Starting phenix.real_space_refine on Thu Feb 22 16:52:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o1v_12697/02_2024/7o1v_12697_updated.pdb" } resolution = 4.31 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14030 atoms to isotropic. 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 5 5.49 5 Mg 88 5.21 5 S 77 5.16 5 C 14809 2.51 5 N 2821 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 67": "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: 20914 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5787 Classifications: {'peptide': 739} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 706} Chain: "B" Number of atoms: 5770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5770 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 699} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 600 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1102 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 130} Chain: "E" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 579 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 80, 573 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 80, 573 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 76} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 577 Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 238 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "A" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 2915 Unusual residues: {'BCR': 7, 'CLA': 44, 'LHG': 2, 'LMG': 1, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 56} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 505 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'CLA:plan-5': 9} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 3049 Unusual residues: {'BCR': 7, 'CLA': 42, 'ECH': 1, 'LHG': 2, 'LMG': 2, 'PQN': 1, 'SQD': 1} Classifications: {'undetermined': 56} Link IDs: {None: 55} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 22 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: "K" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 225 Unusual residues: {'BCR': 1, 'CLA': 2, 'LMG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'ECH': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10172 SG CYS B 565 52.260 54.264 69.749 1.00 76.47 S ATOM 4460 SG CYS A 583 55.090 51.432 65.757 1.00 76.47 S ATOM 4405 SG CYS A 574 51.382 53.937 62.737 1.00 76.47 S ATOM 10117 SG CYS B 556 49.046 49.708 66.761 1.00 76.47 S ATOM 11924 SG CYS C 51 46.989 46.605 55.869 1.00 76.47 S ATOM 11705 SG CYS C 21 43.836 44.434 52.400 1.00 84.93 S ATOM 11950 SG CYS C 54 41.602 45.907 55.559 1.00 80.98 S ATOM 11907 SG CYS C 48 44.453 40.300 57.240 1.00 86.60 S ATOM 11977 SG CYS C 58 32.877 51.403 57.772 1.00 80.34 S ATOM 11676 SG CYS C 17 35.764 47.099 54.893 1.00 95.90 S ATOM 11654 SG CYS C 14 32.602 52.201 52.888 1.00 99.11 S ATOM 11636 SG CYS C 11 29.055 46.822 54.499 1.00 94.23 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS K 27 " occ=0.25 ... (10 atoms not shown) pdb=" SG BCYS K 27 " occ=0.75 Time building chain proxies: 10.96, per 1000 atoms: 0.52 Number of scatterers: 20914 At special positions: 0 Unit cell: (124.92, 124.087, 149.071, 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 77 16.00 P 5 15.00 Mg 88 11.99 O 3102 8.00 N 2821 7.00 C 14809 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=28, symmetry=0 Number of additional bonds: simple=28, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A3001 " pdb="FE2 SF4 A3001 " - pdb=" SG CYS A 583 " pdb="FE4 SF4 A3001 " - pdb=" SG CYS B 556 " pdb="FE3 SF4 A3001 " - pdb=" SG CYS A 574 " pdb="FE1 SF4 A3001 " - pdb=" SG CYS B 565 " pdb=" SF4 C3002 " pdb="FE2 SF4 C3002 " - pdb=" SG CYS C 21 " pdb="FE1 SF4 C3002 " - pdb=" SG CYS C 51 " pdb="FE3 SF4 C3002 " - pdb=" SG CYS C 54 " pdb="FE4 SF4 C3002 " - pdb=" SG CYS C 48 " pdb=" SF4 C3003 " pdb="FE4 SF4 C3003 " - pdb=" SG CYS C 11 " pdb="FE1 SF4 C3003 " - pdb=" SG CYS C 58 " pdb="FE3 SF4 C3003 " - pdb=" SG CYS C 14 " pdb="FE2 SF4 C3003 " - pdb=" SG CYS C 17 " Number of angles added : 36 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 75 helices and 6 sheets defined 51.