND : bond 0.00239 ( 4) SS BOND : angle 3.28778 ( 8) covalent geometry : bond 0.00303 (17293) covalent geometry : angle 0.65275 (23280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 285 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 42 ARG cc_start: 0.8966 (mtt180) cc_final: 0.8766 (ptp-170) REVERT: D 46 LYS cc_start: 0.8232 (mttt) cc_final: 0.7711 (tppt) REVERT: D 73 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8256 (mm-30) REVERT: D 87 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9006 (pm20) REVERT: D 88 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8697 (mtmm) REVERT: D 104 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8443 (pm20) REVERT: D 105 GLN cc_start: 0.9409 (mt0) cc_final: 0.9197 (mm-40) REVERT: D 111 GLN cc_start: 0.9549 (tt0) cc_final: 0.9293 (mm-40) REVERT: E 72 LYS cc_start: 0.9178 (pttt) cc_final: 0.8856 (ptpp) REVERT: E 73 TYR cc_start: 0.8333 (p90) cc_final: 0.8053 (p90) REVERT: E 164 TYR cc_start: 0.8626 (t80) cc_final: 0.8335 (t80) REVERT: F 30 ASN cc_start: 0.9267 (m-40) cc_final: 0.8619 (p0) REVERT: F 31 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8839 (mmmt) REVERT: F 130 LYS cc_start: 0.9225 (mttt) cc_final: 0.8994 (mtmm) REVERT: F 166 MET cc_start: 0.8503 (pmm) cc_final: 0.7906 (pmm) REVERT: J 88 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8233 (mtm110) REVERT: J 255 THR cc_start: 0.8678 (m) cc_final: 0.8352 (p) REVERT: J 280 ASP cc_start: 0.8533 (p0) cc_final: 0.8331 (p0) REVERT: K 20 MET cc_start: 0.8557 (mtm) cc_final: 0.7921 (ttt) REVERT: K 30 ASN cc_start: 0.8409 (m-40) cc_final: 0.8019 (t0) REVERT: L 10 LYS cc_start: 0.8467 (tppt) cc_final: 0.8242 (tptt) REVERT: P 37 ASP cc_start: 0.8362 (t0) cc_final: 0.7894 (t0) REVERT: R 77 MET cc_start: 0.7566 (mmm) cc_final: 0.7042 (mmm) REVERT: R 109 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8284 (tm-30) REVERT: R 112 GLN cc_start: 0.8788 (pp30) cc_final: 0.8330 (pp30) REVERT: V 29 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6960 (tpp-160) REVERT: X 34 LEU cc_start: 0.9410 (mt) cc_final: 0.9208 (mp) REVERT: X 50 LEU cc_start: 0.8883 (mt) cc_final: 0.8453 (pp) REVERT: Z 21 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8341 (mmm160) REVERT: Z 29 ARG cc_start: 0.8820 (tpt170) cc_final: 0.8317 (ptp-110) REVERT: Z 41 THR cc_start: 0.8648 (m) cc_final: 0.8409 (m) REVERT: B 214 PHE cc_start: 0.8874 (m-80) cc_final: 0.8238 (m-80) REVERT: B 220 MET cc_start: 0.8849 (mtm) cc_final: 0.8568 (mtm) REVERT: B 221 MET cc_start: 0.8145 (mmm) cc_final: 0.7821 (mmm) REVERT: B 379 TRP cc_start: 0.8226 (t60) cc_final: 0.7958 (t60) outliers start: 36 outliers final: 24 residues processed: 314 average time/residue: 0.2939 time to fit residues: 137.3069 Evaluate side-chains 277 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 138 CYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 186 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 193 optimal weight: 0.2980 chunk 180 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.108511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072693 restraints weight = 46416.363| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.74 r_work: 0.3117 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17297 Z= 0.140 Angle : 0.630 9.371 23288 Z= 0.324 Chirality : 0.043 0.263 2559 Planarity : 0.004 0.050 2928 Dihedral : 10.221 87.245 2703 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 14.08 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.69 (0.19), residues: 2085 helix: 2.08 (0.20), residues: 658 sheet: 1.23 (0.18), residues: 817 loop : -0.04 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 86 HIS 0.004 0.001 HIS J 112 PHE 0.019 0.001 PHE B 70 TYR 0.015 0.001 TYR F 206 ARG 0.007 0.000 ARG R 60 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 1098) hydrogen bonds : angle 4.85210 ( 3114) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.45452 ( 8) covalent geometry : bond 0.00307 (17293) covalent geometry : angle 0.62956 (23280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8808 (pp20) cc_final: 0.8425 (pp20) REVERT: D 68 LYS cc_start: 0.9519 (pttp) cc_final: 0.9241 (pttp) REVERT: D 73 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 87 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9046 (pm20) REVERT: D 105 GLN cc_start: 0.9420 (mt0) cc_final: 0.9155 (mt0) REVERT: E 293 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7494 (tp30) REVERT: F 30 ASN cc_start: 0.9227 (m-40) cc_final: 0.8588 (p0) REVERT: F 31 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8839 (mmmt) REVERT: F 130 LYS cc_start: 0.9284 (mttt) cc_final: 0.8970 (mtmm) REVERT: F 166 MET cc_start: 0.8609 (pmm) cc_final: 0.7978 (pmm) REVERT: F 200 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: I 280 ASP cc_start: 0.8466 (p0) cc_final: 0.8084 (p0) REVERT: J 88 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8204 (mtm110) REVERT: J 255 THR cc_start: 0.8679 (m) cc_final: 0.8402 (p) REVERT: K 20 MET cc_start: 0.8519 (mtm) cc_final: 0.7815 (ttt) REVERT: K 30 ASN cc_start: 0.8422 (m-40) cc_final: 0.8040 (t0) REVERT: L 10 LYS cc_start: 0.8439 (tppt) cc_final: 0.8237 (tptt) REVERT: N 9 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7759 (mmtm) REVERT: P 37 ASP cc_start: 0.8463 (t0) cc_final: 0.7999 (t0) REVERT: R 77 MET cc_start: 0.7558 (mmm) cc_final: 0.7032 (mmm) REVERT: R 108 MET cc_start: 0.9382 (mmm) cc_final: 0.9114 (tpp) REVERT: R 109 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8228 (tm-30) REVERT: R 112 GLN cc_start: 0.8860 (pp30) cc_final: 0.8211 (pp30) REVERT: V 29 ARG cc_start: 0.7518 (ttm-80) cc_final: 0.7042 (tpp-160) REVERT: X 50 LEU cc_start: 0.8879 (mt) cc_final: 0.8489 (pp) REVERT: Z 21 ARG cc_start: 0.8884 (tpp80) cc_final: 0.8377 (mmm160) REVERT: Z 41 THR cc_start: 0.8776 (m) cc_final: 0.8551 (m) REVERT: B 71 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7261 (tpp-160) REVERT: B 214 PHE cc_start: 0.8845 (m-80) cc_final: 0.8244 (m-80) REVERT: B 379 TRP cc_start: 0.8331 (t60) cc_final: 0.7962 (t60) REVERT: B 476 GLU cc_start: 0.8741 (pm20) cc_final: 0.8476 (tp30) outliers start: 41 outliers final: 32 residues processed: 302 average time/residue: 0.2857 time to fit residues: 127.6693 Evaluate side-chains 287 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain N residue 10 GLN Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 70 SER Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 162 optimal weight: 0.0060 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.107590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071405 restraints weight = 46692.277| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.74 r_work: 0.3091 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17297 Z= 0.172 Angle : 0.635 10.265 23288 Z= 0.324 Chirality : 0.043 0.318 2559 Planarity : 0.004 0.050 2928 Dihedral : 10.327 87.521 2703 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.32 % Allowed : 14.92 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.71 (0.19), residues: 2085 helix: 2.18 (0.20), residues: 658 sheet: 1.21 (0.18), residues: 817 loop : -0.07 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 86 HIS 0.006 0.001 HIS E 284 PHE 0.018 0.001 PHE B 70 TYR 0.013 0.001 TYR E 164 ARG 0.008 0.000 ARG B 543 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 1098) hydrogen bonds : angle 4.78815 ( 3114) SS BOND : bond 0.00360 ( 4) SS BOND : angle 1.89007 ( 8) covalent geometry : bond 0.00387 (17293) covalent geometry : angle 0.63448 (23280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8336 (mm-30) REVERT: D 87 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9056 (pm20) REVERT: D 102 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 105 GLN cc_start: 0.9388 (mt0) cc_final: 0.9063 (mt0) REVERT: D 121 MET cc_start: 0.9192 (ptp) cc_final: 0.8820 (ptp) REVERT: E 74 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7465 (pttm) REVERT: F 26 ARG cc_start: 0.8315 (mtm110) cc_final: 0.7959 (mtm-85) REVERT: F 30 ASN cc_start: 0.9224 (m-40) cc_final: 0.8558 (p0) REVERT: F 