Starting phenix.real_space_refine on Sun Feb 18 07:17:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lu1_0977/02_2024/6lu1_0977_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 2 5.49 5 Mg 82 5.21 5 S 80 5.16 5 C 14981 2.51 5 N 2942 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 689": "OE1" <-> "OE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "M GLU 28": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21198 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5819 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 712} Chain: "B" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5685 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 31, 'TRANS': 681} Chain breaks: 1 Chain: "C" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1075 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 124} Chain: "E" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 539 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "F" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "I" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "J" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 67 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "L" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 994 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "M" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 241 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 2993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 2993 Unusual residues: {'BCR': 14, 'CLA': 44, 'LHG': 2, 'PQN': 1} Classifications: {'undetermined': 61} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 564 Unresolved non-hydrogen angles: 715 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'BCR:plan-2': 2, 'CLA:plan-3': 3, 'CLA:plan-4': 6, 'CLA:plan-5': 10, 'BCR:plan-4': 2, 'BCR:plan-5': 1, 'BCR:plan-9': 3, 'BCR:plan-7': 2, 'BCR:plan-6': 2, 'BCR:plan-1': 4, 'BCR:plan-3': 2, 'BCR:plan-8': 3} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 2258 Unusual residues: {'BCR': 6, 'CLA': 35, 'LMG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 44} Link IDs: {None: 43} Unresolved non-hydrogen bonds: 354 Unresolved non-hydrogen angles: 434 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 6, 'CLA:plan-5': 14, 'BCR:plan-2': 1} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'BCR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 176 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-3': 1, 'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 19 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4440 SG CYS A 578 69.872 48.928 75.101 1.00 9.54 S ATOM 10068 SG CYS B 565 69.435 49.660 82.273 1.00 13.03 S Time building chain proxies: 11.52, per 1000 atoms: 0.54 Number of scatterers: 21198 At special positions: 0 Unit cell: (117.48, 114.81, 153.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 80 16.00 P 2 15.00 Mg 82 11.99 O 3099 8.00 N 2942 7.00 C 14981 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 custom bonds: simple=55, symmetry=0 Number of additional bonds: simple=55, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.14 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 804 " pdb="FE4 SF4 B 804 " - pdb=" SG CYS B 565 " pdb="FE3 SF4 B 804 " - pdb=" SG CYS A 578 " pdb="FE2 SF4 B 804 " - pdb=" SG CYS A 587 " pdb="FE1 SF4 B 804 " - pdb=" SG CYS B 574 " pdb=" SF4 C 101 " pdb="FE2 SF4 C 101 " - pdb=" SG CYS C 20 " pdb="FE3 SF4 C 101 " - pdb=" SG CYS C 53 " pdb="FE4 SF4 C 101 " - pdb=" SG CYS C 47 " pdb="FE1 SF4 C 101 " - pdb=" SG CYS C 50 " pdb=" SF4 C 102 " pdb="FE2 SF4 C 102 " - pdb=" SG CYS C 16 " pdb="FE4 SF4 C 102 " - pdb=" SG CYS C 10 " pdb="FE3 SF4 C 102 " - pdb=" SG CYS C 13 " pdb="FE1 SF4 C 102 " - pdb=" SG CYS C 57 " Number of angles added : 36 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 7 sheets defined 46.