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 65 through 96 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 155 through 181 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.819A pdb=" N GLY A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 261 through 264 No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 290 through 309 removed outlier: 4.469A pdb=" N HIS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 348 through 370 Processing helix chain 'A' and resid 383 through 413 Processing helix chain 'A' and resid 425 through 431 Processing helix chain 'A' and resid 433 through 464 removed outlier: 3.575A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 481 through 496 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 529 through 556 removed outlier: 3.929A pdb=" N ALA A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 587 through 615 removed outlier: 4.161A pdb=" N PHE A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 651 through 658 removed outlier: 3.825A pdb=" N ALA A 655 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 687 removed outlier: 3.899A pdb=" N LEU A 683 " --> pdb=" O PHE A 679 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 Processing helix chain 'A' and resid 720 through 748 Processing helix chain 'B' and resid 10 through 12 No H-bonds generated for 'chain 'B' and resid 10 through 12' Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 39 through 70 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 132 through 157 removed outlier: 3.914A pdb=" N LEU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 184 through 196 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 270 through 287 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 321 through 324 No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 328 through 350 Processing helix chain 'B' and resid 363 through 394 Processing helix chain 'B' and resid 405 through 444 removed outlier: 5.657A pdb=" N GLU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 444 " --> pdb=" O VAL B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 456 through 464 Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 511 through 536 Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 569 through 600 removed outlier: 4.455A pdb=" N PHE B 578 " --> pdb=" O TYR B 574 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TRP B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.663A pdb=" N SER B 610 " --> pdb=" O PHE B 606 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N THR B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 623 through 632 removed outlier: 4.394A pdb=" N GLN B 627 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 628 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 629 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 630 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 631 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR B 632 " --> pdb=" O ILE B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 662 removed outlier: 4.577A pdb=" N PHE B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 681 Processing helix chain 'B' and resid 699 through 729 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'K' and resid 27 through 38 Processing helix chain 'K' and resid 63 through 84 Processing helix chain 'M' and resid 5 through 30 removed outlier: 4.754A pdb=" N LEU M 17 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Proline residue: M 18 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 16 through 18 Processing sheet with id= B, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= C, first strand: chain 'C' and resid 26 through 30 Processing sheet with id= D, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.519A pdb=" N TRP D 32 " --> pdb=" O ASN D 55 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N HIS D 98 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG D 87 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TYR D 96 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR D 89 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 94 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 39 through 41 Processing sheet with id= F, first strand: chain 'E' and resid 66 through 68 removed outlier: 6.743A pdb=" N ILE E 38 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN E 59 " --> pdb=" O VAL E 39 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 2010 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: 5.34 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 9159 1.42 - 1.64: 12454 1.64 - 1.86: 110 1.86 - 2.08: 176 2.08 - 2.30: 212 Bond restraints: 22111 Sorted by residual: bond pdb=" C42 LMG B5002 " pdb=" C43 LMG B5002 " ideal model delta sigma weight residual 1.526 1.327 0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C36 LMG K5009 " pdb=" C37 LMG K5009 " ideal model delta sigma weight residual 1.526 1.329 0.197 2.00e-02 2.50e+03 9.75e+01 bond pdb=" C42 LMG K5009 " pdb=" C43 LMG K5009 " ideal model delta sigma weight residual 1.526 1.329 0.197 2.00e-02 2.50e+03 9.66e+01 bond pdb=" C39 LMG B5002 " pdb=" C40 LMG B5002 " ideal model delta sigma weight residual 1.523 1.327 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C36 LMG B5002 " pdb=" C37 LMG B5002 " ideal model delta sigma weight residual 1.526 1.330 0.196 2.00e-02 2.50e+03 9.59e+01 ... (remaining 22106 not shown) Histogram of bond angle deviations from ideal: 73.32 - 94.64: 392 94.64 - 115.96: 