Starting phenix.real_space_refine on Mon Aug 25 02:36:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eas_27984/08_2025/8eas_27984.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eas_27984/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eas_27984/08_2025/8eas_27984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eas_27984/08_2025/8eas_27984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eas_27984/08_2025/8eas_27984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eas_27984/08_2025/8eas_27984.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1} 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, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2} 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: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'TYR: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: 4.84, per 1000 atoms: 0.20 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.48 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: 4.31 Time building geometry restraints manager: 2.83 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: 2.740 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: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.160 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG a 799 TYR 0.031 0.002 TYR a 141 PHE 0.028 0.002 PHE d 192 TRP 0.117 0.003 TRP c 77 HIS 0.007 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00579 (25284) covalent geometry : angle 0.63902 (34323) hydrogen bonds : bond 0.10202 ( 1978) hydrogen bonds : angle 5.23394 ( 5847) *********************** 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 : 0.595 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: 0.5767 time to fit residues: 257.5865 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 : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.156308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104080 restraints weight = 25450.046| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.38 r_work: 0.3094 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25284 Z= 0.159 Angle : 0.521 7.890 34323 Z= 0.278 Chirality : 0.039 0.147 4076 Planarity : 0.004 0.044 4288 Dihedral : 4.281 31.905 3503 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.50 % Allowed : 7.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.14), residues: 3193 helix: 1.80 (0.10), residues: 2344 sheet: 0.56 (0.66), residues: 66 loop : -0.22 (0.20), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 112 TYR 0.024 0.001 TYR o 127 PHE 0.032 0.001 PHE c 80 TRP 0.029 0.001 TRP c 77 HIS 0.003 0.001 HIS a 796 Details of bonding type rmsd covalent geometry : bond 0.00338 (25284) covalent geometry : angle 0.52090 (34323) hydrogen bonds : bond 0.05422 ( 1978) hydrogen bonds : angle 4.63348 ( 5847) *********************** 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 390 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 351 time to evaluate : 0.656 Fit side-chains REVERT: A 74 MET cc_start: 0.8273 (ptt) cc_final: 0.7941 (ptt) REVERT: B 3 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6155 (mm-30) REVERT: B 33 LEU cc_start: 0.7805 (tp) cc_final: 0.7373 (pt) REVERT: B 102 GLU cc_start: 0.7042 (tt0) cc_final: 0.6254 (tp30) REVERT: a 75 LEU cc_start: 0.6708 (mt) cc_final: 0.6480 (mt) REVERT: a 124 MET cc_start: 0.7737 (mtt) cc_final: 0.7345 (mtt) REVERT: a 128 THR cc_start: 0.6939 (t) cc_final: 0.6733 (t) REVERT: a 134 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6534 (tp40) REVERT: a 355 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6403 (tp30) REVERT: a 481 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7666 (t70) REVERT: a 565 MET cc_start: 0.6208 (tpt) cc_final: 0.5998 (mmt) REVERT: a 714 HIS cc_start: 0.5966 (t70) cc_final: 0.5537 (t-90) REVERT: a 769 MET cc_start: 0.7476 (ttt) cc_final: 0.7174 (tpp) REVERT: c 208 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8621 (mtmm) REVERT: e 24 MET cc_start: 0.7738 (mtp) cc_final: 0.7031 (ptt) REVERT: e 47 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8229 (ttt) REVERT: e 64 ARG cc_start: 0.8493 (ptm160) cc_final: 0.8251 (ptm160) REVERT: l 124 ARG cc_start: 0.8445 (mtm180) cc_final: 0.8069 (mtm180) REVERT: n 113 ASP cc_start: 0.8284 (t0) cc_final: 0.8017 (t0) REVERT: n 117 ARG cc_start: 0.6633 (mtm-85) cc_final: 0.6145 (mtp180) REVERT: o 152 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8712 (tmm) outliers start: 39 outliers final: 13 residues processed: 366 average time/residue: 0.5493 time to fit residues: 231.5395 Evaluate side-chains 332 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 