Starting phenix.real_space_refine on Mon Sep 30 04:39:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0o_28775/09_2024/8f0o_28775.cif" } resolution = 2.99 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= 0.003 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 15416 2.51 5 N 3940 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24030 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "C" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "D" Number of atoms: 5888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5888 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 27, 'TRANS': 714} Chain breaks: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.81, per 1000 atoms: 0.57 Number of scatterers: 24030 At special positions: 0 Unit cell: (127.2, 146.28, 181.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4554 8.00 N 3940 7.00 C 15416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A1001 " - " ASN A 412 " " NAG B1001 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG D1001 " - " ASN D 412 " " NAG E 1 " - " ASN A 381 " " NAG F 1 " - " ASN A 430 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN C 378 " " NAG J 1 " - " ASN C 430 " " NAG K 1 " - " ASN C 275 " " NAG L 1 " - " ASN D 378 " Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.9 seconds 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5536 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 28 sheets defined 46.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 210 through 220 removed outlier: 4.258A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 264 removed outlier: 3.638A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 336 removed outlier: 3.582A pdb=" N ALA A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 423 through 427 removed outlier: 4.466A pdb=" N ASP A 426 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 423 through 427' Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.712A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.781A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 Processing helix chain 'A' and resid 632 through 664 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.625A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 removed outlier: 3.534A pdb=" N LYS A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.553A pdb=" N ARG A 712 " --> pdb=" O PHE A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.758A pdb=" N THR A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 772 through 789 removed outlier: 4.094A pdb=" N ASP A 776 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 822 through 839 Processing helix chain 'B' and resid 51 through 66 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.552A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 185 through 195 Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 220 removed outlier: 4.565A pdb=" N LEU B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.814A pdb=" N ARG B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 302 removed outlier: 4.073A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.921A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 454 through 457 removed outlier: 3.880A pdb=" N ASP B 457 " --> pdb=" O TYR B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.967A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 4.016A pdb=" N ASP B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 Processing helix chain 'B' and resid 562 through 580 Processing helix chain 'B' and resid 632 through 665 Processing helix chain 'B' and resid 670 through 677 Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 720 through 730 removed outlier: 3.678A pdb=" N ILE B 725 " --> pdb=" O ASN B 721 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN B 726 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 780 through 789 removed outlier: 4.036A pdb=" N GLU B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 796 Processing helix chain 'B' and resid 818 through 839 Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 152 through 168 Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.764A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 removed outlier: 3.712A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Proline residue: C 192 - end of helix Processing helix chain 'C' and resid 210 through 220 removed outlier: 4.299A pdb=" N LEU C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 286 through 301 removed outlier: 3.775A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.716A pdb=" N ALA C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.583A pdb=" N ARG C 503 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 560 through 578 Processing helix chain 'C' and resid 632 through 664 Processing helix chain 'C' and resid 669 through 676 removed outlier: 3.700A pdb=" N ASP C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 696 removed outlier: 3.689A pdb=" N THR C 692 " --> pdb=" O GLY C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 