Starting phenix.real_space_refine on Sat Jun 21 09:12:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.map" model { file = "/net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eas_27984/06_2025/8eas_27984.cif" } resolution = 2.6 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= 0.007 sd= 0.311 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: 4 Type Number sf(0) Gaussians S 146 5.16 5 C 16186 2.51 5 N 4005 2.21 5 O 4465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24802 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1044 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 799 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 196 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'TRANS': 38} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'UNK:plan-1': 38} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 919 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "a" Number of atoms: 5948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5948 Classifications: {'peptide': 742} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 21, 'TRANS': 720} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "b" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 385 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "c" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1473 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "d" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2740 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 565 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "f" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 506 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 67} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "g" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "h" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "i" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "j" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1136 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "k" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1136 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1129 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "m" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "n" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1139 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain: "o" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1140 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.82, per 1000 atoms: 0.56 Number of scatterers: 24802 At special positions: 0 Unit cell: (121.54, 162.74, 153.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 146 16.00 O 4465 8.00 N 4005 7.00 C 16186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 3.1 seconds 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 78.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 15 through 50 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 143 through 177 removed outlier: 3.654A pdb=" N ARG A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Proline residue: A 158 - end of helix Processing helix chain 'B' and resid 7 through 18 removed outlier: 3.994A pdb=" N LYS B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 38 Processing helix chain 'B' and resid 41 through 53 Processing helix chain 'B' and resid 84 through 107 Processing helix chain 'B' and resid 124 through 151 removed outlier: 3.546A pdb=" N UNK B 132 " --> pdb=" O UNK B 128 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N UNK B 135 " --> pdb=" O UNK B 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 24 Processing helix chain 'F' and resid 46 through 59 removed outlier: 3.607A pdb=" N ILE F 50 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 77 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 102 through 105 Processing helix chain 'F' and resid 106 through 115 removed outlier: 3.529A pdb=" N LYS F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 37 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 104 through 146 removed outlier: 3.643A pdb=" N ASP a 108 " --> pdb=" O GLY a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 153 Processing helix chain 'a' and resid 195 through 207 Processing helix chain 'a' and resid 242 through 256 Processing helix chain 'a' and resid 267 through 269 No H-bonds generated for 'chain 'a' and resid 267 through 269' Processing helix chain 'a' and resid 270 through 325 removed outlier: 3.714A pdb=" N THR a 294 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 360 Processing helix chain 'a' and resid 387 through 398 removed outlier: 4.188A pdb=" N TYR a 397 " --> pdb=" O ILE a 393 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY a 398 " --> pdb=" O CYS a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 407 through 423 removed outlier: 4.444A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 425 through 442 Processing helix chain 'a' and resid 442 through 447 Processing helix chain 'a' and resid 453 through 461 Processing helix chain 'a' and resid 461 through 480 Processing helix chain 'a' and resid 519 through 523 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.665A pdb=" N SER a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 571 Processing helix chain 'a' and resid 571 through 596 removed outlier: 3.807A pdb=" N GLY a 575 " --> pdb=" O ASN a 571 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 597 through 602 Processing helix chain 'a' and resid 607 through 618 removed outlier: 3.734A pdb=" N PHE a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 629 through 658 removed outlier: 3.704A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 4.706A pdb=" N LYS a 652 " --> pdb=" O LEU a 648 " (cutoff:3.500A) Proline residue: a 653 - end of helix Processing helix chain 'a' and resid 710 through 733 removed outlier: 3.801A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR a 730 " --> pdb=" O CYS a 726 " (cutoff:3.500A) Processing helix chain 'a' and resid 733 through 753 removed outlier: 4.373A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 759 removed outlier: 3.558A pdb=" N ALA a 758 " --> pdb=" O THR a 754 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE a 759 " --> pdb=" O ILE a 755 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 754 through 759' Processing helix chain 'a' and resid 762 through 785 Processing helix chain 'a' and resid 787 through 803 Processing helix chain 'a' and resid 805 through 810 removed outlier: 3.997A pdb=" N PHE a 809 " --> pdb=" O SER a 805 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 833 Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 90 removed outlier: 