314 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 g residue 2 THR 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 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 95 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 295 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.153582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101040 restraints weight = 25421.501| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.37 r_work: 0.3036 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25284 Z= 0.231 Angle : 0.560 7.229 34323 Z= 0.296 Chirality : 0.041 0.166 4076 Planarity : 0.004 0.039 4288 Dihedral : 4.373 35.394 3503 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.12 % Allowed : 9.10 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.14), residues: 3193 helix: 1.68 (0.10), residues: 2342 sheet: 0.49 (0.68), residues: 60 loop : -0.26 (0.20), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 266 TYR 0.019 0.002 TYR o 127 PHE 0.033 0.002 PHE c 80 TRP 0.024 0.002 TRP c 77 HIS 0.006 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00532 (25284) covalent geometry : angle 0.55984 (34323) hydrogen bonds : bond 0.05751 ( 1978) hydrogen bonds : angle 4.69011 ( 5847) *********************** 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: 55 poor density : 327 time to evaluate : 0.824 Fit side-chains REVERT: A 74 MET cc_start: 0.8233 (ptt) cc_final: 0.7870 (ptt) REVERT: B 3 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6261 (mm-30) REVERT: B 33 LEU cc_start: 0.7794 (tp) cc_final: 0.7418 (pp) REVERT: B 100 GLU cc_start: 0.8052 (tp30) cc_final: 0.7777 (tp30) REVERT: B 102 GLU cc_start: 0.7010 (tt0) cc_final: 0.6218 (tp30) REVERT: a 124 MET cc_start: 0.7685 (mtt) cc_final: 0.7185 (mtt) REVERT: a 128 THR cc_start: 0.6905 (t) cc_final: 0.6689 (t) REVERT: a 333 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7616 (ptmm) REVERT: a 355 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6312 (tp30) REVERT: a 432 MET cc_start: 0.8253 (ttp) cc_final: 0.7957 (ttm) REVERT: a 481 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7685 (t70) REVERT: a 714 HIS cc_start: 0.5951 (t70) cc_final: 0.5521 (t-90) REVERT: a 753 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5768 (mmm) REVERT: a 769 MET cc_start: 0.7414 (ttt) cc_final: 0.7194 (tpp) REVERT: c 132 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8052 (m-40) REVERT: c 208 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8673 (mtmm) REVERT: d 1 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6119 (tmt) REVERT: e 24 MET cc_start: 0.7844 (mtp) cc_final: 0.7171 (ptt) REVERT: e 64 ARG cc_start: 0.8477 (ptm160) cc_final: 0.8178 (ptm160) REVERT: g 3 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7000 (mt-10) REVERT: l 124 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7974 (mtm180) REVERT: n 113 ASP cc_start: 0.8290 (t0) cc_final: 0.7998 (t0) REVERT: n 117 ARG cc_start: 0.6566 (mtm-85) cc_final: 0.5994 (mtp180) REVERT: o 152 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8655 (tmm) outliers start: 55 outliers final: 27 residues processed: 350 average time/residue: 0.5508 time to fit residues: 223.2239 Evaluate side-chains 347 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 333 LYS Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 481 ASP Chi-restraints excluded: chain a residue 563 ASN 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 a residue 753 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 c residue 208 LYS Chi-restraints excluded: chain d residue 1 MET 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 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 120 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 191 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 213 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 27 ASN f 29 HIS n 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101276 restraints weight = 25329.124| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.36 r_work: 0.3039 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25284 Z= 0.218 Angle : 0.543 7.283 34323 Z= 0.289 Chirality : 0.041 0.161 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.377 38.746 3503 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.39 % Allowed : 10.42 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.14), residues: 3193 helix: 1.66 (0.10), residues: 2346 sheet: 0.37 (0.68), residues: 60 loop : -0.28 (0.20), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 112 TYR 0.020 0.002 TYR o 127 PHE 0.031 0.002 PHE c 80 TRP 0.015 0.002 TRP