removed outlier: 3.892A pdb=" N ARG C 712 " --> pdb=" O PHE C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 717 removed outlier: 3.891A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.733A pdb=" N GLY C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 725 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 747 removed outlier: 4.064A pdb=" N ILE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 788 Processing helix chain 'C' and resid 789 through 797 Processing helix chain 'C' and resid 818 through 839 removed outlier: 3.711A pdb=" N ILE C 823 " --> pdb=" O ASN C 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 211 through 220 Processing helix chain 'D' and resid 231 through 244 Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.827A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 336 removed outlier: 3.649A pdb=" N GLN D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 365 Processing helix chain 'D' and resid 415 through 419 removed outlier: 4.116A pdb=" N GLY D 419 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 474 removed outlier: 3.570A pdb=" N GLU D 469 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 520 through 527 Processing helix chain 'D' and resid 563 through 581 Processing helix chain 'D' and resid 632 through 665 Processing helix chain 'D' and resid 670 through 677 removed outlier: 3.659A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 removed outlier: 3.832A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.796A pdb=" N ARG D 712 " --> pdb=" O PHE D 708 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 776 through 782 removed outlier: 3.591A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 796 Processing helix chain 'D' and resid 821 through 839 removed outlier: 4.068A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 6.168A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 83 removed outlier: 7.261A pdb=" N GLY A 39 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 203 removed outlier: 6.480A pdb=" N VAL A 172 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG A 202 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 171 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 227 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 173 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP A 229 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 479 through 480 removed outlier: 3.863A pdb=" N VAL A 514 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 515 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 765 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 517 " --> pdb=" O GLY A 763 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY A 763 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.666A pdb=" N LEU A 536 " --> pdb=" O LYS A 762 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.714A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.699A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU B 149 " --> pdb=" O HIS B 129 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLN B 131 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ARG B 384 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N SER B 148 " --> pdb=" O ARG B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.613A pdb=" N HIS B 225 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET B 276 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU B 389 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 404 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 391 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 368 through 370 removed outlier: 3.874A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 432 through 433 Processing sheet with id=AB3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB4, first strand: chain 'B' and resid 682 through 683 removed outlier: 7.447A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU B 738 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 75 through 83 removed outlier: 5.704A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N ALA C 105 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ARG C 37 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N PHE C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY C 39 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 198 through 203 removed outlier: 6.711A pdb=" N VAL C 172 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ARG C 202 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N HIS C 225 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 254 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N PHE C 279 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N PHE C 256 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET C 276 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C 389 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR C 404 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 368 through 370 Processing sheet with