3.645A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 95 No H-bonds generated for 'chain 'c' and resid 93 through 95' Processing helix chain 'c' and resid 96 through 123 removed outlier: 4.818A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 133 removed outlier: 3.553A pdb=" N MET c 133 " --> pdb=" O ALA c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 180 through 206 removed outlier: 3.880A pdb=" N ILE c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU c 194 " --> pdb=" O PHE c 190 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 6 removed outlier: 3.576A pdb=" N PHE d 6 " --> pdb=" O GLU d 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 2 through 6' Processing helix chain 'd' and resid 6 through 23 removed outlier: 3.548A pdb=" N GLY d 11 " --> pdb=" O ASN d 7 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N PHE d 12 " --> pdb=" O ILE d 8 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE d 13 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 35 Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 88 through 116 removed outlier: 3.942A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 126 Processing helix chain 'd' and resid 136 through 141 removed outlier: 3.510A pdb=" N SER d 140 " --> pdb=" O PRO d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 152 Processing helix chain 'd' and resid 158 through 163 removed outlier: 3.734A pdb=" N LYS d 163 " --> pdb=" O PRO d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 Processing helix chain 'd' and resid 201 through 228 removed outlier: 3.755A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 240 removed outlier: 3.542A pdb=" N SER d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 257 Processing helix chain 'd' and resid 261 through 270 Processing helix chain 'd' and resid 283 through 300 Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.184A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 25 removed outlier: 3.907A pdb=" N VAL e 7 " --> pdb=" O SER e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 55 removed outlier: 3.638A pdb=" N GLN e 55 " --> pdb=" O THR e 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 33 Processing helix chain 'f' and resid 35 through 40 Processing helix chain 'f' and resid 48 through 76 Processing helix chain 'g' and resid 8 through 46 removed outlier: 4.045A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 49 through 54 Processing helix chain 'g' and resid 54 through 77 removed outlier: 4.027A pdb=" N ILE g 63 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 122 Processing helix chain 'g' and resid 124 through 154 removed outlier: 4.171A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 43 removed outlier: 4.007A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 48 No H-bonds generated for 'chain 'h' and resid 46 through 48' Processing helix chain 'h' and resid 49 through 54 Processing helix chain 'h' and resid 54 through 76 Processing helix chain 'h' and resid 83 through 122 removed outlier: 3.997A pdb=" N GLN h 121 " --> pdb=" O ARG h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 153 removed outlier: 4.324A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 46 removed outlier: 4.001A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU i 45 " --> pdb=" O ALA i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 76 Processing helix chain 'i' and resid 83 through 122 removed outlier: 3.785A pdb=" N GLN i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 153 removed outlier: 4.376A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 43 removed outlier: 4.058A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 77 Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 124 through 155 removed outlier: 4.249A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.118A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 48 No H-bonds generated for 'chain 'k' and resid 46 through 48' Processing helix chain 'k' and resid 49 through 54 Processing helix chain 'k' and resid 54 through 77 Processing helix chain 'k' and resid 83 through 122 Processing helix chain 'k' and resid 124 through 152 removed outlier: 4.424A pdb=" N GLY k 128 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 43 removed outlier: 4.161A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 48 No H-bonds generated for 'chain 'l' and resid 46 through 48' Processing helix chain 'l' and resid 49 through 54 Processing helix chain 'l' and resid 54 through 77 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.648A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.189A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 43 removed outlier: 4.089A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 45 No H-bonds generated for 'chain 'm' and resid 44 through 45' Processing helix chain 'm' and resid 46 through 50 Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 83 through 120 Processing helix chain 'm' and resid 124 through 155 removed outlier: 4.194A pdb=" N GLY m 128 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR m 155 " --> pdb=" O ASN m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 44 removed outlier: 4.142A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 46 through 48 No H-bonds generated for 'chain 'n' and resid 46 through 48' Processing helix chain 'n' and resid 49 through 54 Processing helix chain 'n' and resid 54 through 78 Processing helix chain 'n' and resid 83 through 122 removed outlier: 3.740A pdb=" N GLN n 121 " --> pdb=" O ARG n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 153 removed outlier: 4.330A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 49 removed outlier: 3.921A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 84 removed outlier: 3.660A pdb=" N ASN o 83 " --> pdb=" O LEU o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 130 removed outlier: 4.768A pdb=" N ARG o 125 " --> pdb=" O ASP o 121 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS o 126 " --> pdb=" O VAL o 122 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN o 130 " --> pdb=" O LYS o 126 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 164 removed outlier: 4.085A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 40 removed outlier: 4.018A pdb=" N GLU B 70 " --> pdb=" O LYS B 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 37 through 39 removed outlier: 8.131A pdb=" N PHE F 38 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL F 10 " --> pdb=" O PHE F 38 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU F 7 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA F 65 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU F 92 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 67 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE F 94 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE F 69 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA5, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA6, first strand: chain 'a' and resid 213 through 217 removed outlier: 4.332A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 222 through 224 Processing sheet with id=AA8, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA9, first strand: chain 'a' and resid 506 through 507 1980 hydrogen bonds defined for protein. 