c 77 HIS 0.005 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00499 (25284) covalent geometry : angle 0.54299 (34323) hydrogen bonds : bond 0.05636 ( 1978) hydrogen bonds : angle 4.65610 ( 5847) *********************** 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 391 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 329 time to evaluate : 0.680 Fit side-chains REVERT: A 74 MET cc_start: 0.8266 (ptt) cc_final: 0.7907 (ptt) REVERT: B 3 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6296 (mm-30) REVERT: B 33 LEU cc_start: 0.7796 (tp) cc_final: 0.7413 (pp) REVERT: B 102 GLU cc_start: 0.7029 (tt0) cc_final: 0.6253 (tp30) REVERT: a 124 MET cc_start: 0.7690 (mtt) cc_final: 0.7223 (mtt) REVERT: a 128 THR cc_start: 0.6969 (t) cc_final: 0.6752 (t) REVERT: a 355 GLU cc_start: 0.6916 (tm-30) cc_final: 0.6368 (tp30) REVERT: a 453 GLU cc_start: 0.7373 (tp30) cc_final: 0.7117 (mm-30) REVERT: a 481 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7656 (t70) REVERT: a 714 HIS cc_start: 0.5977 (t70) cc_final: 0.5557 (t-90) REVERT: a 753 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5667 (mmm) REVERT: a 769 MET cc_start: 0.7303 (ttt) cc_final: 0.7074 (tpp) REVERT: c 132 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8057 (m-40) REVERT: c 208 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8688 (mtmm) REVERT: d 1 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.5986 (tmt) REVERT: e 24 MET cc_start: 0.7833 (mtp) cc_final: 0.7195 (ptt) REVERT: e 64 ARG cc_start: 0.8487 (ptm160) cc_final: 0.8279 (ptm160) REVERT: g 3 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: l 124 ARG cc_start: 0.8342 (mtm180) cc_final: 0.8139 (mtm180) REVERT: n 113 ASP cc_start: 0.8279 (t0) cc_final: 0.8056 (t0) REVERT: n 117 ARG cc_start: 0.6643 (mtm-85) cc_final: 0.6223 (mtp180) REVERT: o 152 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8670 (tmm) outliers start: 62 outliers final: 34 residues processed: 361 average time/residue: 0.4994 time to fit residues: 209.9960 Evaluate side-chains 349 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 28 ASP Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 481 ASP 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 a residue 753 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 c residue 201 VAL Chi-restraints excluded: chain c residue 208 LYS Chi-restraints excluded: chain d residue 1 MET 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 15 SER Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain h residue 120 SER 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 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 199 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.156377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106285 restraints weight = 25447.880| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.79 r_work: 0.3075 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1222 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= 0.147 Angle : 0.486 7.154 34323 Z= 0.261 Chirality : 0.038 0.150 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.187 39.819 3503 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.16 % Allowed : 11.50 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.14), residues: 3193 helix: 1.90 (0.10), residues: 2348 sheet: 1.15 (0.76), residues: 50 loop : -0.27 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 112 TYR 0.021 0.001 TYR o 127 PHE 0.027 0.001 PHE c 80 TRP 0.012 0.001 TRP e 48 HIS 0.003 0.001 HIS a 796 Details of bonding type rmsd covalent geometry : bond 0.00311 (25284) covalent geometry : angle 0.48571 (34323) hydrogen bonds : bond 0.05112 ( 1978) hydrogen bonds : angle 4.47950 ( 5847) *********************** 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 405 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 0.951 Fit side-chains REVERT: A 74 MET cc_start: 0.8261 (ptt) cc_final: 0.7886 (ptt) REVERT: B 3 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6296 (mm-30) REVERT: B 33 LEU cc_start: 0.7724 (tp) cc_final: 0.7379 (pp) REVERT: B 51 GLU cc_start: 0.6408 (tp30) cc_final: 0.5911 (tp30) REVERT: B 102 GLU cc_start: 0.7012 (tt0) cc_final: 0.6331 (tp30) REVERT: a 75 LEU cc_start: 0.7204 (mt) cc_final: 0.6909 (mt) REVERT: a 128 THR cc_start: 0.6915 (t) cc_final: 0.6693 (t) REVERT: a 134 GLN cc_start: 0.7162 (tt0) cc_final: 0.6724 (tp40) REVERT: a 329 ASP cc_start: 0.5684 (t0) cc_final: 0.5385 (t0) REVERT: a 355 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6312 (tp30) REVERT: a 481 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7670 (t70) REVERT: a 714 HIS cc_start: 0.5999 (t70) cc_final: 0.5572 (t-90) REVERT: a 769 MET cc_start: 0.7299 (ttt) cc_final: 0.7059 (tpp) REVERT: d 1 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.5910 (tmt) REVERT: e 24 MET cc_start: 0.7735 (mtp) cc_final: 0.7186 (ptt) REVERT: g 3 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: h 45 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8019 (mt) REVERT: h 121 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7411 (mm-40) REVERT: k 59 MET cc_start: 0.8024 (mtp) cc_final: 0.7488 (mtt) REVERT: l 4 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7986 (pp) REVERT: l 124 ARG cc_start: 0.8341 (mtm180) cc_final: 0.8079 (mtm180) REVERT: o 152 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8737 (tmm) outliers start: 56 outliers final: 21 residues processed: 375 average time/residue: 0.5535 time to fit residues: 242.1138 Evaluate side-chains 345 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 316 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 651 VAL 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 1 MET 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 g residue 3 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 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 o residue 50 THR 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 14 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 23 optimal weight: 40.0000 chunk 214 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 f 29 HIS f 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.100323 restraints weight = 25325.485| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.34 r_work: 0.2991 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25284 Z= 0.262 Angle : 0.578 7.599 34323 Z= 0.306 Chirality : 0.042 0.170 4076 Planarity : 0.004 0.042 4288 Dihedral : 4.414 40.377 3503 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.58 % Allowed : 11.84 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.14), residues: 3193 helix: 1.56 (0.10), residues: 2375 sheet: 1.04 (0.76), residues: 50 loop : -0.33 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 112 TYR 0.020 0.002 TYR c 22 PHE 0.032 0.002 PHE c 80 TRP 0.016 0.002 TRP e 48 HIS 0.007 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00610 (25284) covalent geometry : angle 0.57772 (34323) hydrogen bonds : bond 0.05833 ( 1978) hydrogen bonds : angle 4.68999 ( 5847) *********************** 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 395 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 328 time to evaluate : 0.788 Fit side-chains REVERT: A 59 ASN cc_start: 0.8446 (t0) cc_final: 0.8211 (t0) REVERT: A 67 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: A 74 MET cc_start: 0.8295 (ptt) cc_final: 0.7921 (ptt) REVERT: B 3 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6388 (mm-30) REVERT: B 33 LEU cc_start: 0.7716 (tp) cc_final: 0.7350 (pp) REVERT: B 102 GLU cc_start: 0.7115 (tt0) cc_final: 0.6359 (tp30) REVERT: F 47 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7485 (ttmm) REVERT: a 134 GLN cc_start: 0.7149 (tt0) cc_final: 0.6642 (tp40) REVERT: a 355 GLU cc_start: 0.6930 (tm-30) cc_final: 0.6384 (tp30) REVERT: a 481 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7474 (t70) REVERT: a 714 HIS cc_start: 0.5935 (t70) cc_final: 0.5500 (t-90) REVERT: a 753 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5587 (mmm) REVERT: a 769 MET cc_start: 0.7192 (ttt) cc_final: 0.6851 (tpp) REVERT: c 108 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: c 132 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8089 (m-40) REVERT: d 1 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.5982 (tmt) REVERT: e 24 MET cc_start: 0.7770 (mtp) cc_final: 0.7177 (ptt) REVERT: g 3 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: k 59 MET cc_start: 0.8204 (mtp) cc_final: 0.7516 (mtt) REVERT: k 137 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: l 124 ARG cc_start: 0.8325 (mtm180) cc_final: 0.8055 (mtm180) REVERT: n 113 ASP cc_start: 0.8333 (t0) cc_final: 0.7869 (t0) REVERT: o 152 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8632 (tmm) outliers start: 67 outliers final: 36 residues processed: 364 average time/residue: 0.5219 time to fit residues: 221.6758 Evaluate side-chains 365 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 320 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain a residue 28 ASP Chi-restraints excluded: chain a residue 215 THR Chi-restraints excluded: chain a residue 216 VAL Chi-restraints excluded: chain a residue 245 ILE Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 