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.598A pdb=" N ALA A 29 " --> pdb=" O GLU A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 37 through 40 removed outlier: 4.102A pdb=" N ARG A 40 " --> pdb=" O THR A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 40' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.751A pdb=" N ASN A 50 " --> pdb=" O TRP A 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS A 52 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 53 " --> pdb=" O ASN A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 67 through 96 removed outlier: 4.019A pdb=" N PHE A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.507A pdb=" N LEU A 126 " --> pdb=" O GLN A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.644A pdb=" N ARG A 148 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.516A pdb=" N ILE A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 190 No H-bonds generated for 'chain 'A' and resid 187 through 190' Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.752A pdb=" N HIS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 212 through 218 removed outlier: 3.890A pdb=" N ILE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.646A pdb=" N ASP A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 265 through 268 No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.712A pdb=" N ALA A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.534A pdb=" N LEU A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 348 No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 355 through 361 removed outlier: 4.022A pdb=" N LEU A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.563A pdb=" N ILE A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 418 removed outlier: 3.664A pdb=" N PHE A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 411 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 415 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.866A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 467 removed outlier: 4.305A pdb=" N HIS A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.946A pdb=" N ASN A 492 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 533 through 558 removed outlier: 3.762A pdb=" N HIS A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 572 No H-bonds generated for 'chain 'A' and resid 569 through 572' Processing helix chain 'A' and resid 592 through 620 removed outlier: 3.654A pdb=" N LEU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 608 " --> pdb=" O ASN A 604 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 642 No H-bonds generated for 'chain 'A' and resid 639 through 642' Processing helix chain 'A' and resid 646 through 651 Processing helix chain 'A' and resid 659 through 662 No H-bonds generated for 'chain 'A' and resid 659 through 662' Processing helix chain 'A' and resid 668 through 690 removed outlier: 4.473A pdb=" N ALA A 671 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 675 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 676 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 677 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 678 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 679 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 680 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 682 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP A 683 " --> pdb=" O HIS A 680 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 684 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A 686 " --> pdb=" O TRP A 683 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 690 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 709 removed outlier: 3.755A pdb=" N GLU A 699 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 754 removed outlier: 3.563A pdb=" N ARG A 728 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 731 " --> pdb=" O GLY A 727 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 742 " --> pdb=" O GLY A 738 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 750 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.863A pdb=" N ILE B 55 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 103 No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 119 through 125 removed outlier: 3.708A pdb=" N THR B 125 " --> pdb=" O HIS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 144 removed outlier: 3.624A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.793A pdb=" N TRP B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 171 through 178 removed outlier: 3.668A pdb=" N HIS B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 192 through 195 No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.696A pdb=" N THR B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 229 through 233 removed outlier: 3.729A pdb=" N TYR B 232 " --> pdb=" O TRP B 229 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 233 " --> pdb=" O GLY B 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 233' Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.561A pdb=" N ALA B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.556A pdb=" N LEU B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.503A