id=AB8, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AB9, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC1, first strand: chain 'C' and resid 513 through 519 removed outlier: 7.189A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 765 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 763 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 768 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 528 " --> pdb=" O THR C 768 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 513 through 519 removed outlier: 7.189A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 765 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY C 763 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 540 through 543 Processing sheet with id=AC4, first strand: chain 'C' and resid 682 through 683 removed outlier: 3.585A pdb=" N GLY C 683 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 83 removed outlier: 10.065A pdb=" N ALA D 105 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG D 37 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N PHE D 107 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY D 39 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS D 129 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 149 " --> pdb=" O HIS D 129 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N GLN D 131 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ARG D 384 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER D 148 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 203 removed outlier: 6.238A pdb=" N VAL D 172 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ARG D 202 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N HIS D 225 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N MET D 276 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU D 389 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR D 404 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 368 through 370 removed outlier: 3.641A pdb=" N TRP D 368 " --> pdb=" O ILE D 375 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 432 through 437 removed outlier: 6.274A pdb=" N LEU D 433 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG D 481 " --> pdb=" O LEU D 433 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL D 435 " --> pdb=" O ARG D 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 513 through 517 removed outlier: 4.358A pdb=" N ALA D 515 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY D 765 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 681 through 683 removed outlier: 6.802A pdb=" N GLU D 681 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N LEU D 736 " --> pdb=" O GLU D 681 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N TYR D 733 " --> pdb=" O ARG D 543 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG D 543 " --> pdb=" O TYR D 733 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2994 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: 8.23 Time building geometry restraints manager: 6.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7382 1.34 - 1.46: 4689 1.46 - 1.58: 12254 1.58 - 1.69: 5 1.69 - 1.81: 216 Bond restraints: 24546 Sorted by residual: bond pdb=" C3 BMA I 3 " pdb=" O3 BMA I 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.591 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.585 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C3 BMA G 3 " pdb=" O3 BMA G 3 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.64e+00 bond pdb=" C5 MAN I 5 " pdb=" O5 MAN I 5 " ideal model delta sigma weight residual 1.418 1.479 -0.061 2.00e-02 2.50e+03 9.40e+00 ... (remaining 24541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 32108 1.91 - 3.83: 902 3.83 - 5.74: 149 5.74 - 7.66: 58 7.66 - 9.57: 21 Bond angle restraints: 33238 Sorted by residual: angle pdb=" C GLY D 547 " pdb=" N THR D 548 " pdb=" CA THR D 548 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C LYS A 379 " pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C PRO A 667 " pdb=" N ILE A 668 " pdb=" CA ILE A 668 " ideal model delta sigma weight residual 121.97 129.96 -7.99 1.80e+00 3.09e-01 1.97e+01 angle pdb=" C PRO B 561 " pdb=" N ASP B 562 " pdb=" CA ASP B 562 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C ALA B 707 " pdb=" N PHE B 708 " pdb=" CA PHE B 708 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 33233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.58: 13955 23.58 - 47.16: 939 47.16 - 70.74: 101 70.74 - 94.32: 67 94.32 - 117.89: 53 Dihedral angle restraints: 15115 sinusoidal: 6511 harmonic: 8604 Sorted by residual: dihedral pdb=" CA PRO B 442 " pdb=" C PRO B 442 " pdb=" N TYR B 443 " pdb=" CA TYR B 443 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA A 191 " pdb=" C ALA A 191 " pdb=" N PRO A 192 " pdb=" CA PRO A 192 " ideal model delta harmonic sigma weight residual 180.00 154.22 25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA HIS C 111 " pdb=" C HIS C 111 " pdb=" N SER C 112 " pdb=" CA SER C 112 