481 ASP 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 a residue 753 MET Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 108 GLU 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 1 MET 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 15 SER Chi-restraints excluded: chain g residue 3 GLU Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain g residue 158 VAL Chi-restraints excluded: chain h residue 45 LEU 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 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 50 THR 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 55 optimal weight: 1.9990 chunk 305 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 210 optimal weight: 0.6980 chunk 246 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 246 ASN f 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.106859 restraints weight = 25355.074| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.70 r_work: 0.3086 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25284 Z= 0.143 Angle : 0.486 7.274 34323 Z= 0.260 Chirality : 0.038 0.144 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.167 42.188 3503 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.85 % Allowed : 12.62 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.14), residues: 3193 helix: 1.85 (0.10), residues: 2378 sheet: 0.25 (0.63), residues: 69 loop : -0.24 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG a 112 TYR 0.021 0.001 TYR o 127 PHE 0.025 0.001 PHE c 80 TRP 0.013 0.001 TRP e 48 HIS 0.003 0.001 HIS a 743 Details of bonding type rmsd covalent geometry : bond 0.00301 (25284) covalent geometry : angle 0.48574 (34323) hydrogen bonds : bond 0.05028 ( 1978) hydrogen bonds : angle 4.44420 ( 5847) *********************** 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 391 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 343 time to evaluate : 0.903 Fit side-chains REVERT: A 59 ASN cc_start: 0.8494 (t0) cc_final: 0.8283 (t0) REVERT: A 67 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 74 MET cc_start: 0.8188 (ptt) cc_final: 0.7820 (ptt) REVERT: B 3 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6160 (mm-30) REVERT: B 33 LEU cc_start: 0.7710 (tp) cc_final: 0.7364 (pp) REVERT: B 51 GLU cc_start: 0.6537 (tp30) cc_final: 0.6035 (tp30) REVERT: B 72 GLU cc_start: 0.6932 (tt0) cc_final: 0.6461 (pt0) REVERT: B 102 GLU cc_start: 0.6944 (tt0) cc_final: 0.6302 (tp30) REVERT: F 47 LYS cc_start: 0.7810 (ttmm) cc_final: 0.7559 (ttmm) REVERT: a 75 LEU cc_start: 0.7122 (mt) cc_final: 0.6842 (mt) REVERT: a 109 ASP cc_start: 0.7111 (m-30) cc_final: 0.6877 (m-30) REVERT: a 112 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7697 (mtp-110) REVERT: a 134 GLN cc_start: 0.7121 (tt0) cc_final: 0.6677 (tp40) REVERT: a 329 ASP cc_start: 0.5668 (t0) cc_final: 0.5385 (t0) REVERT: a 355 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6311 (tp30) REVERT: a 714 HIS cc_start: 0.6064 (t70) cc_final: 0.5683 (t-90) REVERT: a 769 MET cc_start: 0.7203 (ttt) cc_final: 0.6976 (tpp) REVERT: d 1 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.5785 (tmt) REVERT: d 14 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: d 260 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6173 (mp10) REVERT: e 24 MET cc_start: 0.7670 (mtp) cc_final: 0.7178 (ptt) REVERT: g 121 GLN cc_start: 0.8555 (mm110) cc_final: 0.8285 (mm110) REVERT: g 153 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7927 (ttt90) REVERT: h 45 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8113 (mt) REVERT: h 121 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7432 (mm-40) REVERT: k 59 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7721 (mmt) REVERT: l 4 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7904 (pp) REVERT: l 117 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7795 (mtt180) REVERT: l 124 ARG cc_start: 0.8303 (mtm180) cc_final: 0.7988 (mtm180) REVERT: o 152 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8741 (tmm) outliers start: 48 outliers final: 23 residues processed: 365 average time/residue: 0.5158 time to fit residues: 218.8127 Evaluate side-chains 354 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 321 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU 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 651 VAL 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 1 MET 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 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 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 59 MET 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 