Starting phenix.real_space_refine on Wed May 8 22:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r5h_18915/05_2024/8r5h_18915_updated.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 71 5.16 5 Cl 1 4.86 5 C 7225 2.51 5 N 1926 2.21 5 O 2051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 11277 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 4918 Classifications: {'peptide': 631} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 17, 'TRANS': 613} Chain breaks: 3 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 25, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 180 Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 587 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1476 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 16, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'UNK:plan-1': 16, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 759 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 93} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 104} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 95} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1205 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5105 SG CYS R 42 52.292 71.426 64.049 1.00 67.35 S ATOM 5121 SG CYS R 45 49.840 69.266 66.363 1.00 77.17 S ATOM 5339 SG CYS R 83 49.456 72.954 66.113 1.00 81.07 S ATOM 5268 SG CYS R 75 59.869 81.569 57.203 1.00 77.02 S ATOM 5424 SG CYS R 94 58.480 81.685 60.878 1.00 78.76 S ATOM 5177 SG CYS R 53 45.098 70.965 64.633 1.00104.29 S ATOM 5196 SG CYS R 56 41.358 70.236 64.534 1.00113.59 S ATOM 5222 SG CYS R 68 43.244 71.906 61.490 1.00 84.39 S Time building chain proxies: 6.72, per 1000 atoms: 0.60 Number of scatterers: 11277 At special positions: 0 Unit cell: (101.293, 125.978, 173.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Cl 1 17.00 S 71 16.00 O 2051 8.00 N 1926 7.00 C 7225 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 C1101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " Number of angles added : 6 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 9 sheets defined 45.6% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.999A pdb=" N THR A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 removed outlier: 4.157A pdb=" N PHE A 39 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 75 Processing helix chain 'A' and resid 83 through 104 removed outlier: 3.746A pdb=" N GLU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N CYS A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 139 through 170 removed outlier: 3.665A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 4.557A pdb=" N ALA A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.992A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 228 removed outlier: 5.721A pdb=" N SER A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 232 through 253 removed outlier: 4.182A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 291 through 301 removed outlier: 4.183A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 337 through 357 Processing helix chain 'A' and resid 362 through 376 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 408 through 424 removed outlier: 4.385A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 445 removed outlier: 3.975A pdb=" N HIS A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 4.345A pdb=" N GLU A 455 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 471 through 493 removed outlier: 5.254A pdb=" N MET A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 533 No H-bonds generated for 'chain 'A' and resid 531 through 533' Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'A' and resid 579 through 589 removed outlier: 3.621A pdb=" N PHE A 588 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 607 through 619 Processing helix chain 'R' and resid 54 through 57 No H-bonds generated for 'chain 'R' and resid 54 through 57' Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 142 through 154 Processing helix chain 'C' and resid 160 through 179 Processing helix chain 'U' and resid 23 through 33 