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 15112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 3791 0.136 - 0.273: 74 0.273 - 0.409: 4 0.409 - 0.545: 0 0.545 - 0.682: 1 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" CB ILE B 519 " pdb=" CA ILE B 519 " pdb=" CG1 ILE B 519 " pdb=" CG2 ILE B 519 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 381 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.71 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 3867 not shown) Planarity restraints: 4140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 275 " -0.034 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN A 275 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 275 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 275 " 0.030 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 191 " 0.058 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO D 192 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 441 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 442 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 442 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 442 " -0.045 5.00e-02 4.00e+02 ... (remaining 4137 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6182 2.80 - 3.32: 20392 3.32 - 3.85: 40366 3.85 - 4.37: 43750 4.37 - 4.90: 75381 Nonbonded interactions: 186071 Sorted by model distance: nonbonded pdb=" O VAL C 716 " pdb=" OH TYR C 733 " model vdw 2.274 3.040 nonbonded pdb=" OE2 GLU C 738 " pdb=" OH TYR C 764 " model vdw 2.320 3.040 nonbonded pdb=" O ALA D 656 " pdb=" OG1 THR D 660 " model vdw 2.328 3.040 nonbonded pdb=" O ASP C 528 " pdb=" OG1 THR C 768 " model vdw 2.336 3.040 nonbonded pdb=" O VAL B 327 " pdb=" OG SER B 331 " model vdw 2.336 3.040 ... (remaining 186066 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 7.640 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: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.500 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.005 0.078 24546 Z= 0.299 Angle : 0.803 9.572 33238 Z= 0.409 Chirality : 0.053 0.682 3870 Planarity : 0.006 0.087 4128 Dihedral : 17.633 117.895 9570 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -2.73 (0.13), residues: 2944 helix: -1.85 (0.11), residues: 1260 sheet: -0.52 (0.26), residues: 408 loop : -2.08 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 296 HIS 0.010 0.001 HIS A 253 PHE 0.038 0.002 PHE A 642 TYR 0.027 0.002 TYR D 251 ARG 0.005 0.000 ARG B 712 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 705 MET cc_start: 0.9082 (mtp) cc_final: 0.8813 (mtm) REVERT: A 709 MET cc_start: 0.9419 (mtt) cc_final: 0.9142 (mtm) REVERT: B 691 MET cc_start: 0.9035 (tmm) cc_final: 0.8537 (tmm) REVERT: C 50 MET cc_start: 0.7387 (mtm) cc_final: 0.7165 (mtp) REVERT: C 247 MET cc_start: 0.8334 (mtp) cc_final: 0.8042 (ttp) REVERT: C 501 MET cc_start: 0.9021 (mtm) cc_final: 0.8817 (mtt) REVERT: C 664 MET cc_start: 0.8777 (mmm) cc_final: 0.8479 (tmm) REVERT: C 705 MET cc_start: 0.9132 (mmt) cc_final: 0.8922 (mmt) REVERT: D 794 MET cc_start: 0.6711 (mtm) cc_final: 0.6355 (ptp) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 1.6208 time to fit residues: 242.5607 Evaluate side-chains 100 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 232 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 98 GLN ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 GLN C 81 GLN C 98 GLN C 196 ASN C 328 HIS D 81 GLN D 98 GLN D 203 GLN D 677 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24546 Z= 0.325 Angle : 0.661 10.352 33238 Z= 0.328 Chirality : 0.042 0.225 3870 Planarity : 0.004 0.052 4128 Dihedral : 13.069 109.700 3966 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.66 % Allowed : 7.00 % Favored : 92.34 % 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: -1.00 (0.15), residues: 2944 helix: 0.26 (0.14), residues: 1275 sheet: -0.39 (0.27), residues: 396 loop : -1.69 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 296 HIS 0.006 0.001 HIS D 225 PHE 0.024 0.002 PHE A 642 TYR 0.023 0.001 TYR D 571 ARG 0.006 0.001 ARG D 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 MET cc_start: 0.7862 (ttp) cc_final: 0.7308 (mtm) REVERT: A 433 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8566 (mm) REVERT: A 501 MET cc_start: 0.9321 (mtt) cc_final: 0.9069 (mtt) REVERT: B 691 MET cc_start: 0.8911 (tmm) cc_final: 0.8341 (tmm) REVERT: B 794 MET cc_start: 0.6075 (tpt) cc_final: 0.5506 (tpt) REVERT: C 50 MET cc_start: 0.7379 (mtm) cc_final: 0.7161 (mtp) REVERT: C 247 MET cc_start: 0.8449 (mtp) cc_final: 0.8053 (mtp) REVERT: C 298 MET cc_start: 0.8965 (mmm) cc_final: 0.8715 (mpm) REVERT: C 664 MET cc_start: 0.8825 (mmm) cc_final: 0.8494 (tmm) REVERT: C 737 MET cc_start: 0.8502 (ppp) cc_final: 0.8187 (pp-130) REVERT: D 247 MET cc_start: 0.8826 (mmt) cc_final: 0.8577 (mmt) REVERT: D 534 MET cc_start: 0.6717 (pmm) cc_final: 0.6452 (pmm) REVERT: D 565 MET cc_start: 0.8070 (mpp) cc_final: 0.7794 (mmm) REVERT: D 709 MET cc_start: 0.8669 (ppp) cc_final: 0.8282 (ppp) outliers start: 17 outliers final: 2 residues processed: 107 average time/residue: 1.5271 time to fit residues: 187.5503 Evaluate side-chains 102 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 534 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 290 optimal weight: 0.0010 chunk 239 optimal weight: 0.0470 chunk 267 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 overall best weight: 1.