31 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8816 (mmmt) REVERT: F 166 MET cc_start: 0.8706 (pmm) cc_final: 0.8155 (pmm) REVERT: F 200 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8468 (tp30) REVERT: F 291 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6957 (tm-30) REVERT: I 280 ASP cc_start: 0.8413 (p0) cc_final: 0.8053 (p0) REVERT: J 88 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8226 (mtm110) REVERT: J 255 THR cc_start: 0.8712 (m) cc_final: 0.8471 (p) REVERT: K 20 MET cc_start: 0.8568 (mtm) cc_final: 0.7697 (ttt) REVERT: K 30 ASN cc_start: 0.8427 (m-40) cc_final: 0.8055 (t0) REVERT: L 22 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8600 (tm-30) REVERT: L 45 LEU cc_start: 0.9496 (mp) cc_final: 0.9254 (mp) REVERT: P 37 ASP cc_start: 0.8607 (t0) cc_final: 0.8117 (t0) REVERT: R 77 MET cc_start: 0.7532 (mmm) cc_final: 0.7244 (mmm) REVERT: R 108 MET cc_start: 0.9383 (mmm) cc_final: 0.9121 (tpp) REVERT: R 109 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8212 (tm-30) REVERT: R 112 GLN cc_start: 0.8860 (pp30) cc_final: 0.8189 (pp30) REVERT: V 29 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7046 (tpp-160) REVERT: X 50 LEU cc_start: 0.8912 (mt) cc_final: 0.8464 (pp) REVERT: Z 21 ARG cc_start: 0.8885 (tpp80) cc_final: 0.8467 (mmm160) REVERT: Z 41 THR cc_start: 0.8843 (m) cc_final: 0.8627 (m) REVERT: Z 43 PHE cc_start: 0.8548 (m-80) cc_final: 0.8307 (m-80) REVERT: B 71 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7119 (tpp-160) REVERT: B 111 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9068 (mp) REVERT: B 214 PHE cc_start: 0.8809 (m-80) cc_final: 0.8237 (m-80) REVERT: B 379 TRP cc_start: 0.8318 (t60) cc_final: 0.7917 (t60) outliers start: 41 outliers final: 27 residues processed: 304 average time/residue: 0.2966 time to fit residues: 133.8234 Evaluate side-chains 288 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain N residue 10 GLN Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 105 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 177 optimal weight: 0.4980 chunk 174 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.106730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070568 restraints weight = 46451.730| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.72 r_work: 0.3073 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17297 Z= 0.187 Angle : 0.672 17.090 23288 Z= 0.338 Chirality : 0.043 0.364 2559 Planarity : 0.004 0.059 2928 Dihedral : 10.401 87.128 2703 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.54 % Allowed : 16.00 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.67 (0.19), residues: 2085 helix: 2.21 (0.20), residues: 656 sheet: 1.15 (0.18), residues: 818 loop : -0.13 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 86 HIS 0.005 0.001 HIS E 284 PHE 0.022 0.002 PHE D 69 TYR 0.016 0.001 TYR F 206 ARG 0.015 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1098) hydrogen bonds : angle 4.73731 ( 3114) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.10084 ( 8) covalent geometry : bond 0.00423 (17293) covalent geometry : angle 0.67119 (23280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLU cc_start: 0.8854 (pp20) cc_final: 0.8502 (pp20) REVERT: D 68 LYS cc_start: 0.9517 (pttp) cc_final: 0.9033 (pttp) REVERT: D 87 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9124 (pm20) REVERT: D 104 GLN cc_start: 0.9014 (pp30) cc_final: 0.8260 (pm20) REVERT: E 72 LYS cc_start: 0.9276 (pttt) cc_final: 0.9068 (ptpp) REVERT: E 74 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7323 (pttm) REVERT: F 30 ASN cc_start: 0.9216 (m-40) cc_final: 0.8641 (p0) REVERT: F 166 MET cc_start: 0.8705 (pmm) cc_final: 0.8070 (pmm) REVERT: F 200 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8263 (tp30) REVERT: F 291 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6871 (tm-30) REVERT: I 280 ASP cc_start: 0.8405 (p0) cc_final: 0.8112 (p0) REVERT: J 88 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8200 (mtm110) REVERT: J 319 ASP cc_start: 