Processing helix chain 'U' and resid 38 through 40 No H-bonds generated for 'chain 'U' and resid 38 through 40' Processing helix chain 'U' and resid 56 through 59 Processing helix chain 'D' and resid 33 through 38 removed outlier: 4.184A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 46 Processing helix chain 'D' and resid 67 through 82 removed outlier: 4.099A pdb=" N LYS D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 110 Processing helix chain 'F' and resid 350 through 364 Processing helix chain 'F' and resid 374 through 377 Processing helix chain 'F' and resid 382 through 385 No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 390 through 393 No H-bonds generated for 'chain 'F' and resid 390 through 393' Processing helix chain 'F' and resid 400 through 407 Processing helix chain 'F' and resid 415 through 432 removed outlier: 3.793A pdb=" N ALA F 429 " --> pdb=" O MET F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 455 Processing helix chain 'G' and resid 24 through 35 removed outlier: 5.234A pdb=" N ARG G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'H' and resid 158 through 169 Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 182 through 189 removed outlier: 4.060A pdb=" N GLU H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 208 Processing sheet with id= A, first strand: chain 'A' and resid 561 through 565 Processing sheet with id= B, first strand: chain 'A' and resid 593 through 595 Processing sheet with id= C, first strand: chain 'C' and resid 60 through 63 Processing sheet with id= D, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.612A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 28 through 32 Processing sheet with id= F, first strand: chain 'G' and resid 3 through 9 removed outlier: 3.921A pdb=" N THR G 16 " --> pdb=" O LEU G 5 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 43 through 45 Processing sheet with id= H, first strand: chain 'H' and resid 106 through 112 removed outlier: 6.573A pdb=" N ILE H 147 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N CYS H 77 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA H 149 " --> pdb=" O CYS H 77 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 84 through 88 449 hydrogen bonds defined for protein. 1323 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: 2.98 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3639 1.34 - 1.46: 2386 1.46 - 1.58: 5394 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 11536 Sorted by residual: bond pdb=" CCH 759 H 301 " pdb=" SBR 759 H 301 " ideal model delta sigma weight residual 1.530 1.751 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CBZ 759 H 301 " pdb=" NBI 759 H 301 " ideal model delta sigma weight residual 1.542 1.325 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" CAV 759 H 301 " pdb=" NBI 759 H 301 " ideal model delta sigma weight residual 1.642 1.441 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" CBZ 759 H 301 " pdb=" CCH 759 H 301 " ideal model delta sigma weight residual 1.578 1.377 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" CA 759 H 301 " pdb=" CB 759 H 301 " ideal model delta sigma weight residual 1.364 1.537 -0.173 2.00e-02 2.50e+03 7.49e+01 ... (remaining 11531 not shown) Histogram of bond angle deviations from ideal: 90.16 - 98.96: 2 98.96 - 107.75: 488 107.75 - 116.54: 7447 116.54 - 125.34: 7550 125.34 - 134.13: 198 Bond angle restraints: 15685 Sorted by residual: angle pdb=" CCC 759 H 301 " pdb=" SBS 759 H 301 " pdb=" CCJ 759 H 301 " ideal model delta sigma weight residual 107.55 90.80 16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N LEU A 473 " pdb=" CA LEU A 473 " pdb=" C LEU A 473 " ideal model delta sigma weight residual 113.18 106.05 7.13 1.33e+00 5.65e-01 2.87e+01 angle pdb=" N ARG H 177 " pdb=" CA ARG H 177 " pdb=" C ARG H 177 " ideal model delta sigma weight residual 114.09 106.57 7.52 1.55e+00 4.16e-01 2.35e+01 angle pdb=" CAV 759 H 301 " pdb=" SBR 759 H 301 " pdb=" CCH 759 H 301 " ideal model delta sigma weight residual 104.58 90.16 14.42 