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 GLN C 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24546 Z= 0.187 Angle : 0.556 9.150 33238 Z= 0.272 Chirality : 0.040 0.262 3870 Planarity : 0.003 0.044 4128 Dihedral : 11.014 100.364 3966 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.85 % Allowed : 9.56 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2944 helix: 0.94 (0.15), residues: 1281 sheet: -0.17 (0.27), residues: 391 loop : -1.54 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 564 HIS 0.003 0.001 HIS C 232 PHE 0.024 0.001 PHE A 642 TYR 0.019 0.001 TYR D 571 ARG 0.006 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6712 (mtp) cc_final: 0.6468 (mmt) REVERT: A 234 MET cc_start: 0.8708 (tpp) cc_final: 0.8469 (tpp) REVERT: A 316 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7246 (mtm) REVERT: A 433 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8601 (mm) REVERT: A 501 MET cc_start: 0.9318 (mtt) cc_final: 0.8878 (mtt) REVERT: A 534 MET cc_start: 0.8048 (mtm) cc_final: 0.7560 (mtm) REVERT: B 565 MET cc_start: 0.8936 (tpp) cc_final: 0.8618 (mpp) REVERT: B 691 MET cc_start: 0.8936 (tmm) cc_final: 0.8342 (tmm) REVERT: B 793 MET cc_start: 0.8976 (tpp) cc_final: 0.8335 (pp-130) REVERT: B 794 MET cc_start: 0.6119 (tpt) cc_final: 0.4121 (tpt) REVERT: C 50 MET cc_start: 0.7310 (mtm) cc_final: 0.7094 (mtp) REVERT: C 81 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: C 247 MET cc_start: 0.8352 (mtp) cc_final: 0.7911 (ttp) REVERT: C 298 MET cc_start: 0.8954 (mmm) cc_final: 0.8732 (tpp) REVERT: C 664 MET cc_start: 0.8835 (mmm) cc_final: 0.8462 (tmm) REVERT: C 737 MET cc_start: 0.8534 (ppp) cc_final: 0.8225 (pp-130) REVERT: D 413 MET cc_start: 0.8415 (mmm) cc_final: 0.8006 (mmm) REVERT: D 501 MET cc_start: 0.8008 (mmm) cc_final: 0.7538 (mpp) REVERT: D 534 MET cc_start: 0.6961 (pmm) cc_final: 0.6615 (pmm) REVERT: D 794 MET cc_start: 0.6611 (ptp) cc_final: 0.6351 (ptt) outliers start: 22 outliers final: 5 residues processed: 107 average time/residue: 1.5564 time to fit residues: 190.7929 Evaluate side-chains 106 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 793 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 139 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24546 Z= 0.396 Angle : 0.685 9.983 33238 Z= 0.340 Chirality : 0.043 0.331 3870 Planarity : 0.004 0.043 4128 Dihedral : 10.326 99.274 3966 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 1.55 % Allowed : 11.80 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 2944 helix: 1.00 (0.14), residues: 1286 sheet: -0.22 (0.28), residues: 378 loop : -1.61 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 564 HIS 0.007 0.001 HIS D 225 PHE 0.024 0.002 PHE B 42 TYR 0.028 0.002 TYR A 774 ARG 0.011 0.001 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8842 (tpp) cc_final: 0.8569 (tpp) REVERT: A 316 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7454 (mtm) REVERT: A 360 MET cc_start: 0.9079 (mmm) cc_final: 0.8799 (mmm) REVERT: A 433 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8485 (mm) REVERT: A 501 MET cc_start: 0.9330 (mtt) cc_final: 0.8942 (mtt) REVERT: B 691 MET cc_start: 0.9022 (tmm) cc_final: 0.8433 (tmm) REVERT: B 737 MET cc_start: 0.6300 (tpt) cc_final: 0.6033 (tpt) REVERT: B 794 MET cc_start: 0.6518 (tpt) cc_final: 0.6142 (tpt) REVERT: C 50 MET cc_start: 0.7305 (mtm) cc_final: 0.7093 (mtp) REVERT: C 81 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: C 298 MET cc_start: 0.8985 (mmm) cc_final: 0.8767 (tpp) REVERT: C 360 MET cc_start: 0.9016 (mmm) cc_final: 0.8783 (mmm) REVERT: C 664 MET cc_start: 0.8791 (mmm) cc_final: 0.8461 (tmm) REVERT: D 413 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8045 (mmm) REVERT: D 438 ILE cc_start: 0.4528 (OUTLIER) cc_final: 0.4274 (tp) REVERT: D 565 MET cc_start: 0.7950 (mpp) cc_final: 0.7647 (mmm) outliers start: 40 outliers final: 8 residues processed: 122 average time/residue: 1.4454 time to fit residues: 203.5515 Evaluate side-chains 111 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24546 Z= 0.166 Angle : 0.559 11.025 33238 Z= 0.272 Chirality : 0.041 0.344 3870 Planarity : 0.003 0.038 4128 Dihedral : 9.393 93.855 3966 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.04 % Allowed : 14.05 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2944 helix: 1.31 (0.15), residues: 1287 sheet: -0.08 (0.28), residues: 359 loop : -1.49 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 564 HIS 0.003 0.001 HIS B 225 PHE 0.027 0.001 PHE C 735 TYR 0.022 0.001 TYR D 571 ARG 0.005 