0.8922 (t0) cc_final: 0.8704 (t70) REVERT: K 20 MET cc_start: 0.8646 (mtm) cc_final: 0.7710 (ttt) REVERT: L 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8575 (tm-30) REVERT: P 37 ASP cc_start: 0.8707 (t0) cc_final: 0.8264 (t0) REVERT: R 77 MET cc_start: 0.7539 (mmm) cc_final: 0.7261 (mmm) REVERT: R 108 MET cc_start: 0.9329 (mmm) cc_final: 0.8886 (tpp) REVERT: R 109 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8210 (tm-30) REVERT: R 112 GLN cc_start: 0.9004 (pp30) cc_final: 0.8514 (pp30) REVERT: V 29 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7007 (tpp-160) REVERT: X 50 LEU cc_start: 0.8933 (mt) cc_final: 0.8490 (pp) REVERT: Z 21 ARG cc_start: 0.8825 (tpp80) cc_final: 0.8353 (mmm160) REVERT: Z 41 THR cc_start: 0.8898 (m) cc_final: 0.8688 (m) REVERT: Z 43 PHE cc_start: 0.8637 (m-80) cc_final: 0.8235 (m-80) REVERT: B 71 ARG cc_start: 0.7714 (tpp80) cc_final: 0.6892 (tpp-160) REVERT: B 111 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 214 PHE cc_start: 0.8858 (m-80) cc_final: 0.8368 (m-80) REVERT: B 379 TRP cc_start: 0.8371 (t60) cc_final: 0.7900 (t60) outliers start: 45 outliers final: 33 residues processed: 296 average time/residue: 0.3146 time to fit residues: 137.9473 Evaluate side-chains 275 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 138 CYS Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain I residue 159 SER Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain N residue 10 GLN Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 103 optimal weight: 0.0070 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 HIS T 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.108463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072493 restraints weight = 45573.307| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.71 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17297 Z= 0.119 Angle : 0.646 12.782 23288 Z= 0.325 Chirality : 0.043 0.380 2559 Planarity : 0.004 0.054 2928 Dihedral : 10.145 85.116 2703 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.04 % Allowed : 16.73 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.76 (0.19), residues: 2085 helix: 2.18 (0.20), residues: 656 sheet: 1.26 (0.18), residues: 818 loop : -0.04 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.008 0.001 HIS E 284 PHE 0.016 0.001 PHE J 288 TYR 0.015 0.001 TYR X 33 ARG 0.018 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03155 ( 1098) hydrogen bonds : angle 4.60747 ( 3114) SS BOND : bond 0.00271 ( 4) SS BOND : angle 1.74935 ( 8) covalent geometry : bond 0.00260 (17293) covalent geometry : angle 0.64578 (23280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 268 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9135 (tm-30) REVERT: D 105 GLN cc_start: 0.9557 (mm110) cc_final: 0.9318 (mm-40) REVERT: E 72 LYS cc_start: 0.9261 (pttt) cc_final: 0.9057 (ptpp) REVERT: E 74 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7305 (pttm) REVERT: F 30 ASN cc_start: 0.9212 (m-40) cc_final: 0.8705 (p0) REVERT: F 164 TYR cc_start: 0.8394 (t80) cc_final: 0.8130 (t80) REVERT: F 166 MET cc_start: 0.8773 (pmm) cc_final: 0.8017 (pmm) REVERT: F 291 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6920 (tm-30) REVERT: I 135 TYR cc_start: 0.8906 (t80) cc_final: 0.8505 (t80) REVERT: I 280 ASP cc_start: 0.8317 (p0) cc_final: 0.8039 (p0) REVERT: K 20 MET cc_start: 0.8655 (mtm) cc_final: 0.7713 (ttt) REVERT: L 22 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8556 (tm-30) REVERT: P 37 ASP cc_start: 0.8751 (t0) cc_final: 0.8378 (t0) REVERT: R 77 MET cc_start: 0.7526 (mmm) cc_final: 0.7011 (mmm) REVERT: R 108 MET cc_start: 0.9368 (mmm) cc_final: 0.9100 (tpp) REVERT: R 109 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8087 (tm-30) REVERT: R 112 GLN cc_start: 0.9019 (pp30) cc_final: 0.8443 (pp30) REVERT: V 29 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7045 (tpp-160) REVERT: X 50 LEU cc_start: 0.8936 (mt) cc_final: 0.8494 (pp) REVERT: Z 21 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8217 (tpt90) REVERT: Z 43 PHE cc_start: 0.8655 (m-80) cc_final: 0.8261 (m-80) REVERT: B 71 ARG cc_start: 0.7850 (tpp80) cc_final: 0.7074 (tpp-160) REVERT: B 111 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9040 (mp) REVERT: B 214 PHE cc_start: 0.8826 (m-80) cc_final: 0.8368 (m-80) REVERT: B 379 TRP cc_start: 0.8268 (t60) cc_final: 0.7872 (t60) outliers start: 36 outliers final: 28 residues processed: 293 average time/residue: 0.2897 time to fit residues: 126.9789 Evaluate side-chains 280 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 138 CYS Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 556 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 0.0000 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 123 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 124 optimal weight: 0.0770 chunk 18 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 overall best weight: 0.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN E 192 HIS ** T 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.108356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.072801 restraints weight = 45513.708| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.13 r_work: 0.3100 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17297 Z= 0.117 Angle : 0.657 13.551 23288 Z= 0.332 Chirality : 0.042 0.385 2559 Planarity : 0.004 0.054 2928 Dihedral : 9.964 85.537 2703 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.04 % Allowed : 17.58 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.73 (0.19), residues: 2085 helix: 2.12 (0.20), residues: 662 sheet: 1.29 (0.18), residues: 822 loop : -0.11 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 222 HIS 0.004 0.001 HIS B 360 PHE 0.021 0.001 PHE D 69 TYR 0.016 0.001 TYR F 206 ARG 0.015 0.001 ARG D 42 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1098) hydrogen bonds : angle 4.51598 ( 3114) SS BOND : bond 0.00337 ( 4) SS BOND : angle 1.81578 ( 8) covalent geometry : bond 0.00259 (17293) covalent geometry : angle 0.65626 (23280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7529 (pttm) REVERT: F 30 ASN cc_start: 0.9218 (m-40) cc_final: 0.8723 (p0) REVERT: F 164 TYR cc_start: 0.8403 (t80) cc_final: 0.8137 (t80) REVERT: F 166 MET cc_start: 0.8717 (pmm) cc_final: 0.7949 (pmm) REVERT: F 291 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6918 (tm-30) REVERT: I 135 TYR cc_start: 0.8927 (t80) cc_final: 0.8512 (t80) REVERT: I 280 ASP cc_start: 0.8346 (p0) cc_final: 0.8072 (p0) REVERT: J 88 ARG cc_start: 0.8412 (mtm110) cc_final: 0.7884 (mtm110) REVERT: K 20 MET cc_start: 0.8679 (mtm) cc_final: 0.7640 (ttt) REVERT: L 22 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8545 (tm-30) REVERT: P 37 ASP cc_start: 0.8779 (t0) cc_final: 0.8406 (t0) REVERT: R 77 MET cc_start: 0.7536 (mmm) cc_final: 0.7025 (mmm) REVERT: R 108 MET cc_start: 0.9400 (mmm) cc_final: 0.9124 (tpp) REVERT: R 109 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8082 (tm-30) REVERT: R 112 GLN cc_start: 0.9021 (pp30) cc_final: 0.8425 (pp30) REVERT: T 77 MET cc_start: 0.8491 (ppp) cc_final: 0.8267 (ppp) REVERT: V 29 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7094 (tpp-160) REVERT: X 32 ILE cc_start: 0.9206 (pt) cc_final: 0.9003 (pt) REVERT: X 50 LEU cc_start: 0.8935 (mt) cc_final: 0.8493 (pp) REVERT: Z 21 ARG cc_start: 0.8729 (tpp80) cc_final: 0.8484 (mtp85) REVERT: Z 43 PHE cc_start: 0.8669 (m-80) cc_final: 0.8286 (m-80) REVERT: B 71 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7045 (tpp-160) REVERT: B 111 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9099 (mp) REVERT: B 214 PHE cc_start: 0.8836 (m-80) cc_final: 0.8382 (m-80) REVERT: B 379 TRP cc_start: 0.8271 (t60) cc_final: 0.7865 (t60) outliers start: 36 outliers final: 26 residues processed: 277 average time/residue: 0.2887 time to fit residues: 119.4039 Evaluate side-chains 265 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 76 CYS Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 45 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.0570 