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C GLU D 54 " pdb=" CA GLU D 54 " pdb=" CB GLU D 54 " ideal model delta sigma weight residual 115.89 110.43 5.46 1.32e+00 5.74e-01 1.71e+01 ... (remaining 15680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 6630 27.36 - 54.73: 267 54.73 - 82.09: 21 82.09 - 109.45: 1 109.45 - 136.81: 3 Dihedral angle restraints: 6922 sinusoidal: 2627 harmonic: 4295 Sorted by residual: dihedral pdb=" CA HIS A 73 " pdb=" C HIS A 73 " pdb=" N LYS A 74 " pdb=" CA LYS A 74 " ideal model delta harmonic sigma weight residual 180.00 154.79 25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA CYS F 368 " pdb=" C CYS F 368 " pdb=" N HIS F 369 " pdb=" CA HIS F 369 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C SY8 C1101 " pdb=" C1 SY8 C1101 " pdb=" C2 SY8 C1101 " pdb=" C3 SY8 C1101 " ideal model delta sinusoidal sigma weight residual 62.79 -160.40 -136.81 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 6919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1632 0.074 - 0.147: 138 0.147 - 0.221: 3 0.221 - 0.294: 0 0.294 - 0.368: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CCN 759 H 301 " pdb=" CBW 759 H 301 " pdb=" CCQ 759 H 301 " pdb=" NBN 759 H 301 " both_signs ideal model delta sigma weight residual False 2.61 2.24 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG 759 H 301 " pdb=" CB 759 H 301 " pdb=" OD1 759 H 301 " pdb=" CD2 759 H 301 " both_signs ideal model delta sigma weight residual False -2.52 -2.68 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1771 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 255 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 256 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" N 759 H 301 " 0.016 2.00e-02 2.50e+03 1.96e-02 5.76e+00 pdb=" CA 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 759 H 301 " -0.026 2.00e-02 2.50e+03 pdb=" CBW 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" CCN 759 H 301 " 0.013 2.00e-02 2.50e+03 pdb=" OAK 759 H 301 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 98 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO H 99 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 99 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 99 " 0.030 5.00e-02 4.00e+02 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 11 2.34 - 2.98: 5535 2.98 - 3.62: 15862 3.62 - 4.26: 22564 4.26 - 4.90: 38523 Nonbonded interactions: 82495 Sorted by model distance: nonbonded pdb=" SG CYS F 368 " pdb=" C SY8 C1101 " model vdw 1.705 3.820 nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.992 2.230 nonbonded pdb=" OG1 THR A 520 " pdb=" OH TYR A 558 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASP A 633 " pdb=" OG SER A 636 " model vdw 2.252 2.440 nonbonded pdb=" NE2 GLN A 581 " pdb=" OG SER A 616 " model vdw 2.272 2.520 ... (remaining 82490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.230 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 35.430 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.007 0.221 11536 Z= 0.419 Angle : 0.772 16.753 15685 Z= 0.416 Chirality : 0.041 0.368 1774 Planarity : 0.005 0.110 2006 Dihedral : 14.293 136.812 4121 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1413 helix: 1.19 (0.21), residues: 652 sheet: -0.92 (0.49), residues: 116 loop : -1.97 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.007 0.001 HIS A 71 PHE 0.015 0.001 PHE D 52 TYR 0.017 0.001 TYR A 194 ARG 0.008 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.238 Fit side-chains REVERT: A 74 LYS cc_start: 0.7452 (ttpp) cc_final: 0.7219 (ttpp) REVERT: A 206 ILE cc_start: 0.8104 (tt) cc_final: 0.7880 (tt) REVERT: A 369 ASP cc_start: 0.6902 (m-30) cc_final: 0.6577 (m-30) REVERT: A 608 LYS cc_start: 0.8425 (ptpp) cc_final: 0.8223 (ptpp) REVERT: C 14 MET cc_start: 0.6235 (ptp) cc_final: 0.5834 (ptp) REVERT: F 364 MET cc_start: 0.5728 (ttm) cc_final: 0.5495 (ttm) REVERT: G 77 LEU cc_start: 0.7922 (tp) cc_final: 0.7581 (tp) REVERT: H 69 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7634 (mtm110) REVERT: H 72 SER cc_start: 0.8067 (p) cc_final: 