pdb=" N ALA B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR B 375 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 418 through 447 removed outlier: 3.587A pdb=" N SER B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 439 " --> pdb=" O HIS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.518A pdb=" N ALA B 468 " --> pdb=" O GLN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 501 through 507 removed outlier: 3.740A pdb=" N ASP B 505 " --> pdb=" O PRO B 501 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 545 removed outlier: 3.873A pdb=" N LEU B 524 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 582 No H-bonds generated for 'chain 'B' and resid 579 through 582' Processing helix chain 'B' and resid 587 through 607 removed outlier: 3.525A pdb=" N TRP B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 606 " --> pdb=" O TRP B 602 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 620 removed outlier: 3.556A pdb=" N SER B 619 " --> pdb=" O PHE B 615 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR B 620 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 627 removed outlier: 3.772A pdb=" N LEU B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 633 No H-bonds generated for 'chain 'B' and resid 630 through 633' Processing helix chain 'B' and resid 650 through 671 removed outlier: 3.899A pdb=" N LEU B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 664 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 667 " --> pdb=" O TRP B 663 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET B 668 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE B 669 " --> pdb=" O THR B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 689 removed outlier: 3.946A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 736 removed outlier: 3.501A pdb=" N ARG B 712 " --> pdb=" O ILE B 708 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 716 " --> pdb=" O ARG B 712 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 726 " --> pdb=" O GLY B 722 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 727 " --> pdb=" O TYR B 723 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 46 No H-bonds generated for 'chain 'C' and resid 44 through 46' Processing helix chain 'C' and resid 52 through 55 No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 73 through 76 No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'D' and resid 61 through 70 removed outlier: 3.558A pdb=" N LEU D 67 " --> pdb=" O GLN D 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'F' and resid 69 through 80 removed outlier: 3.640A pdb=" N ILE F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 86 No H-bonds generated for 'chain 'F' and resid 83 through 86' Processing helix chain 'I' and resid 10 through 18 Proline residue: I 16 - end of helix Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.883A pdb=" N LEU I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 25 through 33 removed outlier: 3.539A pdb=" N PHE L 30 " --> pdb=" O LEU L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 54 removed outlier: 3.886A pdb=" N GLY L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU L 49 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 53 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 63 No H-bonds generated for 'chain 'L' and resid 60 through 63' Processing helix chain 'L' and resid 76 through 99 removed outlier: 3.565A pdb=" N SER L 81 " --> pdb=" O GLY L 77 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL L 88 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY L 97 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU L 98 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 137 removed outlier: 3.579A pdb=" N VAL L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE L 133 " --> pdb=" O MET L 129 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 135 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE L 136 " --> pdb=" O ALA L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 14 removed outlier: 3.512A pdb=" N TYR M 9 " --> pdb=" O ASP M 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA M 11 " --> pdb=" O GLN M 7 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL M 13 " --> pdb=" O TYR M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 29 removed outlier: 4.074A pdb=" N PHE M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 623 through 625 Processing sheet with id= B, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.210A pdb=" N