o residue 50 THR 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 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 chunk 291 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 23 optimal weight: 40.0000 chunk 133 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN f 29 HIS f 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103481 restraints weight = 25256.903| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.37 r_work: 0.3063 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25284 Z= 0.166 Angle : 0.506 6.975 34323 Z= 0.269 Chirality : 0.039 0.149 4076 Planarity : 0.004 0.041 4288 Dihedral : 4.167 41.378 3503 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.85 % Allowed : 13.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.14), residues: 3193 helix: 1.83 (0.10), residues: 2378 sheet: 0.29 (0.63), residues: 69 loop : -0.24 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 112 TYR 0.019 0.001 TYR c 22 PHE 0.028 0.001 PHE c 80 TRP 0.011 0.001 TRP e 48 HIS 0.004 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00366 (25284) covalent geometry : angle 0.50580 (34323) hydrogen bonds : bond 0.05179 ( 1978) hydrogen bonds : angle 4.46956 ( 5847) *********************** 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 374 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 326 time to evaluate : 0.847 Fit side-chains REVERT: A 59 ASN cc_start: 0.8511 (t0) cc_final: 0.8291 (t0) REVERT: A 67 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 74 MET cc_start: 0.8208 (ptt) cc_final: 0.7870 (ptt) REVERT: B 3 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6245 (mm-30) REVERT: B 33 LEU cc_start: 0.7706 (tp) cc_final: 0.7347 (pp) REVERT: B 51 GLU cc_start: 0.6470 (tp30) cc_final: 0.5983 (tp30) REVERT: B 72 GLU cc_start: 0.6941 (tt0) cc_final: 0.6479 (pt0) REVERT: B 102 GLU cc_start: 0.6887 (tt0) cc_final: 0.6262 (tp30) REVERT: F 47 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7496 (ttmm) REVERT: a 75 LEU cc_start: 0.7126 (mt) cc_final: 0.6823 (mt) REVERT: a 134 GLN cc_start: 0.7131 (tt0) cc_final: 0.6684 (tp40) REVERT: a 355 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6318 (tp30) REVERT: a 714 HIS cc_start: 0.6140 (t70) cc_final: 0.5765 (t-90) REVERT: a 769 MET cc_start: 0.7248 (ttt) cc_final: 0.6996 (tpp) REVERT: c 100 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8340 (m110) REVERT: c 132 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: d 14 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: d 260 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6202 (mp10) REVERT: e 24 MET cc_start: 0.7593 (mtp) cc_final: 0.7149 (ptt) REVERT: g 121 GLN cc_start: 0.8580 (mm110) cc_final: 0.8295 (mm110) REVERT: g 153 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7906 (ttt90) REVERT: h 45 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7957 (mt) REVERT: h 121 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: k 59 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7690 (mmt) REVERT: l 4 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7921 (pp) REVERT: l 117 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7792 (mtt180) REVERT: l 124 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7956 (mtm180) REVERT: o 152 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8688 (tmm) outliers start: 48 outliers final: 28 residues processed: 349 average time/residue: 0.5035 time to fit residues: 205.0309 Evaluate side-chains 356 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU 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 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 100 ASN 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 316 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 GLU Chi-restraints excluded: chain g residue 158 VAL 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 59 MET 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 50 THR 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 48 optimal weight: 7.9990 chunk 175 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 305 optimal weight: 0.5980 chunk 192 optimal weight: 2.9990 chunk 150 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 f 29 HIS f 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107812 restraints weight = 25392.700| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.68 r_work: 0.3067 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25284 Z= 0.138 Angle : 0.482 7.414 34323 Z= 0.257 Chirality : 0.038 0.139 4076 Planarity : 0.004 0.040 4288 Dihedral : 4.058 41.916 3503 