0.7831 (p) REVERT: H 136 PHE cc_start: 0.7730 (t80) cc_final: 0.7343 (t80) REVERT: H 202 THR cc_start: 0.6959 (m) cc_final: 0.6696 (m) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.3058 time to fit residues: 90.6039 Evaluate side-chains 209 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0020 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN A 463 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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 0.040 11536 Z= 0.208 Angle : 0.603 13.371 15685 Z= 0.296 Chirality : 0.042 0.401 1774 Planarity : 0.005 0.092 2006 Dihedral : 9.909 173.981 1587 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.39 % Allowed : 8.02 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1413 helix: 1.24 (0.21), residues: 657 sheet: -0.94 (0.49), residues: 122 loop : -1.94 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 374 HIS 0.007 0.001 HIS A 255 PHE 0.027 0.002 PHE A 350 TYR 0.011 0.001 TYR A 219 ARG 0.005 0.000 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 215 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8463 (tp) cc_final: 0.8247 (tt) REVERT: A 41 ASP cc_start: 0.7564 (m-30) cc_final: 0.7332 (m-30) REVERT: A 206 ILE cc_start: 0.8069 (tt) cc_final: 0.7731 (tt) REVERT: A 651 PHE cc_start: 0.7673 (p90) cc_final: 0.7351 (p90) REVERT: R 27 TRP cc_start: 0.7199 (t60) cc_final: 0.6854 (t60) REVERT: C 14 MET cc_start: 0.6111 (ptp) cc_final: 0.5744 (ptp) REVERT: U 1 MET cc_start: 0.6285 (ppp) cc_final: 0.5958 (ppp) REVERT: F 362 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7637 (mmmm) REVERT: H 69 ARG cc_start: 0.7864 (mtm110) cc_final: 0.7637 (mtm110) REVERT: H 72 SER cc_start: 0.8042 (p) cc_final: 0.7819 (p) REVERT: H 136 PHE cc_start: 0.7803 (t80) cc_final: 0.7377 (t80) outliers start: 16 outliers final: 9 residues processed: 218 average time/residue: 0.2876 time to fit residues: 83.6361 Evaluate side-chains 219 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 210 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN F 447 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11536 Z= 0.195 Angle : 0.575 12.577 15685 Z= 0.281 Chirality : 0.041 0.391 1774 Planarity : 0.005 0.086 2006 Dihedral : 9.840 177.944 1587 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.27 % Allowed : 10.46 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1413 helix: 1.33 (0.21), residues: 663 sheet: -0.83 (0.50), residues: 119 loop : -1.99 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.008 0.001 HIS A 255 PHE 0.028 0.001 PHE A 350 TYR 0.020 0.001 TYR A 558 ARG 0.003 0.000 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7894 (t) cc_final: 0.7622 (t) REVERT: A 206 ILE cc_start: 0.8035 (tt) cc_final: 0.7766 (tt) REVERT: A 581 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6784 (mm110) REVERT: A 651 PHE cc_start: 0.7635 (p90) cc_final: 0.7318 (p90) REVERT: R 27 TRP cc_start: 0.7226 (t60) cc_final: 0.6913 (t60) REVERT: C 14 MET cc_start: 0.6133 (ptp) cc_final: 0.5754 (ptp) REVERT: U 1 MET cc_start: 0.6292 (ppp) cc_final: 0.5994 (ppp) REVERT: F 362 LYS cc_start: 0.7924 (mmmm) cc_final: 0.7627 (mmmm) REVERT: F 442 MET cc_start: 0.5949 (ptp) cc_final: 0.5679 (mtm) REVERT: H 72 SER cc_start: 0.8021 (p) cc_final: 0.7800 (p) REVERT: H 136 PHE cc_start: 0.7772 (t80) cc_final: 0.7330 (t80) outliers start: 26 outliers final: 16 residues processed: 226 average time/residue: 0.2966 time to fit residues: 89.5270 Evaluate side-chains 223 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 206 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 137 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11536 Z= 0.220 Angle : 0.586 12.675 15685 Z= 0.287 Chirality : 0.041 0.392 1774 Planarity : 0.005 0.084 2006 Dihedral : 9.803 177.775 1587 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.79 % Allowed : 12.47 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1413 helix: 1.39 (0.21), residues: 658 sheet: -0.86 (0.50), residues: 119 loop : -1.96 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 374 HIS 0.006 0.001 HIS A 255 