VAL A 520 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'C' and resid 26 through 29 Processing sheet with id= E, first strand: chain 'D' and resid 81 through 85 removed outlier: 3.858A pdb=" N ALA D 28 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.826A pdb=" N GLY D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 6 through 8 removed outlier: 6.898A pdb=" N ILE E 37 " --> pdb=" O ALA E 24 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1275 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: 5.61 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 9460 1.41 - 1.63: 12448 1.63 - 1.85: 118 1.85 - 2.07: 328 2.07 - 2.28: 36 Bond restraints: 22390 Sorted by residual: bond pdb=" NA CLA L1502 " pdb="MG CLA L1502 " ideal model delta sigma weight residual 2.089 1.944 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" NA CLA L1501 " pdb="MG CLA L1501 " ideal model delta sigma weight residual 2.089 1.948 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" NA CLA B 836 " pdb="MG CLA B 836 " ideal model delta sigma weight residual 2.089 1.948 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" NA CLA B 814 " pdb="MG CLA B 814 " ideal model delta sigma weight residual 2.089 1.950 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" NA CLA A 811 " pdb="MG CLA A 811 " ideal model delta sigma weight residual 2.089 1.950 0.139 2.00e-02 2.50e+03 4.85e+01 ... (remaining 22385 not shown) Histogram of bond angle deviations from ideal: 73.44 - 92.81: 361 92.81 - 112.19: 10767 112.19 - 131.57: 20080 131.57 - 150.94: 370 150.94 - 170.32: 164 Bond angle restraints: 31742 Sorted by residual: angle pdb=" C19 BCR F 201 " pdb=" C20 BCR F 201 " pdb=" C21 BCR F 201 " ideal model delta sigma weight residual 122.60 143.51 -20.91 3.00e+00 1.11e-01 4.86e+01 angle pdb=" CBD CLA A 840 " pdb=" CGD CLA A 840 " pdb=" O1D CLA A 840 " ideal model delta sigma weight residual 127.77 110.73 17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" N ILE B 55 " pdb=" CA ILE B 55 " pdb=" C ILE B 55 " ideal model delta sigma weight residual 112.96 107.36 5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" NB CLA A 812 " pdb="MG CLA A 812 " pdb=" ND CLA A 812 " ideal model delta sigma weight residual 176.90 160.79 16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" NB CLA B 829 " pdb="MG CLA B 829 " pdb=" ND CLA B 829 " ideal model delta sigma weight residual 176.90 160.84 16.06 3.00e+00 1.11e-01 2.87e+01 ... (remaining 31737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.20: 9378 24.20 - 48.41: 766 48.41 - 72.61: 219 72.61 - 96.82: 54 96.82 - 121.02: 15 Dihedral angle restraints: 10432 sinusoidal: 4797 harmonic: 5635 Sorted by residual: dihedral pdb=" CA TRP B 673 " pdb=" C TRP B 673 " pdb=" N ARG B 674 " pdb=" CA ARG B 674 " ideal model delta harmonic sigma weight residual -180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA THR B 479 " pdb=" C THR B 479 " pdb=" N LEU B 480 " pdb=" CA LEU B 480 " ideal model delta harmonic sigma weight residual -180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE C 61 " pdb=" C PHE C 61 " pdb=" N LEU C 62 " pdb=" CA LEU C 62 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 10429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2092 0.067 - 0.134: 474 0.134 - 0.201: 100 0.201 - 0.268: 38 0.268 - 0.336: 9 Chirality restraints: 2713 Sorted by residual: chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 LMG B 843 " pdb=" C2 LMG B 843 " pdb=" O1 LMG B 843 " pdb=" O6 LMG B 843 " both_signs ideal model delta sigma weight residual False 2.29 2.62 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C2 LMG B 843 " pdb=" C1 LMG B 843 " pdb=" C3 LMG B 843 " pdb=" O2 LMG B 843 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2710 not shown) Planarity restraints: 4168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CLA L1502 " -0.039 2.00e-02 2.50e+03 2.29e-01 7.83e+02 pdb=" C2A CLA L1502 " -0.330 2.00e-02 2.50e+03 pdb=" C4A CLA L1502 " 0.313 2.00e-02 2.50e+03 pdb=" CHA CLA L1502 " 0.240 2.00e-02 2.50e+03 pdb=" NA CLA L1502 " 0.032 2.00e-02 2.50e+03 pdb="MG CLA L1502 " -0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PQN B 837 " -0.071 2.00e-02 2.50e+03 1.49e-01 7.76e+02 pdb=" C10 PQN B 837 " -0.028 2.00e-02 2.50e+03 pdb=" C11 PQN B 837 " -0.269 2.00e-02 2.50e+03 pdb=" C2 PQN B 837 " 0.090 2.00e-02 2.50e+03 pdb=" C2M PQN B 837 " 0.391 2.00e-02 2.50e+03 pdb=" C3 PQN B 837 " -0.046 2.00e-02 2.50e+03 pdb=" C4 PQN B 837 " 0.011 2.00e-02 2.50e+03 