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.62 % Allowed : 13.27 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.14), residues: 3193 helix: 1.96 (0.10), residues: 2373 sheet: 0.33 (0.63), residues: 69 loop : -0.21 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 112 TYR 0.021 0.001 TYR c 22 PHE 0.025 0.001 PHE c 80 TRP 0.011 0.001 TRP e 48 HIS 0.003 0.001 HIS a 796 Details of bonding type rmsd covalent geometry : bond 0.00288 (25284) covalent geometry : angle 0.48211 (34323) hydrogen bonds : bond 0.04902 ( 1978) hydrogen bonds : angle 4.36682 ( 5847) *********************** 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 379 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 0.747 Fit side-chains REVERT: A 35 GLN cc_start: 0.7806 (tp40) cc_final: 0.7602 (tp-100) REVERT: A 59 ASN cc_start: 0.8492 (t0) cc_final: 0.8267 (t0) REVERT: A 74 MET cc_start: 0.8181 (ptt) cc_final: 0.7837 (ptt) REVERT: B 3 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6197 (mm-30) REVERT: B 51 GLU cc_start: 0.6788 (tp30) cc_final: 0.6335 (tp30) REVERT: B 72 GLU cc_start: 0.6826 (tt0) cc_final: 0.6450 (pt0) REVERT: B 102 GLU cc_start: 0.6927 (tt0) cc_final: 0.6309 (tp30) REVERT: F 47 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7573 (ttmm) REVERT: a 75 LEU cc_start: 0.6999 (mt) cc_final: 0.6671 (mt) REVERT: a 109 ASP cc_start: 0.7101 (m-30) cc_final: 0.6797 (m-30) REVERT: a 134 GLN cc_start: 0.7095 (tt0) cc_final: 0.6653 (tp40) REVERT: a 206 VAL cc_start: 0.7738 (p) cc_final: 0.7506 (m) REVERT: a 329 ASP cc_start: 0.5840 (t0) cc_final: 0.5540 (t0) REVERT: a 355 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6442 (tp30) REVERT: a 714 HIS cc_start: 0.6036 (t70) cc_final: 0.5676 (t-90) REVERT: a 769 MET cc_start: 0.7219 (ttt) cc_final: 0.6960 (tpp) REVERT: c 21 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7334 (tm) REVERT: c 100 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8234 (m110) REVERT: c 132 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8066 (m-40) REVERT: d 14 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8115 (tm-30) REVERT: d 260 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: e 24 MET cc_start: 0.7729 (mtp) cc_final: 0.7403 (ptt) REVERT: g 3 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7279 (mt-10) REVERT: g 121 GLN cc_start: 0.8522 (mm110) cc_final: 0.8238 (mm110) REVERT: g 153 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7885 (ttt90) REVERT: h 45 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7908 (mt) REVERT: h 121 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (mm-40) REVERT: k 59 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7643 (mmt) REVERT: l 4 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7890 (pp) REVERT: l 117 ARG cc_start: 0.8060 (mtt180) cc_final: 0.7720 (mtt180) REVERT: l 124 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7893 (mtm180) REVERT: m 52 LYS cc_start: 0.8057 (tttt) cc_final: 0.7710 (tttt) REVERT: o 152 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8678 (tmm) outliers start: 42 outliers final: 22 residues processed: 355 average time/residue: 0.5481 time to fit residues: 226.5291 Evaluate side-chains 353 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 651 VAL Chi-restraints excluded: chain a residue 711 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 100 ASN 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 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 137 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 37 VAL Chi-restraints excluded: chain k residue 59 MET 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 o residue 50 THR 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 92 optimal weight: 0.0040 chunk 77 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 160 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 634 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 = 0.3858 r_free = 0.3858 target = 0.159434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.110579 restraints weight = 25492.266| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.84 r_work: 0.3117 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1713 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= 0.125 Angle : 0.474 7.265 34323 Z= 0.253 Chirality : 0.037 0.137 4076 Planarity : 0.003 0.039 4288 Dihedral : 3.954 40.850 3503 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.43 % Allowed : 13.93 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.14), residues: 3193 helix: 2.17 (0.10), residues: 2339 sheet: 0.29 (0.61), residues: 72 loop : -0.19 