PHE 0.031 0.001 PHE A 350 TYR 0.012 0.001 TYR D 79 ARG 0.004 0.000 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7894 (t) cc_final: 0.7618 (t) REVERT: A 206 ILE cc_start: 0.8063 (tt) cc_final: 0.7783 (tt) REVERT: A 288 GLN cc_start: 0.7486 (mp10) cc_final: 0.7242 (mp10) REVERT: A 377 ASN cc_start: 0.7398 (m110) cc_final: 0.6895 (t0) REVERT: A 651 PHE cc_start: 0.7586 (p90) cc_final: 0.7260 (p90) REVERT: R 27 TRP cc_start: 0.7248 (t60) cc_final: 0.6981 (t60) REVERT: C 14 MET cc_start: 0.6130 (ptp) cc_final: 0.5780 (ptp) REVERT: U 1 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.6003 (ppp) REVERT: F 362 LYS cc_start: 0.7942 (mmmm) cc_final: 0.7654 (mmmm) REVERT: F 442 MET cc_start: 0.5990 (ptp) cc_final: 0.5772 (mtm) REVERT: H 72 SER cc_start: 0.8018 (p) cc_final: 0.7788 (p) REVERT: H 136 PHE cc_start: 0.7782 (t80) cc_final: 0.7341 (t80) outliers start: 32 outliers final: 20 residues processed: 222 average time/residue: 0.2862 time to fit residues: 85.0271 Evaluate side-chains 231 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0170 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.1980 chunk 117 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 70 optimal weight: 0.0270 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11536 Z= 0.149 Angle : 0.554 12.465 15685 Z= 0.266 Chirality : 0.040 0.395 1774 Planarity : 0.005 0.080 2006 Dihedral : 9.571 177.702 1587 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.35 % Allowed : 14.12 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.23), residues: 1413 helix: 1.60 (0.21), residues: 658 sheet: -0.86 (0.50), residues: 119 loop : -1.89 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 35 HIS 0.006 0.001 HIS A 255 PHE 0.026 0.001 PHE A 350 TYR 0.019 0.001 TYR A 558 ARG 0.004 0.000 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7779 (t) cc_final: 0.7480 (t) REVERT: A 206 ILE cc_start: 0.8011 (tt) cc_final: 0.7715 (tt) REVERT: A 288 GLN cc_start: 0.7466 (mp10) cc_final: 0.7229 (mp10) REVERT: A 361 ASP cc_start: 0.6913 (t0) cc_final: 0.6543 (m-30) REVERT: A 377 ASN cc_start: 0.7403 (m110) cc_final: 0.6931 (t0) REVERT: A 537 VAL cc_start: 0.5922 (OUTLIER) cc_final: 0.4307 (p) REVERT: A 651 PHE cc_start: 0.7564 (p90) cc_final: 0.7248 (p90) REVERT: R 27 TRP cc_start: 0.7196 (t60) cc_final: 0.6876 (t60) REVERT: C 14 MET cc_start: 0.6115 (ptp) cc_final: 0.5752 (ptp) REVERT: C 81 MET cc_start: 0.5692 (tpt) cc_final: 0.4984 (tpt) REVERT: U 1 MET cc_start: 0.6247 (OUTLIER) cc_final: 0.6001 (ppp) REVERT: F 362 LYS cc_start: 0.7866 (mmmm) cc_final: 0.7565 (mmmm) REVERT: H 72 SER cc_start: 0.8046 (p) cc_final: 0.7817 (p) REVERT: H 136 PHE cc_start: 0.7712 (t80) cc_final: 0.7303 (t80) outliers start: 27 outliers final: 18 residues processed: 224 average time/residue: 0.2884 time to fit residues: 86.4683 Evaluate side-chains 231 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 211 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11536 Z= 0.204 Angle : 0.579 12.657 15685 Z= 0.283 Chirality : 0.041 0.388 1774 Planarity : 0.005 0.080 2006 Dihedral : 9.563 176.875 1587 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.31 % Allowed : 14.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1413 helix: 1.52 (0.21), residues: 658 sheet: -0.85 (0.50), residues: 119 loop : -1.90 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.006 0.001 HIS A 255 PHE 0.028 0.001 PHE A 350 TYR 0.011 0.001 TYR D 79 ARG 0.006 0.000 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 218 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7838 (t) cc_final: 0.7539 (t) REVERT: A 192 GLU cc_start: 0.8248 (pt0) cc_final: 0.8017 (pt0) REVERT: A 206 ILE cc_start: 0.8028 (tt) cc_final: 0.7721 (tt) REVERT: A 288 GLN cc_start: 0.7472 (mp10) cc_final: 0.7230 (mp10) REVERT: A 361 ASP cc_start: 0.6879 (t0) cc_final: 0.6583 (m-30) REVERT: A 377 ASN cc_start: 0.7403 (m110) cc_final: 0.6927 (t0) REVERT: A 537 VAL cc_start: 0.5733 (OUTLIER) cc_final: 0.5496 (p) REVERT: R 27 TRP cc_start: 0.7225 (t60) cc_final: 0.6926 (t60) REVERT: C 14 MET cc_start: 