chunk 125 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.107885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072099 restraints weight = 45485.538| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.11 r_work: 0.3088 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17297 Z= 0.133 Angle : 0.677 13.721 23288 Z= 0.339 Chirality : 0.043 0.396 2559 Planarity : 0.004 0.050 2928 Dihedral : 9.961 86.595 2703 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.58 % Allowed : 18.26 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.75 (0.19), residues: 2085 helix: 2.12 (0.20), residues: 662 sheet: 1.31 (0.18), residues: 824 loop : -0.11 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 222 HIS 0.012 0.001 HIS J 112 PHE 0.023 0.001 PHE F 52 TYR 0.026 0.001 TYR X 33 ARG 0.012 0.001 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 1098) hydrogen bonds : angle 4.49232 ( 3114) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.85600 ( 8) covalent geometry : bond 0.00301 (17293) covalent geometry : angle 0.67668 (23280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 73 GLU cc_start: 0.9199 (tt0) cc_final: 0.8542 (tt0) REVERT: D 102 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9145 (tm-30) REVERT: D 104 GLN cc_start: 0.9094 (pp30) cc_final: 0.8841 (pp30) REVERT: D 105 GLN cc_start: 0.9565 (mm110) cc_final: 0.9264 (mm-40) REVERT: E 74 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7478 (pttm) REVERT: F 30 ASN cc_start: 0.9204 (m-40) cc_final: 0.8705 (p0) REVERT: F 164 TYR cc_start: 0.8397 (t80) cc_final: 0.8099 (t80) REVERT: F 166 MET cc_start: 0.8786 (pmm) cc_final: 0.8098 (pmm) REVERT: F 291 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6933 (tm-30) REVERT: I 135 TYR cc_start: 0.8917 (t80) cc_final: 0.8539 (t80) REVERT: I 280 ASP cc_start: 0.8362 (p0) cc_final: 0.8104 (p0) REVERT: J 88 ARG cc_start: 0.8417 (mtm110) cc_final: 0.7835 (mtm110) REVERT: K 20 MET cc_start: 0.8682 (mtm) cc_final: 0.7657 (ttt) REVERT: L 22 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8534 (tm-30) REVERT: P 37 ASP cc_start: 0.8751 (t0) cc_final: 0.8384 (t0) REVERT: R 77 MET cc_start: 0.7484 (mmm) cc_final: 0.6992 (mmm) REVERT: R 108 MET cc_start: 0.9388 (mmm) cc_final: 0.9118 (tpp) REVERT: R 109 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8091 (tm-30) REVERT: R 112 GLN cc_start: 0.9046 (pp30) cc_final: 0.8465 (pp30) REVERT: T 77 MET cc_start: 0.8500 (ppp) cc_final: 0.8289 (ppp) REVERT: V 29 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7099 (tpp-160) REVERT: X 50 LEU cc_start: 0.8969 (mt) cc_final: 0.8532 (pp) REVERT: Z 21 ARG cc_start: 0.8749 (tpp80) cc_final: 0.8510 (mtp85) REVERT: Z 43 PHE cc_start: 0.8712 (m-80) cc_final: 0.8328 (m-80) REVERT: B 71 ARG cc_start: 0.7749 (tpp80) cc_final: 0.6991 (tpp-160) REVERT: B 111 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9064 (mp) REVERT: B 214 PHE cc_start: 0.8870 (m-80) cc_final: 0.8413 (m-80) REVERT: B 379 TRP cc_start: 0.8297 (t60) cc_final: 0.7859 (t60) outliers start: 28 outliers final: 24 residues processed: 276 average time/residue: 0.2907 time to fit residues: 122.1110 Evaluate side-chains 267 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 172 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 135 optimal weight: 0.3980 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.107526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071452 restraints weight = 45843.720| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.72 r_work: 0.3094 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17297 Z= 0.153 Angle : 0.683 13.633 23288 Z= 0.344 Chirality : 0.043 0.406 2559 Planarity : 0.004 0.050 2928 Dihedral : 10.040 87.479 2703 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.70 % Allowed : 18.03 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.71 (0.19), residues: 2085 helix: 2.10 (0.20), residues: 662 sheet: 1.28 (0.18), residues: 824 loop : -0.14 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 222 HIS 0.016 0.001 HIS J 112 PHE 0.020 0.001 PHE J 288 TYR 0.022 0.001 TYR X 33 ARG 0.008 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 1098) hydrogen bonds : angle 4.49957 ( 3114) SS BOND : bond 0.00270 ( 4) SS BOND : angle 1.99278 ( 8) covalent geometry : bond 0.00350 (17293) covalent geometry : angle 0.68208 (23280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4170 Ramachandran restraints generated. 