pdb=" C5 PQN B 837 " 0.015 2.00e-02 2.50e+03 pdb=" C6 PQN B 837 " 0.054 2.00e-02 2.50e+03 pdb=" C7 PQN B 837 " 0.058 2.00e-02 2.50e+03 pdb=" C8 PQN B 837 " 0.019 2.00e-02 2.50e+03 pdb=" C9 PQN B 837 " -0.024 2.00e-02 2.50e+03 pdb=" O1 PQN B 837 " -0.245 2.00e-02 2.50e+03 pdb=" O4 PQN B 837 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA B 814 " 0.030 2.00e-02 2.50e+03 2.08e-01 6.51e+02 pdb=" C2A CLA B 814 " 0.302 2.00e-02 2.50e+03 pdb=" C4A CLA B 814 " -0.281 2.00e-02 2.50e+03 pdb=" CHA CLA B 814 " -0.220 2.00e-02 2.50e+03 pdb=" NA CLA B 814 " -0.031 2.00e-02 2.50e+03 pdb="MG CLA B 814 " 0.200 2.00e-02 2.50e+03 ... (remaining 4165 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4133 2.78 - 3.31: 15551 3.31 - 3.84: 33850 3.84 - 4.37: 43461 4.37 - 4.90: 74480 Nonbonded interactions: 171475 Sorted by model distance: nonbonded pdb=" OG SER A 590 " pdb=" OD1 ASP A 593 " model vdw 2.254 2.440 nonbonded pdb=" OG SER B 577 " pdb=" OD1 ASP B 580 " model vdw 2.304 2.440 nonbonded pdb=" O SER B 61 " pdb=" OG SER B 61 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR A 280 " pdb=" OG SER A 295 " model vdw 2.311 2.440 nonbonded pdb=" OD2 ASP A 386 " pdb=" OG1 THR A 389 " model vdw 2.314 2.440 ... (remaining 171470 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=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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.790 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 59.370 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 : 0.022 0.145 22390 Z= 1.157 Angle : 1.765 20.907 31742 Z= 0.647 Chirality : 0.067 0.336 2713 Planarity : 0.032 0.245 4168 Dihedral : 20.122 121.023 6842 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % 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: -5.98 (0.12), residues: 1964 helix: -4.71 (0.06), residues: 1013 sheet: -2.55 (0.65), residues: 57 loop : -2.99 (0.17), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 59 HIS 0.018 0.002 HIS A 373 PHE 0.022 0.002 PHE A 453 TYR 0.015 0.002 TYR B 723 ARG 0.008 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.916 Fit side-chains REVERT: L 49 GLU cc_start: 0.6884 (tt0) cc_final: 0.6625 (tt0) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.3683 time to fit residues: 105.8692 Evaluate side-chains 152 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 61 HIS A 135 HIS A 286 ASN A 359 ASN A 373 HIS A 542 HIS A 718 GLN B 13 GLN B 205 HIS B 639 ASN C 15 GLN D 54 ASN D 70 GLN D 71 GLN E 18 ASN E 56 ASN L 16 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22390 Z= 0.347 Angle : 0.820 14.760 31742 Z= 0.352 Chirality : 0.049 0.345 2713 Planarity : 0.007 0.066 4168 Dihedral : 19.803 111.134 3516 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.19 % Allowed : 10.38 % Favored : 88.43 % 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: -4.57 (0.15), residues: 1964 helix: -3.33 (0.11), residues: 1027 sheet: -1.97 (0.65), residues: 66 loop : -2.58 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 503 HIS 0.020 0.003 HIS A 436 PHE 0.020 0.002 PHE A 394 TYR 0.020 0.002 TYR B 599 ARG 0.002 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 2.173 Fit side-chains REVERT: A 424 MET cc_start: 0.6720 (ttm) cc_final: 0.6481 (ttp) REVERT: B 205 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7074 (t-90) REVERT: D 80 TYR cc_start: 0.8858 (p90) cc_final: 0.8605 (p90) outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 0.3620 time to fit residues: 100.1605 Evaluate side-chains 171 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain L residue 16 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 119 optimal weight: 0.0970 chunk 48 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 282 ASN A 426 GLN B 205 HIS C 15 GLN L 16 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22390 Z= 0.251 Angle : 0.705 13.665 31742 Z= 0.301 Chirality : 0.045 0.304 2713 Planarity : 0.006 0.059 4168 Dihedral : 18.425 109.615 3516 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.31 % Allowed : 13.01 % Favored : 85.68 % 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: -3.71 (0.16), residues: 1964 helix: -2.50 (0.13), residues: 1026 sheet: -1.68 (0.78), residues: 54 loop : -2.34 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.017 0.002 HIS A 135 PHE 0.017 0.002 PHE B 719 TYR 0.013 0.001 TYR B 599 ARG 0.004 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.766 Fit side-chains REVERT: A 424 MET cc_start: 0.6651 (ttm) cc_final: 0.6413 (ttp) REVERT: D 80 TYR cc_start: 0.8853 (p90) cc_final: 0.8630 (p90) outliers start: 21 outliers final: 19 residues processed: 180 average time/residue: 0.3399 time to fit residues: 96.1100 Evaluate side-chains 177 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 50 optimal weight: 0.4980 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 GLN B 49 HIS B 75 GLN B 205 HIS C 15 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22390 Z= 0.386 Angle : 0.820 15.573 31742 Z= 0.348 Chirality : 0.050 0.401 2713 Planarity : 0.007 0.057 4168 Dihedral : 18.279 109.817 3516 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.13 % Allowed : 14.32 % Favored : 83.55 % 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: -3.48 (0.17), residues: 1964 helix: -2.27 (0.14), residues: 1031 sheet: -1.39 (0.71), residues: 66 loop : -2.31 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 744 HIS 0.018 0.003 HIS A 436 PHE 0.019 0.002 PHE B 719 TYR 0.017 0.002 TYR B 583 ARG 0.003 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 2.032 Fit side-chains REVERT: A 424 MET cc_start: 0.6723 (ttm) cc_final: 0.6487 (ttp) REVERT: B 205 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7022 (t-90) outliers start: 34 outliers final: 28 residues processed: 188 average time/residue: 0.3367 time to fit residues: 100.1279 Evaluate side-chains 185 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain L residue 16 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.1980 chunk 167 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN C 15 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22390 Z= 0.174 Angle : 0.626 12.325 31742 Z= 0.267 Chirality : 0.042 0.252 2713 Planarity : 0.005 0.049 4168 Dihedral : 17.188 108.791 3516 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.44 % Allowed : 15.82 % Favored : 82.74 % 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: -2.96 (0.17), residues: 1964 helix: -1.81 (0.15), residues: 1029 sheet: -1.26 (0.81), residues: 54 loop : -2.09 (0.19), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 503 HIS 0.016 0.002 HIS B 205 PHE 0.016 0.001 PHE B 644 TYR 0.010 0.001 TYR B 583 ARG 0.002 0.000 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 172 time to evaluate : 1.855 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 188 average time/residue: 0.3359 time to fit residues: 99.5487 Evaluate side-chains 181 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 417 HIS C 15 GLN D 78 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 22390 Z= 0.546 Angle : 0.944 16.082 31742 Z= 0.402 Chirality : 0.057 0.578 2713 Planarity : 0.008 0.058 4168 Dihedral : 18.156 110.214 3516 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.75 % Allowed : 15.76 % Favored : 81.49 % Cbeta Deviations : 0.06 % 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: -3.26 (0.17), residues: 1964 helix: -2.10 (0.14), residues: 1028 sheet: -1.28 (0.70), residues: 68 loop : -2.18 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 663 HIS 0.042 0.003 HIS A 461 PHE 0.023 0.003 PHE C 61 TYR 0.017 0.002 TYR B 583 ARG 0.004 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 1.965 Fit side-chains REVERT: B 205 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.6998 (t-90) outliers start: 44 outliers final: 36 residues processed: 192 average time/residue: 0.3231 time to fit residues: 97.8276 Evaluate side-chains 191 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 446 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 56 ASN Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 0.0010 chunk 113 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 425 ASN A 718 GLN B 205 HIS C 15 GLN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22390 Z= 0.166 Angle : 0.623 11.377 31742 Z= 0.268 Chirality : 0.043 0.371 2713 Planarity : 0.005 0.052 4168 Dihedral : 17.019 108.483 3516 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.88 % Allowed : 16.70 % Favored : 81.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.18), residues: 1964 helix: -1.56 (0.15), residues: 1022 sheet: -1.17 (0.81), residues: 54 loop : -1.98 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 579 HIS 0.022 0.002 HIS A 461 PHE 0.017 0.001 PHE B 644 TYR 0.017 0.001 TYR I 5 ARG 0.002 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.948 Fit side-chains REVERT: I 29 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7780 (mp) outliers start: 30 outliers final: 24 residues processed: 184 average time/residue: 0.3367 time to fit residues: 97.1859 Evaluate side-chains 182 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain I residue 29 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 0.0060 chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 overall best weight: 3.