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 99 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8731 (tpp) cc_final: 0.8446 (tpp) REVERT: A 316 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7173 (mtm) REVERT: A 501 MET cc_start: 0.9292 (mtt) cc_final: 0.9090 (mtt) REVERT: A 737 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8194 (mpt) REVERT: B 565 MET cc_start: 0.8912 (tpp) cc_final: 0.8592 (mpp) REVERT: B 691 MET cc_start: 0.8981 (tmm) cc_final: 0.8378 (tmm) REVERT: B 794 MET cc_start: 0.6352 (tpt) cc_final: 0.5953 (tpt) REVERT: C 81 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: C 298 MET cc_start: 0.8941 (mmm) cc_final: 0.8724 (tpp) REVERT: C 664 MET cc_start: 0.8787 (mmm) cc_final: 0.8453 (tmm) REVERT: C 735 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8030 (t80) REVERT: C 794 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8713 (mmm) REVERT: D 145 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7978 (t80) REVERT: D 413 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8085 (mmm) REVERT: D 438 ILE cc_start: 0.4692 (OUTLIER) cc_final: 0.4170 (tp) REVERT: D 534 MET cc_start: 0.6758 (pmm) cc_final: 0.6474 (pmm) REVERT: D 737 MET cc_start: 0.8108 (ppp) cc_final: 0.7800 (ppp) outliers start: 27 outliers final: 5 residues processed: 113 average time/residue: 1.5160 time to fit residues: 197.4147 Evaluate side-chains 110 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 794 MET Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 286 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 GLN C 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24546 Z= 0.292 Angle : 0.640 11.494 33238 Z= 0.308 Chirality : 0.042 0.342 3870 Planarity : 0.003 0.037 4128 Dihedral : 9.147 91.087 3966 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.43 % Allowed : 14.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.16), residues: 2944 helix: 1.35 (0.15), residues: 1287 sheet: -0.21 (0.28), residues: 370 loop : -1.48 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 296 HIS 0.005 0.001 HIS D 225 PHE 0.030 0.001 PHE C 735 TYR 0.024 0.001 TYR D 571 ARG 0.004 0.000 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8793 (tpp) cc_final: 0.8514 (tpp) REVERT: A 316 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7455 (mtm) REVERT: A 433 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 501 MET cc_start: 0.9340 (mtt) cc_final: 0.9111 (mtt) REVERT: A 691 MET cc_start: 0.8966 (ptt) cc_final: 0.8716 (pmm) REVERT: A 793 MET cc_start: 0.9028 (ptt) cc_final: 0.8735 (pp-130) REVERT: B 565 MET cc_start: 0.8957 (tpp) cc_final: 0.8554 (mpp) REVERT: B 691 MET cc_start: 0.9050 (tmm) cc_final: 0.8473 (tmm) REVERT: B 794 MET cc_start: 0.6572 (tpt) cc_final: 0.6301 (tpt) REVERT: C 81 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: C 247 MET cc_start: 0.8773 (tpp) cc_final: 0.8120 (mmm) REVERT: C 298 MET cc_start: 0.8926 (mmm) cc_final: 0.8687 (tpp) REVERT: C 360 MET cc_start: 0.9051 (mmm) cc_final: 0.8811 (mmm) REVERT: C 664 MET cc_start: 0.8794 (mmm) cc_final: 0.8440 (tmm) REVERT: C 735 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8122 (t80) REVERT: D 145 PHE cc_start: 0.8964 (OUTLIER) cc_final: 0.8452 (t80) REVERT: D 248 MET cc_start: 0.8420 (mmm) cc_final: 0.8159 (mmm) REVERT: D 413 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8095 (mmm) REVERT: D 438 ILE cc_start: 0.4521 (OUTLIER) cc_final: 0.4063 (tp) REVERT: D 534 MET cc_start: 0.6704 (pmm) cc_final: 0.6418 (pmm) REVERT: D 565 MET cc_start: 0.7852 (mpp) cc_final: 0.7596 (mmm) REVERT: D 664 MET cc_start: 0.8952 (mmm) cc_final: 0.8631 (mmt) REVERT: D 737 MET cc_start: 0.8115 (ppp) cc_final: 0.7102 (ppp) outliers start: 37 outliers final: 6 residues processed: 124 average time/residue: 1.3954 time to fit residues: 200.4822 Evaluate side-chains 110 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 3.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 0.0010 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24546 Z= 0.212 Angle : 0.601 11.838 33238 Z= 0.288 Chirality : 0.041 0.336 3870 Planarity : 0.003 0.037 4128 Dihedral : 8.651 86.758 3966 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.97 % Allowed : 15.94 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2944 helix: 1.46 (0.15), residues: 1288 sheet: -0.06 (0.29), residues: 365 loop : -1.40 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 564 HIS 0.003 0.001 HIS D 225 PHE 0.026 0.001 PHE C 735 TYR 0.024 0.001 TYR D 571 ARG 0.003 0.000 ARG D 354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8765 (tpp) cc_final: 0.8482 (tpp) REVERT: A 316 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7408 (mtm) REVERT: A 433 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 691 MET cc_start: 0.8953 (ptt) cc_final: 0.8604 (ptt) REVERT: A 793 MET cc_start: 0.9016 (ptt) cc_final: 0.8730 (pp-130) REVERT: B 248 MET cc_start: 0.8230 (mtp) cc_final: 0.7969 (mtp) REVERT: B 565 MET cc_start: 0.8977 (tpp) cc_final: 0.8572 (mpp) REVERT: B 691 