2085 Oldfield, 0 Emsley, 2085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 52 PHE cc_start: 0.8627 (t80) cc_final: 0.8352 (t80) REVERT: E 74 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7551 (pttm) REVERT: F 30 ASN cc_start: 0.9197 (m-40) cc_final: 0.8717 (p0) REVERT: F 164 TYR cc_start: 0.8412 (t80) cc_final: 0.8167 (t80) REVERT: F 166 MET cc_start: 0.8791 (pmm) cc_final: 0.8124 (pmm) REVERT: F 291 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6972 (tm-30) REVERT: I 135 TYR cc_start: 0.8884 (t80) cc_final: 0.8463 (t80) REVERT: I 280 ASP cc_start: 0.8297 (p0) cc_final: 0.8042 (p0) REVERT: J 88 ARG cc_start: 0.8452 (mtm110) cc_final: 0.7871 (mtm110) REVERT: K 20 MET cc_start: 0.8681 (mtm) cc_final: 0.7698 (ttt) REVERT: L 22 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8510 (tm-30) REVERT: P 37 ASP cc_start: 0.8777 (t0) cc_final: 0.8472 (t0) REVERT: R 77 MET cc_start: 0.7523 (mmm) cc_final: 0.7026 (mmm) REVERT: R 108 MET cc_start: 0.9419 (mmm) cc_final: 0.9196 (tpp) REVERT: R 109 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8141 (tm-30) REVERT: R 112 GLN cc_start: 0.9070 (pp30) cc_final: 0.8478 (pp30) REVERT: V 29 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7098 (tpp-160) REVERT: X 50 LEU cc_start: 0.8987 (mt) cc_final: 0.8555 (pp) REVERT: Z 21 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8522 (mtp85) REVERT: Z 43 PHE cc_start: 0.8713 (m-80) cc_final: 0.8336 (m-80) REVERT: B 71 ARG cc_start: 0.7813 (tpp80) cc_final: 0.7069 (tpp-160) REVERT: B 111 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (mp) REVERT: B 214 PHE cc_start: 0.8900 (m-80) cc_final: 0.8523 (m-80) REVERT: B 379 TRP cc_start: 0.8295 (t60) cc_final: 0.7881 (t60) outliers start: 30 outliers final: 25 residues processed: 266 average time/residue: 0.2828 time to fit residues: 113.1574 Evaluate side-chains 262 residues out of total 1769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 95 ASN Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain I residue 262 THR Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 318 VAL Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain T residue 99 VAL Chi-restraints excluded: chain V residue 45 LEU Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 525 ASP Chi-restraints excluded: chain B residue 556 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 80 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 204 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.106921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.070934 restraints weight = 45637.393| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.70 r_work: 0.3080 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17297 Z= 0.169 Angle : 0.697 14.079 23288 Z= 0.352 Chirality : 0.043 0.389 2559 Planarity : 0.004 0.051 2928 Dihedral : 10.109 87.873 2703 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.75 % Allowed : 18.09 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % 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: 1.65 (0.19), residues: 2085 helix: 2.06 (0.20), residues: 662 sheet: 1.25 (0.18), residues: 825 loop : -0.19 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 222 HIS 0.013 0.001 HIS J 112 PHE 0.019 0.001 PHE J 288 TYR 0.024 0.001 TYR E 18 ARG 0.010 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1098) hydrogen bonds : angle 4.53157 ( 3114) SS BOND : bond 0.00264 ( 4) SS BOND : angle 2.04205 ( 8) covalent geometry : bond 0.00385 (17293) covalent geometry : angle 0.69652 (23280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9622.73 seconds wall clock time: 167 minutes 32.83 seconds (10052.83 seconds total)