14191 115.96 - 137.28: 16333 137.28 - 158.60: 239 158.60 - 179.92: 203 Bond angle restraints: 31358 Sorted by residual: angle pdb=" C10 BCR B4017 " pdb=" C11 BCR B4017 " pdb=" C12 BCR B4017 " ideal model delta sigma weight residual 122.66 179.92 -57.26 3.00e+00 1.11e-01 3.64e+02 angle pdb=" C10 BCR A4008 " pdb=" C11 BCR A4008 " pdb=" C12 BCR A4008 " ideal model delta sigma weight residual 122.66 178.84 -56.18 3.00e+00 1.11e-01 3.51e+02 angle pdb=" C10 BCR A4001 " pdb=" C11 BCR A4001 " pdb=" C12 BCR A4001 " ideal model delta sigma weight residual 122.66 178.50 -55.84 3.00e+00 1.11e-01 3.46e+02 angle pdb=" C10 BCR B4011 " pdb=" C11 BCR B4011 " pdb=" C12 BCR B4011 " ideal model delta sigma weight residual 122.66 178.09 -55.43 3.00e+00 1.11e-01 3.41e+02 angle pdb=" C10 BCR A4019 " pdb=" C11 BCR A4019 " pdb=" C12 BCR A4019 " ideal model delta sigma weight residual 122.66 177.90 -55.24 3.00e+00 1.11e-01 3.39e+02 ... (remaining 31353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 8640 21.96 - 43.91: 1146 43.91 - 65.87: 406 65.87 - 87.83: 53 87.83 - 109.79: 19 Dihedral angle restraints: 10264 sinusoidal: 4953 harmonic: 5311 Sorted by residual: dihedral pdb=" CA TRP B 664 " pdb=" C TRP B 664 " pdb=" N ARG B 665 " pdb=" CA ARG B 665 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG A 560 " pdb=" C ARG A 560 " pdb=" N LEU A 561 " pdb=" CA LEU A 561 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA MET A 310 " pdb=" C MET A 310 " pdb=" N TYR A 311 " pdb=" CA TYR A 311 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 10261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 2521 0.177 - 0.355: 45 0.355 - 0.532: 10 0.532 - 0.710: 65 0.710 - 0.887: 13 Chirality restraints: 2654 Sorted by residual: chirality pdb=" C3A CLA A1139 " pdb=" C2A CLA A1139 " pdb=" C4A CLA A1139 " pdb=" CMA CLA A1139 " both_signs ideal model delta sigma weight residual False -2.76 -1.88 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" C3A CLA B1223 " pdb=" C2A CLA B1223 " pdb=" C4A CLA B1223 " pdb=" CMA CLA B1223 " both_signs ideal model delta sigma weight residual False -2.76 -1.97 -0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" C3A CLA A1113 " pdb=" C2A CLA A1113 " pdb=" C4A CLA A1113 " pdb=" CMA CLA A1113 " both_signs ideal model delta sigma weight residual False -2.76 -2.00 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 2651 not shown) Planarity restraints: 4080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BCR B4017 " -0.349 2.00e-02 2.50e+03 2.00e-01 5.01e+02 pdb=" C11 BCR B4017 " 0.235 2.00e-02 2.50e+03 pdb=" C34 BCR B4017 " 0.088 2.00e-02 2.50e+03 pdb=" C8 BCR B4017 " 0.100 2.00e-02 2.50e+03 pdb=" C9 BCR B4017 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR A4003 " -0.345 2.00e-02 2.50e+03 1.98e-01 4.92e+02 pdb=" C11 BCR A4003 " 0.234 2.00e-02 2.50e+03 pdb=" C34 BCR A4003 " 0.043 2.00e-02 2.50e+03 pdb=" C8 BCR A4003 " 0.131 2.00e-02 2.50e+03 pdb=" C9 BCR A4003 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BCR B4004 " -0.343 2.00e-02 2.50e+03 1.95e-01 4.76e+02 pdb=" C11 BCR B4004 " 0.228 2.00e-02 2.50e+03 pdb=" C34 BCR B4004 " 0.086 2.00e-02 2.50e+03 pdb=" C8 BCR B4004 " 0.096 2.00e-02 2.50e+03 pdb=" C9 BCR B4004 " -0.067 2.00e-02 2.50e+03 ... (remaining 4077 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1672 2.75 - 3.28: 18178 3.28 - 3.82: 37027 3.82 - 4.36: 40468 4.36 - 4.90: 69042 Nonbonded interactions: 166387 Sorted by model distance: nonbonded pdb=" O GLN A 351 " pdb=" ND2 ASN A 355 " model vdw 2.207 2.520 nonbonded pdb=" OD2 ASP C 61 " pdb=" OG SER E 16 " model vdw 2.228 2.440 nonbonded pdb=" O GLY B 558 " pdb=" OG1 THR B 564 " model vdw 2.241 2.440 nonbonded pdb=" OG SER A 719 " pdb=" OG SER E 50 " model vdw 2.267 2.440 nonbonded pdb=" O GLU A 342 " pdb=" OG1 THR A 346 " model vdw 2.290 2.440 ... (remaining 166382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 5.980 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 55.070 Find NCS groups from input model: 0.550 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.025 0.199 22111 Z= 1.296 Angle : 2.769 57.257 31358 Z= 0.979 Chirality : 0.132 0.887 2654 Planarity : 0.016 0.200 4080 Dihedral : 21.507 109.785 6882 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 0.80 % Favored : 99.13 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 1858 helix: -0.38 (0.15), residues: 1000 sheet: -0.69 (0.71), residues: 61 loop : -2.06 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 668 HIS 0.030 0.002 HIS A 608 PHE 0.035 0.003 PHE B 589 TYR 0.056 0.003 TYR A 661 ARG 0.013 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7224 (tp30) cc_final: 0.6722 (mm-30) REVERT: A 192 ASN cc_start: 0.8504 (t0) cc_final: 0.8050 (t0) REVERT: A 241 GLU cc_start: 0.7584 (pp20) cc_final: 0.6507 (tp30) REVERT: A 244 LEU