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 112 TYR 0.022 0.001 TYR c 22 PHE 0.023 0.001 PHE c 80 TRP 0.011 0.001 TRP e 48 HIS 0.003 0.001 HIS a 796 Details of bonding type rmsd covalent geometry : bond 0.00251 (25284) covalent geometry : angle 0.47413 (34323) hydrogen bonds : bond 0.04686 ( 1978) hydrogen bonds : angle 4.28085 ( 5847) ********************** 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 385 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 348 time to evaluate : 1.003 Fit side-chains REVERT: A 59 ASN cc_start: 0.8427 (t0) cc_final: 0.8218 (t0) REVERT: A 74 MET cc_start: 0.8159 (ptt) cc_final: 0.7820 (ptt) REVERT: B 3 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.5938 (mm-30) REVERT: B 51 GLU cc_start: 0.6826 (tp30) cc_final: 0.6398 (tp30) REVERT: B 72 GLU cc_start: 0.6755 (tt0) cc_final: 0.6284 (pp20) REVERT: B 102 GLU cc_start: 0.6898 (tt0) cc_final: 0.6273 (tp30) REVERT: a 75 LEU cc_start: 0.6888 (mt) cc_final: 0.6550 (mt) REVERT: a 109 ASP cc_start: 0.7106 (m-30) cc_final: 0.6819 (m-30) REVERT: a 134 GLN cc_start: 0.7080 (tt0) cc_final: 0.6646 (tp40) REVERT: a 206 VAL cc_start: 0.7599 (p) cc_final: 0.7377 (m) REVERT: a 329 ASP cc_start: 0.5783 (t0) cc_final: 0.5484 (t0) REVERT: a 333 LYS cc_start: 0.8046 (mttp) cc_final: 0.7653 (tptp) REVERT: a 355 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6475 (tp30) REVERT: a 432 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7575 (ttm) REVERT: a 714 HIS cc_start: 0.5902 (t70) cc_final: 0.5548 (t-90) REVERT: a 769 MET cc_start: 0.7121 (ttt) cc_final: 0.6893 (tpp) REVERT: a 815 LEU cc_start: 0.7767 (mm) cc_final: 0.7331 (pp) REVERT: c 21 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7334 (tm) REVERT: c 132 ASN cc_start: 0.8375 (OUTLIER) cc_final: 0.8027 (m-40) REVERT: d 14 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: d 260 GLN cc_start: 0.6711 (OUTLIER) cc_final: 0.6211 (mp10) REVERT: g 3 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7293 (mt-10) REVERT: g 121 GLN cc_start: 0.8419 (mm110) cc_final: 0.8109 (mm110) REVERT: g 153 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7819 (ttt90) REVERT: h 45 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7841 (mt) REVERT: k 59 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: l 4 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7875 (pp) REVERT: l 117 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7769 (mtt180) REVERT: l 124 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7932 (mtm180) REVERT: m 48 ASP cc_start: 0.7612 (p0) cc_final: 0.7350 (p0) REVERT: m 52 LYS cc_start: 0.7970 (tttt) cc_final: 0.7669 (tttt) REVERT: o 152 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8636 (tmm) outliers start: 37 outliers final: 17 residues processed: 363 average time/residue: 0.6030 time to fit residues: 254.8831 Evaluate side-chains 345 residues out of total 2652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 318 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 432 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 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 135 THR Chi-restraints excluded: chain d residue 260 GLN Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 316 LYS Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain h residue 45 LEU Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 59 MET Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain o residue 23 CYS 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 252 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 168 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109885 restraints weight = 25394.293| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.66 r_work: 0.3119 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25284 Z= 0.134 Angle : 0.487 7.151 34323 Z= 0.259 Chirality : 0.038 0.149 4076 Planarity : 0.004 0.039 4288 Dihedral : 3.950 39.713 3503 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.20 % Allowed : 14.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.14), residues: 3193 helix: 2.18 (0.10), residues: 2339 sheet: 0.32 (0.62), residues: 72 loop : -0.18 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 112 TYR 0.020 0.001 TYR c 22 PHE 0.025 0.001 PHE c 80 TRP 0.010 0.001 TRP e 48 HIS 0.003 0.001 HIS a 796 Details of bonding type rmsd covalent geometry : bond 0.00278 (25284) covalent geometry : angle 0.48691 (34323) hydrogen bonds : bond 0.04758 ( 1978) hydrogen bonds : angle 4.27718 ( 5847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8432.80 seconds wall clock time: 144 minutes 22.15 seconds (8662.15 seconds total)