0.6109 (ptp) cc_final: 0.5711 (ptp) REVERT: C 81 MET cc_start: 0.5656 (tpt) cc_final: 0.4978 (tpt) REVERT: H 72 SER cc_start: 0.8035 (p) cc_final: 0.7813 (p) REVERT: H 136 PHE cc_start: 0.7743 (t80) cc_final: 0.7333 (t80) REVERT: H 155 VAL cc_start: 0.7044 (t) cc_final: 0.6773 (p) outliers start: 38 outliers final: 25 residues processed: 232 average time/residue: 0.2888 time to fit residues: 89.8579 Evaluate side-chains 241 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 0.3980 chunk 77 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 136 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11536 Z= 0.162 Angle : 0.559 12.522 15685 Z= 0.268 Chirality : 0.040 0.391 1774 Planarity : 0.004 0.078 2006 Dihedral : 9.453 176.971 1587 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.70 % Allowed : 14.91 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1413 helix: 1.63 (0.21), residues: 658 sheet: -0.86 (0.50), residues: 119 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 374 HIS 0.005 0.001 HIS A 255 PHE 0.009 0.001 PHE F 365 TYR 0.017 0.001 TYR A 558 ARG 0.004 0.000 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7804 (t) cc_final: 0.7519 (t) REVERT: A 206 ILE cc_start: 0.8019 (tt) cc_final: 0.7716 (tt) REVERT: A 288 GLN cc_start: 0.7502 (mp10) cc_final: 0.7248 (mp10) REVERT: A 361 ASP cc_start: 0.6825 (t0) cc_final: 0.6603 (m-30) REVERT: A 377 ASN cc_start: 0.7390 (m110) cc_final: 0.6952 (t0) REVERT: A 487 ASN cc_start: 0.7088 (m-40) cc_final: 0.6884 (m-40) REVERT: A 537 VAL cc_start: 0.5766 (OUTLIER) cc_final: 0.5559 (p) REVERT: R 27 TRP cc_start: 0.7226 (t60) cc_final: 0.6947 (t60) REVERT: C 14 MET cc_start: 0.6096 (ptp) cc_final: 0.5704 (ptp) REVERT: C 81 MET cc_start: 0.5648 (tpt) cc_final: 0.4990 (tpt) REVERT: H 72 SER cc_start: 0.8030 (p) cc_final: 0.7800 (p) REVERT: H 136 PHE cc_start: 0.7694 (t80) cc_final: 0.7266 (t80) REVERT: H 155 VAL cc_start: 0.7033 (t) cc_final: 0.6753 (p) outliers start: 31 outliers final: 23 residues processed: 230 average time/residue: 0.2994 time to fit residues: 93.0812 Evaluate side-chains 242 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 218 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11536 Z= 0.252 Angle : 0.616 12.595 15685 Z= 0.302 Chirality : 0.042 0.384 1774 Planarity : 0.005 0.080 2006 Dihedral : 9.618 176.693 1587 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.23 % Allowed : 14.30 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1413 helix: 1.45 (0.21), residues: 651 sheet: -0.76 (0.52), residues: 114 loop : -2.02 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 374 HIS 0.007 0.001 HIS R 77 PHE 0.015 0.002 PHE A 339 TYR 0.014 0.002 TYR A 203 ARG 0.005 0.000 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7884 (t) cc_final: 0.7597 (t) REVERT: A 206 ILE cc_start: 0.8063 (tt) cc_final: 0.7760 (tt) REVERT: A 288 GLN cc_start: 0.7520 (mp10) cc_final: 0.7256 (mp10) REVERT: A 361 ASP cc_start: 0.6883 (t0) cc_final: 0.6665 (m-30) REVERT: A 377 ASN cc_start: 0.7359 (m110) cc_final: 0.6856 (t0) REVERT: A 487 ASN cc_start: 0.7103 (m-40) cc_final: 0.6869 (m-40) REVERT: A 537 VAL cc_start: 0.6034 (OUTLIER) cc_final: 0.4159 (p) REVERT: R 27 TRP cc_start: 0.7284 (t60) cc_final: 0.7074 (t60) REVERT: C 14 MET cc_start: 0.6117 (ptp) cc_final: 0.5716 (ptp) REVERT: C 81 MET cc_start: 0.5695 (tpt) cc_final: 0.5087 (tpt) REVERT: D 80 LYS cc_start: 0.8076 (tttt) cc_final: 0.7864 (tttp) REVERT: H 72 SER cc_start: 0.8013 (p) cc_final: 0.7784 (p) REVERT: H 136 PHE cc_start: 0.7739 (t80) cc_final: 0.7268 (t80) outliers start: 37 outliers final: 25 residues processed: 230 average time/residue: 0.2722 time to fit residues: 85.0724 Evaluate side-chains 234 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11536 Z= 0.210 Angle : 0.611 12.524 15685 Z= 0.297 Chirality : 0.041 0.393 1774 Planarity : 0.005 0.079 2006 Dihedral : 9.505 175.842 1587 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.35 % Allowed : 15.87 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1413 helix: 1.45 (0.21), residues: 651 sheet: -0.80 (0.52), residues: 114 loop : -1.97 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 374 HIS 0.007 0.001 HIS A 274 PHE 0.034 0.001 PHE A 350 TYR 0.026 0.001 TYR A 558 ARG 0.005 0.000 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7844 (t) cc_final: 0.7576 (t) REVERT: A 206 ILE cc_start: 0.8058 (tt) cc_final: 0.7751 (tt) REVERT: A 288 GLN cc_start: 0.7529 (mp10) cc_final: 0.7256 (mp10) REVERT: A 361 ASP cc_start: 0.6832 (t0) cc_final: 0.6626 (m-30) REVERT: A 377 ASN cc_start: 0.7344 (m110) cc_final: 0.6876 (t0) REVERT: A 487 ASN cc_start: 0.7080 (m-40) cc_final: 0.6875 (m-40) REVERT: A 537 VAL cc_start: 0.5665 (OUTLIER) cc_final: 0.5425 (p) REVERT: R 27 TRP cc_start: 0.7279 (t60) cc_final: 0.7018 (t60) REVERT: C 14 MET cc_start: 0.6109 (ptp) cc_final: 0.5704 (ptp) REVERT: C 81 MET cc_start: 0.5675 (tpt) cc_final: 0.5071 (tpt) REVERT: H 72 SER cc_start: 0.8011 (p) cc_final: 0.7782 (p) REVERT: H 136 PHE cc_start: 0.7682 (t80) cc_final: 0.7241 (t80) outliers start: 27 outliers final: 23 residues processed: 218 average time/residue: 0.3066 time to fit residues: 89.3661 Evaluate side-chains 232 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 50 MET Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain U residue 70 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 130 optimal weight: 0.0170 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.0040 chunk 87 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 100.0000 chunk 120 optimal weight: 0.5980 overall best weight: 0.3030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 255 HIS A 276 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11536 Z= 0.158 Angle : 0.587 12.404 15685 Z= 0.280 Chirality : 0.040 0.391 1774 Planarity : 0.005 0.079 2006 Dihedral : 9.175 170.999 1587 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1413 helix: 1.66 (0.21), residues: 651 sheet: -0.73 (0.51), residues: 114 loop : -1.91 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 374 HIS 0.007 0.001 HIS A 274 PHE 0.031 0.001 PHE A 350 TYR 0.012 0.001 TYR D 79 ARG 0.005 0.000 ARG H 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 VAL cc_start: 0.7762 (t) cc_final: 0.7480 (t) REVERT: A 206 ILE cc_start: 0.8034 (tt) cc_final: 0.7703 (tt) REVERT: A 377 ASN cc_start: 0.7350 (m110) cc_final: 0.6965 (t0) REVERT: A 390 LEU cc_start: 0.7227 (mp) cc_final: 0.6868 (mt) REVERT: R 27 TRP cc_start: 0.7254 (t60) cc_final: 0.6979 (t60) REVERT: C 14 MET cc_start: 0.6096 (ptp) cc_final: 0.5699 (ptp) REVERT: C 81 MET cc_start: 0.5685 (tpt) cc_final: 0.4999 (tpt) REVERT: G 8 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7623 (mtm180) REVERT: H 72 SER cc_start: 0.8002 (p) cc_final: 0.7773 (p) REVERT: H 136 PHE cc_start: 0.7661 (t80) cc_final: 0.7121 (t80) REVERT: H 203 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6058 (mp10) outliers start: 23 outliers final: 18 residues processed: 226 average time/residue: 0.2910 time to fit residues: 87.7499 Evaluate side-chains 234 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 54 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 203 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.2980 chunk 103 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 255 HIS A 276 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.158570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134008 restraints weight = 16673.467| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.44 r_work: 0.3634 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11536 Z= 0.182 Angle : 0.598 12.441 15685 Z= 0.288 Chirality : 0.041 0.389 1774 Planarity : 0.005 0.080 2006 Dihedral : 9.033 167.032 1587 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1413 helix: 1.60 (0.21), residues: 652 sheet: -0.74 (0.51), residues: 114 loop : -1.90 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 374 HIS 0.007 0.001 HIS A 274 PHE 0.011 0.001 PHE A 339 TYR 0.012 0.001 TYR D 79 ARG 0.005 0.000 ARG H 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.63 seconds wall clock time: 54 minutes 20.04 seconds (3260.04 seconds total)