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22390 Z= 0.246 Angle : 0.673 11.447 31742 Z= 0.289 Chirality : 0.045 0.398 2713 Planarity : 0.006 0.051 4168 Dihedral : 17.037 108.093 3516 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.13 % Allowed : 16.70 % Favored : 81.18 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1964 helix: -1.51 (0.15), residues: 1027 sheet: -1.19 (0.80), residues: 54 loop : -1.91 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.022 0.002 HIS A 461 PHE 0.018 0.002 PHE L 136 TYR 0.016 0.001 TYR D 136 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.858 Fit side-chains REVERT: I 29 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7828 (mp) outliers start: 34 outliers final: 29 residues processed: 185 average time/residue: 0.3448 time to fit residues: 99.8660 Evaluate side-chains 189 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain L residue 37 TYR Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22390 Z= 0.142 Angle : 0.577 10.918 31742 Z= 0.249 Chirality : 0.041 0.339 2713 Planarity : 0.005 0.048 4168 Dihedral : 16.369 101.414 3516 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.63 % Allowed : 17.45 % Favored : 80.93 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.18), residues: 1964 helix: -1.13 (0.16), residues: 1014 sheet: -0.96 (0.82), residues: 54 loop : -1.76 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 579 HIS 0.020 0.001 HIS A 461 PHE 0.017 0.001 PHE B 644 TYR 0.016 0.001 TYR I 5 ARG 0.002 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 173 time to evaluate : 1.823 Fit side-chains REVERT: B 386 MET cc_start: 0.9182 (mmm) cc_final: 0.8859 (mmt) outliers start: 26 outliers final: 26 residues processed: 193 average time/residue: 0.3353 time to fit residues: 101.2443 Evaluate side-chains 193 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain L residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 chunk 153 optimal weight: 0.0870 chunk 15 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 4.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22390 Z= 0.307 Angle : 0.716 11.517 31742 Z= 0.309 Chirality : 0.047 0.404 2713 Planarity : 0.006 0.050 4168 Dihedral : 16.926 98.051 3516 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.94 % Allowed : 17.39 % Favored : 80.68 % Cbeta Deviations : 0.06 % 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: -2.41 (0.18), residues: 1964 helix: -1.38 (0.15), residues: 1029 sheet: -1.00 (0.73), residues: 66 loop : -1.81 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 59 HIS 0.023 0.002 HIS A 461 PHE 0.019 0.002 PHE A 267 TYR 0.017 0.002 TYR D 136 ARG 0.005 0.000 ARG C 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.800 Fit side-chains REVERT: I 29 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (mp) outliers start: 31 outliers final: 29 residues processed: 186 average time/residue: 0.3288 time to fit residues: 96.6218 Evaluate side-chains 191 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 574 CYS Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 582 PHE Chi-restraints excluded: chain B residue 735 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain L residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 ASN ** 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 = 0.3435 r_free = 0.3435 target = 0.133852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.111893 restraints weight = 26607.529| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.07 r_work: 0.2876 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22390 Z= 0.192 Angle : 0.627 17.775 31742 Z= 0.272 Chirality : 0.043 0.360 2713 Planarity : 0.005 0.049 4168 Dihedral : 16.452 92.545 3516 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.00 % Allowed : 17.76 % Favored : 80.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1964 helix: -1.17 (0.16), residues: 1026 sheet: -1.02 (0.81), residues: 54 loop : -1.74 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 697 HIS 0.021 0.002 HIS A 461 PHE 0.018 0.001 PHE A 267 TYR 0.022 0.001 TYR D 136 ARG 0.003 0.000 ARG C 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.73 seconds wall clock time: 63 minutes 45.54 seconds (3825.54 seconds total)