5847 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: 9.03 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6924 1.33 - 1.45: 4128 1.45 - 1.57: 14012 1.57 - 1.69: 0 1.69 - 1.81: 220 Bond restraints: 25284 Sorted by residual: bond pdb=" CB GLU i 137 " pdb=" CG GLU i 137 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.38e+00 bond pdb=" CB GLU k 137 " pdb=" CG GLU k 137 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" CB TRP c 77 " pdb=" CG TRP c 77 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.50e+00 bond pdb=" CB VAL c 110 " pdb=" CG1 VAL c 110 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.93e+00 bond pdb=" C ASN d 333 " pdb=" O ASN d 333 " ideal model delta sigma weight residual 1.243 1.229 0.015 9.50e-03 1.11e+04 2.44e+00 ... (remaining 25279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 34024 2.67 - 5.35: 274 5.35 - 8.02: 21 8.02 - 10.70: 3 10.70 - 13.37: 1 Bond angle restraints: 34323 Sorted by residual: angle pdb=" CB MET i 59 " pdb=" CG MET i 59 " pdb=" SD MET i 59 " ideal model delta sigma weight residual 112.70 126.07 -13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C ILE c 79 " pdb=" N PHE c 80 " pdb=" CA PHE c 80 " ideal model delta sigma weight residual 120.31 114.35 5.96 1.52e+00 4.33e-01 1.54e+01 angle pdb=" C TRP c 77 " pdb=" CA TRP c 77 " pdb=" CB TRP c 77 " ideal model delta sigma weight residual 110.96 105.57 5.39 1.54e+00 4.22e-01 1.22e+01 angle pdb=" C PHE a 483 " pdb=" N SER a 484 " pdb=" CA SER a 484 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C ASN d 333 " pdb=" CA ASN d 333 " pdb=" CB ASN d 333 " ideal model delta sigma weight residual 117.23 112.85 4.38 1.36e+00 5.41e-01 1.04e+01 ... (remaining 34318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13638 17.66 - 35.31: 961 35.31 - 52.97: 132 52.97 - 70.62: 33 70.62 - 88.28: 23 Dihedral angle restraints: 14787 sinusoidal: 5439 harmonic: 9348 Sorted by residual: dihedral pdb=" CA ASN A 49 " pdb=" C ASN A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta harmonic sigma weight residual 180.00 151.42 28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA PRO d 201 " pdb=" C PRO d 201 " pdb=" N GLU d 202 " pdb=" CA GLU d 202 " ideal model delta harmonic sigma weight residual -180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA THR a 754 " pdb=" C THR a 754 " pdb=" N ILE a 755 " pdb=" CA ILE a 755 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 14784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2544 0.037 - 0.073: 1186 0.073 - 0.110: 294 0.110 - 0.146: 43 0.146 - 0.183: 9 Chirality restraints: 4076 Sorted by residual: chirality pdb=" CA TRP c 77 " pdb=" N TRP c 77 " pdb=" C TRP c 77 " pdb=" CB TRP c 77 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CG LEU k 144 " pdb=" CB LEU k 144 " pdb=" CD1 LEU k 144 " pdb=" CD2 LEU k 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CG LEU n 144 " pdb=" CB LEU n 144 " pdb=" CD1 LEU n 144 " pdb=" CD2 LEU n 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 4073 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " -0.041 2.00e-02 2.50e+03 4.66e-02 5.42e+01 pdb=" CG TRP c 77 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR a 627 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO a 628 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO a 628 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO a 628 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU k 137 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" CD GLU k 137 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU k 137 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU k 137 " -0.011 2.00e-02 2.50e+03 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 211 2.62 - 3.19: 23283 3.19 - 3.76: 43055 3.76 - 4.33: 60337 4.33 - 4.90: 97687 Nonbonded interactions: 224573 Sorted by model distance: nonbonded pdb=" OD1 ASP d 105 " pdb=" OH TYR d 185 " model vdw 2.044 3.040 nonbonded pdb=" OG SER A 25 " pdb=" OE1 GLN B 43 " model vdw 2.053 3.040 nonbonded pdb=" O LEU g 78 " pdb=" NH2 ARG h 153 " model vdw 2.145 3.120 nonbonded pdb=" OH TYR a 73 " pdb=" OE2 GLU a 828 " model vdw 2.162 3.040 nonbonded pdb=" NH2 ARG d 18 " pdb=" O PHE d 300 " model vdw 2.166 3.120 ... (remaining 224568 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 'g' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'h' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'i' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) selection = (chain 'j' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 159)) selection = (chain 'k' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 49 or (resid 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 through 159)) selection = (chain 'l' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 49 or (resid 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 through 159)) selection = (chain 'm' and (resid 2 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 159)) selection = (chain 'n' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 through 159)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 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: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 54.550 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.130 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:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.006 0.082 25284 Z= 0.249 Angle : 0.639 13.372 34323 Z= 0.343 Chirality : 0.043 0.183 4076 Planarity : 0.004 0.065 4288 Dihedral : 12.905 88.277 8831 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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 (0.14), residues: 3193 helix: 1.57 (0.10), residues: 2324 sheet: 0.59 (0.63), residues: 68 loop : -0.13 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.117 0.003 TRP c 77 HIS 0.007 0.001 HIS a 801 PHE 0.028 0.002 PHE d 192 TYR 0.031 0.002 TYR a 141 ARG 0.007 0.001 ARG a 799 Details of bonding type rmsd hydrogen bonds : bond 0.10202 ( 1978) hydrogen bonds : angle 5.23394 ( 5847) covalent geometry : bond 0.00579 (25284) covalent geometry : angle 0.63902 (34323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 2.661 Fit side-chains REVERT: B 3 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6801 (mm-30) REVERT: B 102 GLU cc_start: 0.6840 (tt0) cc_final: 0.6272 (tp30) REVERT: a 75 LEU cc_start: 0.7407 (mt) cc_final: 0.7109 (mt) REVERT: a 124 MET cc_start: 0.7886 (mtt) cc_final: 0.7497 (mtt) REVERT: a 248 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7487 (tpt170) REVERT: a 355 GLU cc_start: 0.6715 (tm-30) cc_final: 0.6420 (tp30) REVERT: a 714 HIS cc_start: 0.6537 (t70) cc_final: 0.6092 (t-90) REVERT: a 769 MET cc_start: 0.7448 (ttt) cc_final: 0.7164 (tpp) REVERT: f 65 PHE cc_start: 0.7259 (m-80) cc_final: 0.7047 (m-80) REVERT: l 124 ARG cc_start: 0.8264 (mtm180) cc_final: 0.8028 (mtm180) REVERT: n 113 ASP cc_start: 0.7917 (t0) cc_final: 0.7707 (t0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.4864 time to fit residues: 665.5104 Evaluate side-chains 319 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 128 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 184 optimal weight: 0.4980 chunk 287 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 156 GLN l 151 ASN ** o 159 ASN ** 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 = 0.3840 r_free = 0.3840 target = 0.157912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108564 restraints weight = 25368.754| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.77 r_work: 0.3100 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25284 Z= 0.143 Angle : 0.504 7.717 34323 Z= 0.270 Chirality : 0.038 0.151 4076 Planarity : 0.004 0.043 4288 Dihedral : 4.217 32.393 3503 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.47 % Allowed : 7.21 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.02 (0.14), residues: 3193 helix: 1.88 (0.10), residues: 2347 sheet: 0.69 (0.65), residues: 68 loop : -0.17 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP c 77 HIS 0.003 0.001 HIS F 72 PHE 0.031 0.001 PHE c 80 TYR 0.024 0.001 TYR o 127 ARG 0.007 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 1978) hydrogen bonds : angle 4.54811 ( 5847) covalent geometry : bond 0.00285 (25284) covalent geometry : angle 0.50360 (34323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 354 time to evaluate : 2.661 Fit side-chains REVERT: A 66 ASP cc_start: 0.8159 (t0) cc_final: 0.7939 (t0) REVERT: A 74 MET cc_start: 0.8264 (ptt) cc_final: 0.7898 (ptt) REVERT: B 3 GLU cc_start: 0.7233 (mm-30) cc_final: 0.5900 (mm-30) REVERT: B 33 LEU cc_start: 0.7814 (tp) cc_final: 0.7364 (pt) REVERT: B 102 GLU cc_start: 0.7061 (tt0) cc_final: 0.6275 (tp30) REVERT: a 75 LEU cc_start: 0.6731 (mt) cc_final: 0.6469 (mt) REVERT: a 124 MET cc_start: 0.7739 (mtt) cc_final: 0.7348 (mtt) REVERT: a 128 THR cc_start: 0.6914 (t) cc_final: 0.6703 (t) REVERT: a 134 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6557 (tp40) REVERT: a 355 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6480 (tp30) REVERT: a 453 GLU cc_start: 0.7412 (tp30) cc_final: 0.7183 (tp30) REVERT: a 481 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7677 (t70) REVERT: a 714 HIS cc_start: 0.6008 (t70) cc_final: 0.5553 (t-90) REVERT: a 769 MET cc_start: 0.7474 (ttt) cc_final: 0.7186 (tpp) REVERT: c 208 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: e 24 MET cc_start: 0.7584 (mtp) cc_final: 0.6944 (ptt) REVERT: e 47 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8286 (ttp) REVERT: l 59 MET cc_start: 0.8531 (mmm) cc_final: 0.8131 (mmt) REVERT: l 124 ARG cc_start: 0.8463 (mtm180) cc_final: 0.8069 (mtm180) REVERT: n 3 GLU cc_start: 0.8499 (tt0) cc_final: 0.8174 (tp30) REVERT: n 113 ASP cc_start: 0.8221 (t0) cc_final: 0.7953 (t0) REVERT: n 117 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.6160 (mtp180) REVERT: o 152 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8748 (tmm) outliers start: 38 outliers final: 11 residues processed: 369 average time/residue: 1.3637 time to fit residues: 581.6410 Evaluate side-chains 333 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 317 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain a residue 134 GLN Chi-restraints excluded: chain a residue 194 ASP Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain c residue 208 LYS Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain e residue 47 MET Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 81 LYS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 136 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 93 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.157102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107558 restraints weight = 25339.322| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.75 r_work: 0.3057 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25284 Z= 0.151 Angle : 0.490 7.346 34323 Z= 0.261 Chirality : 0.038 0.140 4076 Planarity : 0.004 0.037 4288 Dihedral : 4.108 33.342 3503 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.81 % Allowed : 9.72 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.14 (0.14), residues: 3193 helix: 1.98 (0.10), residues: 2348 sheet: 0.55 (0.64), residues: 68 loop : -0.18 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 77 HIS 0.004 0.001 HIS a 801 PHE 0.031 0.001 PHE c 80 TYR 0.021 0.001 TYR o 127 ARG 0.005 0.000 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.05146 ( 1978) hydrogen bonds : angle 4.45253 ( 5847) covalent geometry : bond 0.00323 (25284) covalent geometry : angle 0.48967 (34323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 335 time to evaluate : 2.591 Fit side-chains REVERT: A 66 ASP cc_start: 0.8152 (t0) cc_final: 0.7948 (t0) REVERT: A 74 MET cc_start: 0.8189 (ptt) cc_final: 0.7798 (ptt) REVERT: B 3 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6080 (mm-30) REVERT: B 33 LEU cc_start: 0.7747 (tp) cc_final: 0.7363 (pp) REVERT: B 100 GLU cc_start: 0.8075 (tp30) cc_final: 0.7775 (tp30) REVERT: B 102 GLU cc_start: 0.7011 (tt0) cc_final: 0.6283 (tp30) REVERT: a 75 LEU cc_start: 0.6688 (mt) cc_final: 0.6438 (mt) REVERT: a 124 MET cc_start: 0.7724 (mtt) cc_final: 0.7325 (mtt) REVERT: a 128 THR cc_start: 0.6949 (t) cc_final: 0.6726 (t) REVERT: a 134 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6621 (tp40) REVERT: a 355 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6323 (tp30) REVERT: a 432 MET cc_start: 0.8178 (ttp) cc_final: 0.7866 (ttm) REVERT: a 481 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7631 (t70) REVERT: a 714 HIS cc_start: 0.5893 (t70) cc_final: 0.5491 (t-90) REVERT: c 21 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7311 (tm) REVERT: c 132 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7986 (m-40) REVERT: e 24 MET cc_start: 0.7603 (mtp) cc_final: 0.7008 (ptt) REVERT: e 47 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (ttt) REVERT: g 3 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6945 (mt-10) REVERT: l 117 ARG cc_start: 0.8154 (mtt180) cc_final: 0.7831 (mtt180) REVERT: l 124 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7972 (mtm180) REVERT: n 3 GLU cc_start: 0.8496 (tt0) cc_final: 0.8164 (tp30) REVERT: o 152 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8703 (tmm) outliers start: 47 outliers final: 22 residues processed: 353 average time/residue: 1.3594 time to fit residues: 558.0613 Evaluate side-chains 344 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 315 time to evaluate : 4.