cc_start: 0.8787 (tt) cc_final: 0.8307 (mt) REVERT: A 338 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7484 (pttp) REVERT: A 606 ILE cc_start: 0.9159 (pt) cc_final: 0.8947 (pt) REVERT: A 613 MET cc_start: 0.8693 (mtp) cc_final: 0.8333 (mtm) REVERT: A 684 MET cc_start: 0.6889 (tpp) cc_final: 0.5531 (tpp) REVERT: B 169 LYS cc_start: 0.7613 (tppt) cc_final: 0.7317 (tppt) REVERT: B 589 PHE cc_start: 0.8790 (m-80) cc_final: 0.8580 (m-80) REVERT: C 39 ILE cc_start: 0.8711 (tt) cc_final: 0.8378 (tt) REVERT: D 1 MET cc_start: 0.5212 (tmm) cc_final: 0.4452 (tmm) REVERT: D 49 ILE cc_start: 0.8630 (mt) cc_final: 0.8347 (tp) REVERT: D 57 LEU cc_start: 0.7823 (tt) cc_final: 0.7613 (tt) REVERT: E 7 ASP cc_start: 0.5964 (m-30) cc_final: 0.5296 (t0) REVERT: E 8 LYS cc_start: 0.7714 (ttmm) cc_final: 0.6979 (ttmt) REVERT: K 38 TYR cc_start: 0.5462 (t80) cc_final: 0.5030 (t80) REVERT: K 70 MET cc_start: 0.7122 (ttt) cc_final: 0.6712 (ttp) REVERT: M 9 LEU cc_start: 0.8693 (mm) cc_final: 0.7969 (tt) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.3011 time to fit residues: 176.7913 Evaluate side-chains 300 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 224 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 679 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22111 Z= 0.170 Angle : 0.665 10.707 31358 Z= 0.286 Chirality : 0.043 0.183 2654 Planarity : 0.005 0.066 4080 Dihedral : 20.684 89.417 3749 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 0.20 % Allowed : 5.13 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.19), residues: 1858 helix: 0.57 (0.16), residues: 986 sheet: -1.49 (0.57), residues: 82 loop : -1.79 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 190 HIS 0.018 0.002 HIS A 543 PHE 0.027 0.002 PHE A 84 TYR 0.018 0.001 TYR B 574 ARG 0.004 0.000 ARG D 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 375 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7340 (m-30) cc_final: 0.7019 (m-30) REVERT: A 66 GLU cc_start: 0.7077 (tp30) cc_final: 0.6854 (tp30) REVERT: A 192 ASN cc_start: 0.8409 (t0) cc_final: 0.7917 (t0) REVERT: A 197 MET cc_start: 0.8450 (mmm) cc_final: 0.7938 (tmm) REVERT: A 241 GLU cc_start: 0.7648 (pp20) cc_final: 0.6662 (tt0) REVERT: A 244 LEU cc_start: 0.8854 (tt) cc_final: 0.8407 (mt) REVERT: A 300 ILE cc_start: 0.9177 (tp) cc_final: 0.8972 (tp) REVERT: A 312 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7222 (ttm170) REVERT: A 352 LEU cc_start: 0.8662 (tt) cc_final: 0.8316 (tt) REVERT: A 478 LEU cc_start: 0.9081 (mp) cc_final: 0.8853 (mp) REVERT: A 532 PHE cc_start: 0.9177 (t80) cc_final: 0.8538 (t80) REVERT: A 719 SER cc_start: 0.8800 (t) cc_final: 0.8585 (m) REVERT: B 326 ASN cc_start: 0.7860 (m-40) cc_final: 0.7512 (t0) REVERT: B 659 MET cc_start: 0.7348 (tpp) cc_final: 0.7011 (tpp) REVERT: C 39 ILE cc_start: 0.8737 (tt) cc_final: 0.8479 (tt) REVERT: C 47 ASP cc_start: 0.7985 (m-30) cc_final: 0.7669 (m-30) REVERT: D 49 ILE cc_start: 0.8515 (mt) cc_final: 0.8265 (tp) REVERT: D 55 ASN cc_start: 0.8347 (m-40) cc_final: 0.8072 (m-40) REVERT: D 122 ILE cc_start: 0.6878 (mm) cc_final: 0.6429 (tp) REVERT: E 7 ASP cc_start: 0.5783 (m-30) cc_final: 0.5260 (t0) REVERT: E 8 LYS cc_start: 0.7613 (ttmm) cc_final: 0.6882 (ttmt) REVERT: E 43 ARG cc_start: 0.8306 (mtm180) cc_final: 0.8072 (mtm180) REVERT: K 38 TYR cc_start: 0.5499 (t80) cc_final: 0.4925 (t80) REVERT: K 43 LYS cc_start: 0.6731 (pttm) cc_final: 0.5590 (pttm) REVERT: K 70 MET cc_start: 0.7212 (ttt) cc_final: 0.6815 (ttp) outliers start: 3 outliers final: 1 residues processed: 376 average time/residue: 0.2891 time to fit residues: 174.9134 Evaluate side-chains 306 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 167 optimal weight: 0.0870 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 224 ASN A 355 ASN A 458 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 ASN B 609 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22111 Z= 0.236 Angle : 0.657 10.228 31358 Z= 0.291 Chirality : 0.044 0.191 2654 Planarity : 0.005 0.062 4080 Dihedral : 19.341 89.866 3749 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1858 helix: 0.74 (0.16), residues: 997 sheet: -1.47 (0.57), residues: 82 loop : -1.65 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 693 HIS 0.014 0.002 HIS B 412 PHE 0.026 0.002 PHE B 429 TYR 0.022 0.001 TYR B 574 ARG 0.004 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8477 (ppp) cc_final: 0.8151 (ppp) REVERT: A 192 ASN cc_start: 0.8758 (t0) cc_final: 0.8305 (t0) REVERT: A 197 MET cc_start: 0.8425 (mmm) cc_final: 0.8175 (tmm) REVERT: A 244 LEU cc_start: 0.8776 (tt) cc_final: 0.8429 (mt) REVERT: A 310 MET cc_start: 0.8938 (tpp) cc_final: 0.8303 (mmm) REVERT: A 311 TYR cc_start: 0.8744 (m-80) cc_final: 0.8460 (m-10) REVERT: A 338 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7524 (pttp) REVERT: A 352 LEU cc_start: 0.8700 (tt) cc_final: 0.8358 (tt) REVERT: A 478 LEU cc_start: 0.9046 (mp) cc_final: 0.8786 (mp) REVERT: A 598 MET cc_start: 0.8896 (tmm) cc_final: 0.8643 (tmm) REVERT: A 613 MET cc_start: 0.8873 (mtp) cc_final: 0.8454 (mtp) REVERT: A 684 MET cc_start: 0.8712 (tpp) cc_final: 0.8162 (tpp) REVERT: A 744 LEU cc_start: 0.8783 (mp) cc_final: 0.8552 (mp) REVERT: B 324 ILE cc_start: 0.8840 (mp) cc_final: 0.8615 (mm) REVERT: B 372 HIS cc_start: 0.8574 (t-90) cc_final: 0.8246 (t70) REVERT: B 582 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7798 (t0) REVERT: B 659 MET cc_start: 0.7561 (tpp) cc_final: 0.7167 (ttt) REVERT: C 47 ASP cc_start: 0.8248 (m-30) cc_final: 0.7713 (m-30) REVERT: C 68 TYR cc_start: 0.8715 (m-80) cc_final: 0.8276 (m-10) REVERT: C 75 ARG cc_start: 0.8013 (tpt-90) cc_final: 0.7701 (tpt170) REVERT: D 42 MET cc_start: 0.8989 (ttt) cc_final: 0.8746 (ttt) REVERT: D 49 ILE cc_start: 0.8567 (mt) cc_final: 0.8203 (tp) REVERT: D 55 ASN cc_start: 0.8361 (m-40) cc_final: 0.8027 (m-40) REVERT: D 72 LEU cc_start: 0.8503 (mp) cc_final: 0.8275 (mp) REVERT: D 122 ILE cc_start: 0.6809 (mm) cc_final: 0.6569 (tp) REVERT: E 7 ASP cc_start: 0.5804 (m-30) cc_final: 0.5293 (t0) REVERT: E 8 LYS cc_start: 0.7552 (ttmm) cc_final: 0.6681 (ttmt) REVERT: E 43 ARG cc_start: 0.8412 (mtm180) cc_final: 0.8076 (mtm180) REVERT: K 38 TYR cc_start: 0.5506 (t80) cc_final: 0.4916 (t80) REVERT: K 58 LYS cc_start: 0.4315 (ptpp) cc_final: 0.3839 (ptpp) REVERT: M 5 ASP cc_start: 0.7663 (p0) cc_final: 0.7313 (p0) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.3390 time to fit residues: 199.9048 Evaluate side-chains 291 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 355 ASN A 457 HIS ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 ASN K 74 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22111 Z= 0.203 Angle : 0.616 10.226 31358 Z= 0.274 Chirality : 0.042 0.175 2654 Planarity : 0.004 0.058 4080 Dihedral : 18.912 88.010 3749 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.19), residues: 1858 helix: 0.90 (0.16), residues: 990 sheet: -1.45 (0.58), residues: 84 loop : -1.53 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 693 HIS 0.013 0.001 HIS B 412 PHE 0.032 0.002 PHE A 84 TYR 0.021 0.001 TYR B 574 ARG 0.005 0.000 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 378 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASN cc_start: 0.8644 (t0) cc_final: 0.8132 (t0) REVERT: A 244 LEU cc_start: 0.8760 (tt) cc_final: 0.8417 (mt) REVERT: A 292 ASP cc_start: 0.8394 (m-30) cc_final: 0.8124 (m-30) REVERT: A 310 MET cc_start: 0.9048 (tpp) cc_final: 0.8621 (mmm) REVERT: A 338 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7532 (pttp) REVERT: A 352 LEU cc_start: 0.8698 (tt) cc_final: 0.8360 (tt) REVERT: A 394 MET cc_start: 0.8924 (mmm) cc_final: 0.8693 (mtp) REVERT: A 568 LEU cc_start: 0.8710 (mp) cc_final: 0.8499 (mp) REVERT: A 598 MET cc_start: 0.8839 (tmm) cc_final: 0.8490 (tmm) REVERT: A 684 MET cc_start: 0.8758 (tpp) cc_final: 0.7954 (tpp) REVERT: B 142 LEU cc_start: 0.9407 (mp) cc_final: 0.9045 (tp) REVERT: B 201 GLU cc_start: 0.5385 (mm-30) cc_final: 0.5078 (mm-30) REVERT: B 290 MET cc_start: 0.7387 (tmm) cc_final: 0.6965 (tmm) REVERT: B 372 HIS cc_start: 0.8549 (t-90) cc_final: 0.7614 (t-170) REVERT: D 1 MET cc_start: 0.4121 (tpp) cc_final: 0.3674 (tpt) REVERT: D 49 ILE cc_start: 0.8565 (mt) cc_final: 0.8199 (tp) REVERT: D 55 ASN cc_start: 0.8243 (m-40) cc_final: 0.7906 (m-40) REVERT: D 57 LEU cc_start: 0.7578 (tt) cc_final: 0.7265 (tt) REVERT: D 72 LEU cc_start: 0.8521 (mp) cc_final: 0.8257 (mp) REVERT: E 7 ASP cc_start: 0.5811 (m-30) cc_final: 0.5374 (t0) REVERT: E 8 LYS cc_start: 0.7534 (ttmm) cc_final: 0.6625 (ttmt) REVERT: E 43 ARG cc_start: 0.8382 (mtm180) cc_final: 0.8124 (mtm180) REVERT: E 52 SER cc_start: 0.8326 (m) cc_final: 0.8106 (m) REVERT: K 38 TYR cc_start: 0.5463 (t80) cc_final: 0.4836 (t80) REVERT: M 5 ASP cc_start: 0.7692 (p0) cc_final: 0.7344 (p0) REVERT: M 28 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7793 (tm-30) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.2886 time to fit residues: 174.9185 Evaluate side-chains 293 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN K 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22111 Z= 0.288 Angle : 0.694 12.772 31358 Z= 0.307 Chirality : 0.046 0.223 2654 Planarity : 0.005 0.055 4080 Dihedral : 18.817 81.390 3749 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1858 helix: 0.82 (0.16), residues: 999 sheet: -1.35 (0.57), residues: 88 loop : -1.52 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 570 HIS 0.019 0.002 HIS A 608 PHE 0.023 0.002 PHE B 647 TYR 0.024 0.002 TYR B 574 ARG 0.005 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8607 (ppp) cc_final: 0.8133 (ppp) REVERT: A 241 GLU cc_start: 0.7849 (pp20) cc_final: 0.7605 (pp20) REVERT: A 244 LEU cc_start: 0.8768 (tt) cc_final: 0.8460 (mt) REVERT: A 352 LEU cc_start: 0.8742 (tt) cc_final: 0.8415 (tt) REVERT: A 412 MET cc_start: 0.8943 (tpp) cc_final: 0.8672 (tpt) REVERT: A 434 ASP cc_start: 0.8786 (p0) cc_final: 0.7746 (p0) REVERT: A 584 GLN cc_start: 0.8738 (mt0) cc_final: 0.8083 (mp10) REVERT: A 598 MET cc_start: 0.9035 (tmm) cc_final: 0.8697 (tmm) REVERT: A 613 MET cc_start: 0.8669 (mtp) cc_final: 0.8355 (mtp) REVERT: A 684 MET cc_start: 0.8719 (tpp) cc_final: 0.8367 (tpp) REVERT: B 262 HIS cc_start: 0.7955 (t-170) cc_final: 0.7457 (t70) REVERT: B 290 MET cc_start: 0.7666 (tmm) cc_final: 0.7304 (tmm) REVERT: B 348 GLN cc_start: 0.9019 (tt0) cc_final: 0.8791 (tt0) REVERT: B 372 HIS cc_start: 0.8603 (t-90) cc_final: 0.8298 (t70) REVERT: B 659 MET cc_start: 0.7709 (ttt) cc_final: 0.6735 (ttp) REVERT: C 47 ASP cc_start: 0.8703 (m-30) cc_final: 0.8333 (m-30) REVERT: D 42 MET cc_start: 0.9197 (ttt) cc_final: 0.8866 (ttt) REVERT: D 57 LEU cc_start: 0.7721 (tt) cc_final: 0.7244 (tt) REVERT: E 8 LYS cc_start: 0.7560 (ttmm) cc_final: 0.7251 (ttmt) REVERT: E 18 TRP cc_start: 0.8176 (m-10) cc_final: 0.7585 (m-10) REVERT: E 52 SER cc_start: 0.8323 (m) cc_final: 0.8082 (m) REVERT: K 38 TYR cc_start: 0.5468 (t80) cc_final: 0.4742 (t80) REVERT: M 5 ASP cc_start: 0.7879 (p0) cc_final: 0.7649 (p0) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.3112 time to fit residues: 178.2142 Evaluate side-chains 286 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 104 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.3980 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN A 224 ASN A 355 ASN A 458 ASN ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 366 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 22111 Z= 0.147 Angle : 0.598 10.183 31358 Z= 0.265 Chirality : 0.041 0.173 2654 Planarity : 0.004 0.053 4080 Dihedral : 18.124 82.892 3749 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 0.07 % Allowed : 2.13 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1858 helix: 1.14 (0.17), residues: 988 sheet: -1.53 (0.55), residues: 90 loop : -1.43 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 591 HIS 0.016 0.001 HIS B 412 PHE 0.036 0.002 PHE B 429 TYR 0.019 0.001 TYR B 574 ARG 0.006 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7295 (tp30) cc_final: 0.6785 (mm-30) REVERT: A 168 MET cc_start: 0.8396 (ppp) cc_final: 0.7986 (ppp) REVERT: A 192 ASN cc_start: 0.8582 (t0) cc_final: 0.8079 (t0) REVERT: A 244 LEU cc_start: 0.8703 (tt) cc_final: 0.8412 (mt) REVERT: A 251 GLU cc_start: 0.6823 (pt0) cc_final: 0.6573 (tp30) REVERT: A 292 ASP cc_start: 0.8406 (m-30) cc_final: 0.8148 (m-30) REVERT: A 310 MET cc_start: 0.9045 (tpp) cc_final: 0.8764 (mmm) REVERT: A 338 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7582 (pttp) REVERT: A 352 LEU cc_start: 0.8586 (tt) cc_final: 0.8195 (tt) REVERT: A 598 MET cc_start: 0.8900 (tmm) cc_final: 0.8253 (tmm) REVERT: A 613 MET cc_start: 0.8684 (mtp) cc_final: 0.8310 (mtm) REVERT: A 684 MET cc_start: 0.8087 (tpp) cc_final: 0.7833 (tpp) REVERT: B 262 HIS cc_start: 0.7888 (t-170) cc_final: 0.7482 (t70) REVERT: B 348 GLN cc_start: 0.8781 (tt0) cc_final: 0.8540 (tt0) REVERT: B 372 HIS cc_start: 0.8424 (t-90) cc_final: 0.8106 (t70) REVERT: B 582 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7326 (t0) REVERT: C 47 ASP cc_start: 0.8492 (m-30) cc_final: 0.7993 (m-30) REVERT: C 77 MET cc_start: 0.7807 (tpp) cc_final: 0.7587 (tpp) REVERT: D 42 MET cc_start: 0.9191 (ttt) cc_final: 0.8895 (ttm) REVERT: D 49 ILE cc_start: 0.8589 (mt) cc_final: 0.8228 (tp) REVERT: D 57 LEU cc_start: 0.7654 (tt) cc_final: 0.7098 (tt) REVERT: E 15 GLU cc_start: 0.6905 (mp0) cc_final: 0.6646 (mp0) REVERT: K 38 TYR cc_start: 0.5384 (t80) cc_final: 0.4762 (t80) REVERT: M 5 ASP cc_start: 0.7771 (p0) cc_final: 0.7567 (p0) outliers start: 1 outliers final: 0 residues processed: 380 average time/residue: 0.2898 time to fit residues: 177.3752 Evaluate side-chains 292 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 355 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 HIS ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 582 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 22111 Z= 0.317 Angle : 0.722 13.568 31358 Z= 0.321 Chirality : 0.047 0.240 2654 Planarity : 0.005 0.057 4080 Dihedral : 18.347 81.177 3749 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.19), residues: 1858 helix: 0.87 (0.16), residues: 993 sheet: -1.54 (0.55), residues: 90 loop : -1.45 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 190 HIS 0.015 0.002 HIS B 412 PHE 0.023 0.002 PHE A 743 TYR 0.028 0.002 TYR A 661 ARG 0.007 0.001 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 