MET cc_start: 0.9045 (tmm) cc_final: 0.8460 (tmm) REVERT: B 794 MET cc_start: 0.6547 (tpt) cc_final: 0.6288 (tpt) REVERT: C 81 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: C 247 MET cc_start: 0.8727 (tpp) cc_final: 0.8251 (mmm) REVERT: C 298 MET cc_start: 0.8939 (mmm) cc_final: 0.8666 (tpp) REVERT: C 360 MET cc_start: 0.9008 (mmm) cc_final: 0.8786 (mmm) REVERT: C 664 MET cc_start: 0.8797 (mmm) cc_final: 0.8461 (tmm) REVERT: C 735 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8054 (t80) REVERT: C 793 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8663 (pp-130) REVERT: D 145 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8348 (t80) REVERT: D 360 MET cc_start: 0.9173 (mtm) cc_final: 0.8895 (mtm) REVERT: D 413 MET cc_start: 0.8513 (mmm) cc_final: 0.8147 (mmm) REVERT: D 438 ILE cc_start: 0.4504 (OUTLIER) cc_final: 0.3945 (tp) REVERT: D 534 MET cc_start: 0.6696 (pmm) cc_final: 0.6383 (pmm) REVERT: D 565 MET cc_start: 0.7861 (mpp) cc_final: 0.7588 (mmm) REVERT: D 737 MET cc_start: 0.8111 (ppp) cc_final: 0.6928 (ppp) REVERT: D 794 MET cc_start: 0.7016 (ptp) cc_final: 0.6788 (ptt) outliers start: 25 outliers final: 7 residues processed: 118 average time/residue: 1.4007 time to fit residues: 191.3614 Evaluate side-chains 111 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain C residue 823 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 chunk 170 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24546 Z= 0.181 Angle : 0.616 12.272 33238 Z= 0.291 Chirality : 0.041 0.338 3870 Planarity : 0.003 0.038 4128 Dihedral : 8.091 82.454 3966 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.74 % Allowed : 16.56 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2944 helix: 1.54 (0.15), residues: 1286 sheet: -0.11 (0.29), residues: 367 loop : -1.34 (0.18), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 706 HIS 0.005 0.001 HIS C 792 PHE 0.021 0.001 PHE C 735 TYR 0.017 0.001 TYR D 571 ARG 0.004 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8745 (tpp) cc_final: 0.8460 (tpp) REVERT: A 316 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7240 (mtm) REVERT: A 433 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8543 (mm) REVERT: A 534 MET cc_start: 0.8034 (mtm) cc_final: 0.7623 (mtm) REVERT: A 691 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8558 (ptt) REVERT: A 737 MET cc_start: 0.9154 (pmm) cc_final: 0.8740 (pmm) REVERT: A 793 MET cc_start: 0.9004 (ptt) cc_final: 0.8730 (pp-130) REVERT: B 248 MET cc_start: 0.8242 (mtp) cc_final: 0.7995 (mtp) REVERT: B 323 MET cc_start: 0.9182 (mmm) cc_final: 0.8887 (tpt) REVERT: B 565 MET cc_start: 0.8978 (tpp) cc_final: 0.8624 (mtp) REVERT: B 691 MET cc_start: 0.9043 (tmm) cc_final: 0.8459 (tmm) REVERT: B 794 MET cc_start: 0.6378 (tpt) cc_final: 0.6129 (tpt) REVERT: C 81 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: C 247 MET cc_start: 0.8747 (tpp) cc_final: 0.8290 (mmm) REVERT: C 664 MET cc_start: 0.8781 (mmm) cc_final: 0.8406 (tmm) REVERT: C 793 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8632 (pp-130) REVERT: D 145 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8338 (t80) REVERT: D 360 MET cc_start: 0.9113 (mtm) cc_final: 0.8853 (mtm) REVERT: D 413 MET cc_start: 0.8474 (mmm) cc_final: 0.8105 (mmm) REVERT: D 438 ILE cc_start: 0.4531 (OUTLIER) cc_final: 0.4028 (tp) REVERT: D 565 MET cc_start: 0.7854 (mpp) cc_final: 0.7583 (mmm) REVERT: D 664 MET cc_start: 0.8876 (mmm) cc_final: 0.8570 (mmt) outliers start: 19 outliers final: 6 residues processed: 112 average time/residue: 1.4551 time to fit residues: 188.8970 Evaluate side-chains 110 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 208 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24546 Z= 0.306 Angle : 0.697 13.437 33238 Z= 0.331 Chirality : 0.042 0.331 3870 Planarity : 0.003 0.037 4128 Dihedral : 8.006 79.957 3966 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.89 % Allowed : 16.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2944 helix: 1.48 (0.15), residues: 1285 sheet: -0.10 (0.28), residues: 378 loop : -1.41 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 640 HIS 0.005 0.001 HIS D 225 PHE 0.027 0.001 PHE B 166 TYR 0.019 0.001 TYR A 774 ARG 0.005 0.000 ARG C 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8798 (tpp) cc_final: 0.8512 (tpp) REVERT: A 316 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7418 (mtm) REVERT: A 433 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 501 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8866 (mtt) REVERT: A 534 MET cc_start: 0.8166 (mtm) cc_final: 0.7744 (mtm) REVERT: A 691 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8539 (ptt) REVERT: A 793 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8728 (pp-130) REVERT: B 248 MET cc_start: 0.8213 (mtp) cc_final: 0.7960 (mtp) REVERT: B 565 MET cc_start: 0.8967 (tpp) cc_final: 0.8541 (mtp) REVERT: B 691 MET cc_start: 0.9094 (tmm) cc_final: 0.8509 (tmm) REVERT: B 794 MET cc_start: 0.6607 (tpt) cc_final: 0.6383 (tpt) REVERT: C 81 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: C 247 MET cc_start: 0.8772 (tpp) cc_final: 0.8214 (mmm) REVERT: C 664 MET cc_start: 0.8800 (mmm) cc_final: 0.8432 (tmm) REVERT: C 793 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8718 (pp-130) REVERT: D 145 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8429 (t80) REVERT: D 360 MET cc_start: 0.9139 (mtm) cc_final: 0.8885 (mtm) REVERT: D 413 MET cc_start: 0.8514 (mmm) cc_final: 0.8138 (mmm) REVERT: D 438 ILE cc_start: 0.4555 (OUTLIER) cc_final: 0.4008 (tp) REVERT: D 565 MET cc_start: 0.7850 (mpp) cc_final: 0.7585 (mmm) REVERT: D 664 MET cc_start: 0.8944 (mmm) cc_final: 0.8620 (mmt) REVERT: D 770 MET cc_start: 0.5789 (mpm) cc_final: 0.5367 (mpp) outliers start: 23 outliers final: 5 residues processed: 112 average time/residue: 1.5109 time to fit residues: 195.2369 Evaluate side-chains 111 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 774 TYR Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 508 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 181 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24546 Z= 0.210 Angle : 0.666 13.917 33238 Z= 0.312 Chirality : 0.041 0.333 3870 Planarity : 0.003 0.037 4128 Dihedral : 7.747 76.588 3966 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.89 % Allowed : 16.72 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2944 helix: 1.51 (0.15), residues: 1290 sheet: -0.07 (0.28), residues: 372 loop : -1.39 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP A 640 HIS 0.003 0.001 HIS D 225 PHE 0.026 0.001 PHE B 166 TYR 0.018 0.001 TYR D 571 ARG 0.003 0.000 ARG A 431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5888 Ramachandran restraints generated. 2944 Oldfield, 0 Emsley, 2944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 3.099 Fit side-chains revert: symmetry clash REVERT: A 234 MET cc_start: 0.8760 (tpp) cc_final: 0.8472 (tpp) REVERT: A 316 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7405 (mtm) REVERT: A 501 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8800 (mtt) REVERT: A 534 MET cc_start: 0.8039 (mtm) cc_final: 0.7620 (mtm) REVERT: A 691 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8524 (ptt) REVERT: A 793 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8735 (pp-130) REVERT: B 247 MET cc_start: 0.8838 (tpp) cc_final: 0.8590 (tpp) REVERT: B 248 MET cc_start: 0.8252 (mtp) cc_final: 0.8012 (mtp) REVERT: B 565 MET cc_start: 0.8984 (tpp) cc_final: 0.8552 (mtp) REVERT: B 691 MET cc_start: 0.9080 (tmm) cc_final: 0.8492 (tmm) REVERT: B 793 MET cc_start: 0.9121 (tpp) cc_final: 0.8477 (pp-130) REVERT: B 794 MET cc_start: 0.6335 (tpt) cc_final: 0.4551 (tpt) REVERT: C 81 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7849 (mp10) REVERT: C 247 MET cc_start: 0.8750 (tpp) cc_final: 0.8290 (mmm) REVERT: C 360 MET cc_start: 0.9208 (mmm) cc_final: 0.8539 (mmp) REVERT: C 664 MET cc_start: 0.8809 (mmm) cc_final: 0.8443 (tmm) REVERT: C 793 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8702 (pp-130) REVERT: D 145 PHE cc_start: 0.9182 (OUTLIER) cc_final: 0.8493 (t80) REVERT: D 360 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8872 (mtm) REVERT: D 413 MET cc_start: 0.8467 (mmm) cc_final: 0.8085 (mmm) REVERT: D 438 ILE cc_start: 0.4484 (OUTLIER) cc_final: 0.3977 (tp) REVERT: D 565 MET cc_start: 0.7852 (mpp) cc_final: 0.7585 (mmm) REVERT: D 664 MET cc_start: 0.8922 (mmm) cc_final: 0.8548 (mmt) REVERT: D 770 MET cc_start: 0.5856 (mpm) cc_final: 0.5444 (mpp) outliers start: 23 outliers final: 4 residues processed: 111 average time/residue: 1.5115 time to fit residues: 192.7838 Evaluate side-chains 109 residues out of total 2584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 793 MET Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 367 HIS Chi-restraints excluded: chain C residue 793 MET Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 718 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.0670 chunk 250 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN D 98 GLN ** D 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.043221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.033376 restraints weight = 219882.101| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 4.73 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24546 Z= 0.149 Angle : 0.663 13.878 33238 Z= 0.305 Chirality : 0.041 0.340 3870 Planarity : 0.003 0.039 4128 Dihedral : 7.326 71.552 3966 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.74 % Allowed : 17.11 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.16), residues: 2944 helix: 1.65 (0.15), residues: 1288 sheet: 0.07 (0.29), residues: 369 loop : -1.33 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 640 HIS 0.002 0.001 HIS C 792 PHE 0.021 0.001 PHE B 166 TYR 0.018 0.001 TYR D 571 ARG 0.007 0.000 ARG A 775 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5271.43 seconds wall clock time: 95 minutes 49.54 seconds (5749.54 seconds total)