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 134 GLN Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain e residue 47 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 81 LYS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain n residue 130 ILE Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 290 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 204 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.107089 restraints weight = 25587.931| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.79 r_work: 0.3082 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25284 Z= 0.160 Angle : 0.493 7.173 34323 Z= 0.263 Chirality : 0.038 0.154 4076 Planarity : 0.004 0.039 4288 Dihedral : 4.112 35.315 3503 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.20 % Allowed : 10.88 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.14 (0.14), residues: 3193 helix: 1.98 (0.10), residues: 2348 sheet: 0.65 (0.67), residues: 62 loop : -0.16 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 77 HIS 0.004 0.001 HIS a 801 PHE 0.030 0.001 PHE c 80 TYR 0.020 0.001 TYR o 127 ARG 0.006 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05167 ( 1978) hydrogen bonds : angle 4.44583 ( 5847) covalent geometry : bond 0.00349 (25284) covalent geometry : angle 0.49260 (34323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 2.737 Fit side-chains REVERT: A 66 ASP cc_start: 0.8208 (t0) cc_final: 0.7997 (t0) REVERT: A 74 MET cc_start: 0.8216 (ptt) cc_final: 0.7840 (ptt) REVERT: B 3 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6214 (mm-30) REVERT: B 33 LEU cc_start: 0.7702 (tp) cc_final: 0.7339 (pp) REVERT: B 51 GLU cc_start: 0.6481 (tp30) cc_final: 0.5888 (tp30) REVERT: B 100 GLU cc_start: 0.8062 (tp30) cc_final: 0.7837 (tp30) REVERT: B 102 GLU cc_start: 0.6983 (tt0) cc_final: 0.6279 (tp30) REVERT: a 75 LEU cc_start: 0.6710 (mt) cc_final: 0.6458 (mt) REVERT: a 128 THR cc_start: 0.6876 (t) cc_final: 0.6665 (t) REVERT: a 262 ASP cc_start: 0.7721 (m-30) cc_final: 0.6935 (t0) REVERT: a 355 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6305 (tp30) REVERT: a 481 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7640 (t70) REVERT: a 714 HIS cc_start: 0.5907 (t70) cc_final: 0.5480 (t-90) REVERT: b 255 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: c 21 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7336 (tm) REVERT: c 132 ASN cc_start: 0.8366 (OUTLIER) cc_final: 0.8046 (m-40) REVERT: e 24 MET cc_start: 0.7724 (mtp) cc_final: 0.7193 (ptt) REVERT: g 3 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: h 121 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7290 (mm-40) REVERT: l 4 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8020 (pp) REVERT: l 124 ARG cc_start: 0.8363 (mtm180) cc_final: 0.7904 (mtm180) REVERT: o 152 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8711 (tmm) outliers start: 57 outliers final: 28 residues processed: 364 average time/residue: 1.2677 time to fit residues: 538.8014 Evaluate side-chains 352 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 639 LEU Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain e residue 47 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 81 LYS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 218 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN d 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.102555 restraints weight = 25384.327| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.37 r_work: 0.3063 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25284 Z= 0.195 Angle : 0.523 7.173 34323 Z= 0.278 Chirality : 0.040 0.159 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.204 37.115 3503 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.20 % Allowed : 11.34 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.93 (0.14), residues: 3193 helix: 1.78 (0.10), residues: 2376 sheet: 1.20 (0.75), residues: 50 loop : -0.20 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 77 HIS 0.006 0.001 HIS a 801 PHE 0.031 0.002 PHE c 80 TYR 0.019 0.002 TYR o 127 ARG 0.006 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05440 ( 1978) hydrogen bonds : angle 4.52818 ( 5847) covalent geometry : bond 0.00442 (25284) covalent geometry : angle 0.52254 (34323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 3.035 Fit side-chains REVERT: A 59 ASN cc_start: 0.8528 (t0) cc_final: 0.8313 (t0) REVERT: A 74 MET cc_start: 0.8174 (ptt) cc_final: 0.7813 (ptt) REVERT: B 3 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6367 (mm-30) REVERT: B 33 LEU cc_start: 0.7708 (tp) cc_final: 0.7345 (pp) REVERT: B 102 GLU cc_start: 0.6943 (tt0) cc_final: 0.6272 (tp30) REVERT: a 128 THR cc_start: 0.6962 (t) cc_final: 0.6749 (t) REVERT: a 134 GLN cc_start: 0.7092 (tt0) cc_final: 0.6639 (tp40) REVERT: a 329 ASP cc_start: 0.5866 (t0) cc_final: 0.5558 (t0) REVERT: a 355 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6291 (tp30) REVERT: a 481 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7652 (t70) REVERT: a 714 HIS cc_start: 0.5945 (t70) cc_final: 0.5517 (t-90) REVERT: b 255 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: c 132 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: d 280 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: e 24 MET cc_start: 0.7679 (mtp) cc_final: 0.7186 (ptt) REVERT: g 3 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: h 121 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7453 (mm-40) REVERT: k 59 MET cc_start: 0.8253 (mtp) cc_final: 0.7625 (mtt) REVERT: l 4 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8027 (pp) REVERT: l 124 ARG cc_start: 0.8317 (mtm180) cc_final: 0.8073 (mtm180) REVERT: o 152 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8658 (tmm) outliers start: 57 outliers final: 32 residues processed: 357 average time/residue: 1.4362 time to fit residues: 595.6058 Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 315 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 639 LEU Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 280 GLU Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 121 GLN Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 81 LYS Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain o residue 137 ILE Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 83 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 316 optimal weight: 0.5980 chunk 278 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106046 restraints weight = 25413.172| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.63 r_work: 0.3041 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25284 Z= 0.162 Angle : 0.495 7.020 34323 Z= 0.265 Chirality : 0.038 0.147 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.139 38.658 3503 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.24 % Allowed : 11.96 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.08 (0.14), residues: 3193 helix: 1.93 (0.10), residues: 2348 sheet: 0.68 (0.68), residues: 60 loop : -0.20 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 48 HIS 0.004 0.001 HIS a 801 PHE 0.028 0.001 PHE c 80 TYR 0.020 0.001 TYR o 127 ARG 0.010 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05184 ( 1978) hydrogen bonds : angle 4.45775 ( 5847) covalent geometry : bond 0.00352 (25284) covalent geometry : angle 0.49491 (34323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 338 time to evaluate : 2.921 Fit side-chains REVERT: A 59 ASN cc_start: 0.8453 (t0) cc_final: 0.8210 (t0) REVERT: A 74 MET cc_start: 0.8077 (ptt) cc_final: 0.7726 (ptt) REVERT: B 3 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: B 33 LEU cc_start: 0.7688 (tp) cc_final: 0.7325 (pp) REVERT: B 51 GLU cc_start: 0.6679 (tp30) cc_final: 0.6224 (tp30) REVERT: B 72 GLU cc_start: 0.6861 (tt0) cc_final: 0.6354 (pt0) REVERT: B 102 GLU cc_start: 0.6817 (tt0) cc_final: 0.6142 (tp30) REVERT: a 128 THR cc_start: 0.6835 (t) cc_final: 0.6628 (t) REVERT: a 134 GLN cc_start: 0.7095 (tt0) cc_final: 0.6605 (tp40) REVERT: a 355 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6269 (tp30) REVERT: a 453 GLU cc_start: 0.7129 (tp30) cc_final: 0.6893 (mm-30) REVERT: a 481 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7549 (t70) REVERT: a 714 HIS cc_start: 0.5848 (t70) cc_final: 0.5433 (t-90) REVERT: b 255 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: c 21 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7230 (tm) REVERT: c 132 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.7944 (m-40) REVERT: d 14 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: d 260 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: d 280 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: e 24 MET cc_start: 0.7621 (mtp) cc_final: 0.7120 (ptt) REVERT: g 3 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: g 153 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7967 (ttt90) REVERT: h 121 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: k 59 MET cc_start: 0.7909 (mtp) cc_final: 0.7619 (mtt) REVERT: l 4 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7908 (pp) REVERT: l 124 ARG cc_start: 0.8284 (mtm180) cc_final: 0.8011 (mtm180) REVERT: o 152 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8619 (tmm) outliers start: 58 outliers final: 29 residues processed: 367 average time/residue: 1.3059 time to fit residues: 560.7788 Evaluate side-chains 361 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 320 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 639 LEU Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 280 GLU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 45 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 114 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 166 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN d 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.107575 restraints weight = 25433.044| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.70 r_work: 0.3085 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25284 Z= 0.141 Angle : 0.481 6.894 34323 Z= 0.257 Chirality : 0.038 0.142 4076 Planarity : 0.003 0.040 4288 Dihedral : 4.054 38.821 3503 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.81 % Allowed : 12.85 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.21 (0.14), residues: 3193 helix: 2.05 (0.10), residues: 2348 sheet: 0.32 (0.63), residues: 69 loop : -0.18 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 48 HIS 0.003 0.001 HIS a 801 PHE 0.026 0.001 PHE c 80 TYR 0.019 0.001 TYR o 127 ARG 0.007 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 1978) hydrogen bonds : angle 4.37240 ( 5847) covalent geometry : bond 0.00296 (25284) covalent geometry : angle 0.48086 (34323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 339 time to evaluate : 2.690 Fit side-chains REVERT: A 59 ASN cc_start: 0.8507 (t0) cc_final: 0.8307 (t0) REVERT: A 74 MET cc_start: 0.8123 (ptt) cc_final: 0.7759 (ptt) REVERT: B 3 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6305 (mm-30) REVERT: B 51 GLU cc_start: 0.6641 (tp30) cc_final: 0.6162 (tp30) REVERT: B 72 GLU cc_start: 0.6887 (tt0) cc_final: 0.6442 (pt0) REVERT: B 102 GLU cc_start: 0.6949 (tt0) cc_final: 0.6312 (tp30) REVERT: F 47 LYS cc_start: 0.7848 (ttmm) cc_final: 0.7641 (ttmm) REVERT: a 75 LEU cc_start: 0.7134 (mt) cc_final: 0.6763 (mt) REVERT: a 128 THR cc_start: 0.6787 (t) cc_final: 0.6582 (t) REVERT: a 134 GLN cc_start: 0.7117 (tt0) cc_final: 0.6679 (tp40) REVERT: a 355 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6399 (tp30) REVERT: a 403 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7593 (mmm160) REVERT: a 481 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7585 (t70) REVERT: a 714 HIS cc_start: 0.5918 (t70) cc_final: 0.5520 (t-90) REVERT: b 255 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6206 (mp0) REVERT: c 21 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7362 (tm) REVERT: d 14 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: d 260 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6297 (mp10) REVERT: e 24 MET cc_start: 0.7660 (mtp) cc_final: 0.7310 (ptt) REVERT: g 153 ARG cc_start: 0.8253 (ttm-80) cc_final: 0.7873 (ttt90) REVERT: h 45 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7891 (mt) REVERT: h 99 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8720 (mt) REVERT: h 121 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7424 (mm-40) REVERT: k 59 MET cc_start: 0.8090 (mtp) cc_final: 0.7416 (mtt) REVERT: k 137 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (mm-30) REVERT: l 4 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7934 (pp) REVERT: l 117 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7848 (mtt180) REVERT: l 124 ARG cc_start: 0.8328 (mtm180) cc_final: 0.8044 (mtm180) REVERT: o 152 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8723 (tmm) outliers start: 47 outliers final: 24 residues processed: 362 average time/residue: 1.3460 time to fit residues: 564.9619 Evaluate side-chains 354 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 121 GLN Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 137 GLU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 268 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 262 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.103083 restraints weight = 25193.176| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.36 r_work: 0.3066 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25284 Z= 0.188 Angle : 0.526 9.162 34323 Z= 0.278 Chirality : 0.039 0.157 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.150 38.974 3503 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.01 % Allowed : 12.85 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.98 (0.14), residues: 3193 helix: 1.83 (0.10), residues: 2376 sheet: 0.21 (0.62), residues: 72 loop : -0.17 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 48 HIS 0.005 0.001 HIS a 801 PHE 0.030 0.001 PHE c 80 TYR 0.020 0.002 TYR c 22 ARG 0.006 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 1978) hydrogen bonds : angle 4.48105 ( 5847) covalent geometry : bond 0.00424 (25284) covalent geometry : angle 0.52613 (34323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 319 time to evaluate : 3.089 Fit side-chains REVERT: A 74 MET cc_start: 0.8142 (ptt) cc_final: 0.7798 (ptt) REVERT: B 3 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6467 (mm-30) REVERT: B 102 GLU cc_start: 0.6930 (tt0) cc_final: 0.6296 (tp30) REVERT: F 47 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7668 (ttmm) REVERT: a 75 LEU cc_start: 0.7130 (mt) cc_final: 0.6767 (mt) REVERT: a 123 GLN cc_start: 0.7441 (tt0) cc_final: 0.7230 (tp40) REVERT: a 134 GLN cc_start: 0.7141 (tt0) cc_final: 0.6696 (tp40) REVERT: a 206 VAL cc_start: 0.7821 (p) cc_final: 0.7593 (m) REVERT: a 355 GLU cc_start: 0.6905 (tm-30) cc_final: 0.6326 (tp30) REVERT: a 403 ARG cc_start: 0.7800 (mmm160) cc_final: 0.7595 (mmm160) REVERT: a 481 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7537 (t70) REVERT: a 714 HIS cc_start: 0.5981 (t70) cc_final: 0.5573 (t-90) REVERT: b 255 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6199 (mp0) REVERT: c 21 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7394 (tm) REVERT: d 14 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: d 260 GLN cc_start: 0.6814 (OUTLIER) cc_final: 0.6306 (mp10) REVERT: d 280 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: e 24 MET cc_start: 0.7688 (mtp) cc_final: 0.7273 (ptt) REVERT: g 153 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.7904 (ttt90) REVERT: h 99 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8767 (mt) REVERT: h 121 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7433 (mm-40) REVERT: k 59 MET cc_start: 0.8180 (mtp) cc_final: 0.7384 (mtt) REVERT: k 137 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: l 4 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7967 (pp) REVERT: l 117 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7766 (mtt180) REVERT: l 124 ARG cc_start: 0.8312 (mtm180) cc_final: 0.8030 (mtm180) REVERT: m 52 LYS cc_start: 0.8131 (tttt) cc_final: 0.7869 (tttt) REVERT: o 152 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8676 (tmm) outliers start: 52 outliers final: 30 residues processed: 345 average time/residue: 1.3273 time to fit residues: 532.1456 Evaluate side-chains 355 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 178 SER Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 280 GLU Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 158 VAL Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 121 GLN Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain k residue 137 GLU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain l residue 159 VAL Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 202 optimal weight: 0.9980 chunk 252 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 260 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN f 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107972 restraints weight = 25519.391| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.72 r_work: 0.3061 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25284 Z= 0.144 Angle : 0.494 8.996 34323 Z= 0.262 Chirality : 0.038 0.140 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.057 40.330 3503 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.77 % Allowed : 13.35 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.21 (0.14), residues: 3193 helix: 2.04 (0.10), residues: 2349 sheet: 0.23 (0.62), residues: 72 loop : -0.14 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 48 HIS 0.003 0.001 HIS a 801 PHE 0.026 0.001 PHE c 80 TYR 0.019 0.001 TYR o 127 ARG 0.008 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 1978) hydrogen bonds : angle 4.38248 ( 5847) covalent geometry : bond 0.00305 (25284) covalent geometry : angle 0.49415 (34323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 332 time to evaluate : 3.483 Fit side-chains REVERT: A 74 MET cc_start: 0.8064 (ptt) cc_final: 0.7701 (ptt) REVERT: B 3 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6087 (mm-30) REVERT: B 72 GLU cc_start: 0.6818 (tt0) cc_final: 0.6253 (pp20) REVERT: B 102 GLU cc_start: 0.6829 (tt0) cc_final: 0.6175 (tp30) REVERT: F 47 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7663 (ttmm) REVERT: a 75 LEU cc_start: 0.6911 (mt) cc_final: 0.6573 (mt) REVERT: a 109 ASP cc_start: 0.7094 (m-30) cc_final: 0.6784 (m-30) REVERT: a 123 GLN cc_start: 0.7339 (tt0) cc_final: 0.7135 (tp40) REVERT: a 134 GLN cc_start: 0.7021 (tt0) cc_final: 0.6576 (tp40) REVERT: a 206 VAL cc_start: 0.7637 (p) cc_final: 0.7389 (m) REVERT: a 355 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6281 (tp30) REVERT: a 403 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7516 (mmm160) REVERT: a 481 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7546 (t70) REVERT: a 714 HIS cc_start: 0.5913 (t70) cc_final: 0.5544 (t-90) REVERT: b 255 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: c 21 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7253 (tm) REVERT: d 14 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: d 260 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: d 280 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: e 24 MET cc_start: 0.7674 (mtp) cc_final: 0.7337 (ptt) REVERT: g 153 ARG cc_start: 0.8182 (ttm-80) cc_final: 0.7763 (ttt90) REVERT: h 45 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7772 (mt) REVERT: h 99 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8600 (mt) REVERT: h 121 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: i 46 ARG cc_start: 0.7728 (mmm160) cc_final: 0.7273 (mmm-85) REVERT: k 59 MET cc_start: 0.7979 (mtp) cc_final: 0.7268 (mtt) REVERT: l 4 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7832 (pp) REVERT: l 117 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7596 (mtt180) REVERT: l 124 ARG cc_start: 0.8193 (mtm180) cc_final: 0.7856 (mtm180) REVERT: m 52 LYS cc_start: 0.7969 (tttt) cc_final: 0.7766 (tttt) REVERT: o 152 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8630 (tmm) outliers start: 46 outliers final: 26 residues processed: 356 average time/residue: 1.3204 time to fit residues: 548.0280 Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 280 GLU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 43 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN f 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103427 restraints weight = 25346.877| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.36 r_work: 0.3070 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25284 Z= 0.182 Angle : 0.529 8.764 34323 Z= 0.280 Chirality : 0.039 0.154 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.140 39.946 3503 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.70 % Allowed : 13.62 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 1.99 (0.14), residues: 3193 helix: 1.84 (0.10), residues: 2376 sheet: 0.23 (0.62), residues: 72 loop : -0.18 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 48 HIS 0.005 0.001 HIS a 801 PHE 0.030 0.001 PHE c 80 TYR 0.023 0.002 TYR c 22 ARG 0.009 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.05265 ( 1978) hydrogen bonds : angle 4.47239 ( 5847) covalent geometry : bond 0.00407 (25284) covalent geometry : angle 0.52882 (34323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6386 Ramachandran restraints generated. 3193 Oldfield, 0 Emsley, 3193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 320 time to evaluate : 2.702 Fit side-chains REVERT: A 59 ASN cc_start: 0.8452 (t0) cc_final: 0.8247 (t0) REVERT: A 74 MET cc_start: 0.8182 (ptt) cc_final: 0.7834 (ptt) REVERT: B 3 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6339 (mm-30) REVERT: B 72 GLU cc_start: 0.6865 (tt0) cc_final: 0.6472 (pt0) REVERT: B 102 GLU cc_start: 0.6951 (tt0) cc_final: 0.6295 (tp30) REVERT: F 47 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7715 (ttmm) REVERT: a 75 LEU cc_start: 0.7067 (mt) cc_final: 0.6696 (mt) REVERT: a 109 ASP cc_start: 0.7076 (m-30) cc_final: 0.6792 (m-30) REVERT: a 134 GLN cc_start: 0.7115 (tt0) cc_final: 0.6693 (tp40) REVERT: a 333 LYS cc_start: 0.8093 (mttp) cc_final: 0.7704 (tptm) REVERT: a 355 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6419 (tp30) REVERT: a 432 MET cc_start: 0.8020 (ttm) cc_final: 0.7744 (ttm) REVERT: a 481 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7546 (t70) REVERT: a 714 HIS cc_start: 0.5964 (t70) cc_final: 0.5564 (t-90) REVERT: b 255 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6213 (mp0) REVERT: c 21 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7369 (tm) REVERT: c 132 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8082 (m-40) REVERT: d 14 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: d 260 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: d 280 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: e 24 MET cc_start: 0.7695 (mtp) cc_final: 0.7356 (ptt) REVERT: g 3 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: g 153 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7855 (ttt90) REVERT: h 99 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8739 (mt) REVERT: h 121 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: k 59 MET cc_start: 0.8068 (mtp) cc_final: 0.7435 (mtt) REVERT: l 4 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7969 (pp) REVERT: l 117 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7718 (mtt180) REVERT: m 52 LYS cc_start: 0.8132 (tttt) cc_final: 0.7908 (tttt) REVERT: o 152 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8673 (tmm) outliers start: 44 outliers final: 27 residues processed: 343 average time/residue: 1.2897 time to fit residues: 514.7026 Evaluate side-chains 352 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 467 LEU Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 565 MET Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain b residue 255 GLU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 34 THR Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 280 GLU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain h residue 121 GLN Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain k residue 26 LEU Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 131 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 152 SER Chi-restraints excluded: chain o residue 139 LEU Chi-restraints excluded: chain o residue 152 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 248 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 304 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 127 optimal weight: 0.0970 chunk 123 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN a 634 GLN f 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.107978 restraints weight = 25455.556| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.79 r_work: 0.3098 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25284 Z= 0.140 Angle : 0.497 8.763 34323 Z= 0.264 Chirality : 0.038 0.219 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.037 40.799 3503 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.77 % Allowed : 13.73 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % 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: 2.23 (0.14), residues: 3193 helix: 2.05 (0.10), residues: 2348 sheet: 0.25 (0.62), residues: 72 loop : -0.13 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 48 HIS 0.003 0.001 HIS a 801 PHE 0.025 0.001 PHE c 80 TYR 0.022 0.001 TYR c 22 ARG 0.009 0.000 ARG a 112 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 1978) hydrogen bonds : angle 4.37117 ( 5847) covalent geometry : bond 0.00295 (25284) covalent geometry : angle 0.49689 (34323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23692.05 seconds wall clock time: 411 minutes 31.25 seconds (24691.25 seconds total)