359 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ILE cc_start: 0.8027 (pt) cc_final: 0.7737 (pt) REVERT: A 168 MET cc_start: 0.8516 (ppp) cc_final: 0.8285 (ppp) REVERT: A 244 LEU cc_start: 0.8736 (tt) cc_final: 0.8373 (mp) REVERT: A 352 LEU cc_start: 0.8723 (tt) cc_final: 0.8440 (tt) REVERT: A 412 MET cc_start: 0.8921 (tpp) cc_final: 0.8417 (tpp) REVERT: A 584 GLN cc_start: 0.8775 (mt0) cc_final: 0.8276 (mt0) REVERT: A 598 MET cc_start: 0.9094 (tmm) cc_final: 0.8757 (tmm) REVERT: A 613 MET cc_start: 0.8757 (mtp) cc_final: 0.8461 (mtp) REVERT: B 23 TYR cc_start: 0.7833 (m-80) cc_final: 0.7611 (m-80) REVERT: B 262 HIS cc_start: 0.8326 (t70) cc_final: 0.7831 (t70) REVERT: B 348 GLN cc_start: 0.9055 (tt0) cc_final: 0.8699 (tt0) REVERT: C 47 ASP cc_start: 0.8562 (m-30) cc_final: 0.8332 (m-30) REVERT: D 57 LEU cc_start: 0.7797 (tt) cc_final: 0.7275 (tt) REVERT: D 72 LEU cc_start: 0.8546 (mp) cc_final: 0.8278 (mp) REVERT: E 3 LEU cc_start: 0.6960 (mt) cc_final: 0.6727 (mt) REVERT: E 5 ARG cc_start: 0.6337 (mmm160) cc_final: 0.5420 (mmp80) REVERT: E 15 GLU cc_start: 0.7144 (mp0) cc_final: 0.6894 (mp0) REVERT: E 18 TRP cc_start: 0.8130 (m-10) cc_final: 0.7513 (m-10) REVERT: K 38 TYR cc_start: 0.5469 (t80) cc_final: 0.4714 (t80) REVERT: M 5 ASP cc_start: 0.7958 (p0) cc_final: 0.7638 (m-30) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.2970 time to fit residues: 170.2565 Evaluate side-chains 291 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN A 355 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN K 74 HIS M 7 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22111 Z= 0.219 Angle : 0.649 10.671 31358 Z= 0.289 Chirality : 0.043 0.196 2654 Planarity : 0.004 0.056 4080 Dihedral : 18.039 83.693 3749 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.07 % Allowed : 0.93 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.19), residues: 1858 helix: 1.00 (0.16), residues: 983 sheet: -1.28 (0.59), residues: 81 loop : -1.40 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 570 HIS 0.015 0.001 HIS B 412 PHE 0.039 0.002 PHE A 532 TYR 0.024 0.001 TYR B 574 ARG 0.007 0.000 ARG D 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8497 (ppp) cc_final: 0.8255 (ppp) REVERT: A 192 ASN cc_start: 0.8688 (t0) cc_final: 0.8229 (t0) REVERT: A 244 LEU cc_start: 0.8741 (tt) cc_final: 0.8444 (mt) REVERT: A 251 GLU cc_start: 0.6766 (pt0) cc_final: 0.6135 (pt0) REVERT: A 268 TRP cc_start: 0.8098 (m-10) cc_final: 0.7555 (m-10) REVERT: A 352 LEU cc_start: 0.8734 (tt) cc_final: 0.8394 (tt) REVERT: A 412 MET cc_start: 0.8873 (tpp) cc_final: 0.8234 (tpp) REVERT: A 461 MET cc_start: 0.8603 (mmm) cc_final: 0.8325 (mmm) REVERT: A 584 GLN cc_start: 0.8736 (mt0) cc_final: 0.8298 (mt0) REVERT: A 598 MET cc_start: 0.9058 (tmm) cc_final: 0.8777 (tmm) REVERT: A 613 MET cc_start: 0.8812 (mtp) cc_final: 0.8460 (mtm) REVERT: A 684 MET cc_start: 0.8755 (tpp) cc_final: 0.8152 (tpp) REVERT: B 37 MET cc_start: 0.7475 (tpt) cc_final: 0.7107 (tpt) REVERT: B 262 HIS cc_start: 0.8123 (t70) cc_final: 0.7600 (t70) REVERT: B 348 GLN cc_start: 0.8850 (tt0) cc_final: 0.8574 (tt0) REVERT: B 372 HIS cc_start: 0.8578 (t-90) cc_final: 0.7613 (t-170) REVERT: B 582 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7715 (t0) REVERT: B 659 MET cc_start: 0.7587 (ttt) cc_final: 0.7014 (ttt) REVERT: D 57 LEU cc_start: 0.7708 (tt) cc_final: 0.7400 (tt) REVERT: D 72 LEU cc_start: 0.8519 (mp) cc_final: 0.8292 (mp) REVERT: E 3 LEU cc_start: 0.6924 (mt) cc_final: 0.6705 (mt) REVERT: E 5 ARG cc_start: 0.6639 (mmm160) cc_final: 0.5522 (mmp80) REVERT: E 15 GLU cc_start: 0.7202 (mp0) cc_final: 0.6906 (mp0) REVERT: E 40 ARG cc_start: 0.8426 (ttm170) cc_final: 0.8116 (ptp-110) REVERT: E 43 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8163 (mtm180) REVERT: K 38 TYR cc_start: 0.5373 (t80) cc_final: 0.4709 (t80) REVERT: M 5 ASP cc_start: 0.7902 (p0) cc_final: 0.7609 (m-30) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.3128 time to fit residues: 178.2697 Evaluate side-chains 291 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 156 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 518 HIS B 582 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22111 Z= 0.351 Angle : 0.750 12.499 31358 Z= 0.335 Chirality : 0.048 0.278 2654 Planarity : 0.005 0.075 4080 Dihedral : 18.354 82.980 3749 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.13 % Allowed : 1.00 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1858 helix: 0.79 (0.16), residues: 980 sheet: -1.37 (0.57), residues: 87 loop : -1.44 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 645 HIS 0.019 0.002 HIS A 297 PHE 0.030 0.002 PHE A 532 TYR 0.030 0.002 TYR A 692 ARG 0.008 0.001 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 359 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.8900 (mt0) cc_final: 0.8687 (mt0) REVERT: A 244 LEU cc_start: 0.8756 (tt) cc_final: 0.8426 (mp) REVERT: A 268 TRP cc_start: 0.8120 (m-10) cc_final: 0.7587 (m-10) REVERT: A 352 LEU cc_start: 0.8708 (tt) cc_final: 0.8415 (tt) REVERT: A 412 MET cc_start: 0.8927 (tpp) cc_final: 0.8233 (tpp) REVERT: A 584 GLN cc_start: 0.8855 (mt0) cc_final: 0.8418 (mt0) REVERT: A 598 MET cc_start: 0.9126 (tmm) cc_final: 0.8832 (tmm) REVERT: A 613 MET cc_start: 0.8870 (mtp) cc_final: 0.8489 (mtm) REVERT: B 262 HIS cc_start: 0.8287 (t70) cc_final: 0.7610 (t70) REVERT: B 348 GLN cc_start: 0.8931 (tt0) cc_final: 0.8483 (tt0) REVERT: B 372 HIS cc_start: 0.8623 (t-90) cc_final: 0.8055 (t70) REVERT: D 57 LEU cc_start: 0.7833 (tt) cc_final: 0.7523 (tt) REVERT: D 72 LEU cc_start: 0.8590 (mp) cc_final: 0.8323 (mp) REVERT: E 5 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5679 (mmp80) REVERT: E 18 TRP cc_start: 0.8228 (m-10) cc_final: 0.7618 (m-10) REVERT: E 40 ARG cc_start: 0.8464 (ttm170) cc_final: 0.8199 (ptp-110) REVERT: K 38 TYR cc_start: 0.5442 (t80) cc_final: 0.4695 (t80) REVERT: M 5 ASP cc_start: 0.7938 (p0) cc_final: 0.7667 (m-30) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.3147 time to fit residues: 180.4375 Evaluate side-chains 294 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN E 60 ASN K 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22111 Z= 0.257 Angle : 0.694 11.996 31358 Z= 0.311 Chirality : 0.046 0.270 2654 Planarity : 0.005 0.055 4080 Dihedral : 18.158 81.914 3749 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 1858 helix: 0.89 (0.16), residues: 974 sheet: -1.22 (0.60), residues: 81 loop : -1.40 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 645 HIS 0.016 0.002 HIS B 412 PHE 0.031 0.002 PHE A 532 TYR 0.026 0.002 TYR B 574 ARG 0.009 0.001 ARG D 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8501 (ppp) cc_final: 0.8242 (ppp) REVERT: A 192 ASN cc_start: 0.8579 (t0) cc_final: 0.8157 (t0) REVERT: A 241 GLU cc_start: 0.7881 (pp20) cc_final: 0.7640 (pp20) REVERT: A 244 LEU cc_start: 0.8737 (tt) cc_final: 0.8408 (mp) REVERT: A 251 GLU cc_start: 0.6887 (pt0) cc_final: 0.6459 (pt0) REVERT: A 268 TRP cc_start: 0.8128 (m-10) cc_final: 0.7655 (m-10) REVERT: A 352 LEU cc_start: 0.8692 (tt) cc_final: 0.8377 (tt) REVERT: A 412 MET cc_start: 0.8941 (tpp) cc_final: 0.8246 (tpp) REVERT: A 584 GLN cc_start: 0.8818 (mt0) cc_final: 0.8424 (mt0) REVERT: A 598 MET cc_start: 0.9088 (tmm) cc_final: 0.8782 (tmm) REVERT: A 613 MET cc_start: 0.8828 (mtp) cc_final: 0.8462 (mtm) REVERT: A 684 MET cc_start: 0.8875 (tpp) cc_final: 0.8252 (tpp) REVERT: B 262 HIS cc_start: 0.8196 (t70) cc_final: 0.7709 (t70) REVERT: B 348 GLN cc_start: 0.8884 (tt0) cc_final: 0.8577 (tt0) REVERT: B 372 HIS cc_start: 0.8589 (t-90) cc_final: 0.8086 (t70) REVERT: B 542 LYS cc_start: 0.8055 (mmmm) cc_final: 0.7762 (mttt) REVERT: B 582 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7560 (t0) REVERT: B 659 MET cc_start: 0.7566 (ttt) cc_final: 0.7005 (ttt) REVERT: C 77 MET cc_start: 0.7785 (tpp) cc_final: 0.7515 (tpp) REVERT: D 1 MET cc_start: 0.3748 (tpp) cc_final: 0.3396 (tpt) REVERT: D 41 GLU cc_start: 0.8548 (pp20) cc_final: 0.8272 (tt0) REVERT: D 57 LEU cc_start: 0.7632 (tt) cc_final: 0.7419 (tt) REVERT: D 72 LEU cc_start: 0.8523 (mp) cc_final: 0.8234 (mp) REVERT: E 5 ARG cc_start: 0.6683 (mmm160) cc_final: 0.5700 (mmp80) REVERT: E 18 TRP cc_start: 0.8190 (m-10) cc_final: 0.7569 (m-10) REVERT: E 42 ASP cc_start: 0.8057 (p0) cc_final: 0.7674 (t0) REVERT: K 38 TYR cc_start: 0.5470 (t80) cc_final: 0.4703 (t80) REVERT: M 5 ASP cc_start: 0.8009 (p0) cc_final: 0.7742 (m-30) outliers start: 3 outliers final: 0 residues processed: 353 average time/residue: 0.3030 time to fit residues: 171.4754 Evaluate side-chains 293 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN K 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.103651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.085636 restraints weight = 43058.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.088509 restraints weight = 20275.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.090375 restraints weight = 12550.350| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22111 Z= 0.282 Angle : 0.708 12.191 31358 Z= 0.317 Chirality : 0.046 0.234 2654 Planarity : 0.005 0.054 4080 Dihedral : 18.067 83.625 3749 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1858 helix: 0.82 (0.16), residues: 977 sheet: -1.25 (0.57), residues: 87 loop : -1.44 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 570 HIS 0.014 0.002 HIS B 412 PHE 0.029 0.002 PHE A 532 TYR 0.026 0.002 TYR B 574 ARG 0.009 0.001 ARG D 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4308.78 seconds wall clock time: 79 minutes 14.05 seconds (4754.05 seconds total)