Starting phenix.real_space_refine on Mon Apr 8 09:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t7h_41092/04_2024/8t7h_41092_updated.pdb" } resolution = 3.3 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= 0.005 sd= 0.032 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 104 5.16 5 C 8288 2.51 5 N 2247 2.21 5 O 2461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 560": "OD1" <-> "OD2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 560": "OD1" <-> "OD2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13100 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5614 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 508 Unresolved non-hydrogen angles: 638 Unresolved non-hydrogen dihedrals: 421 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "B" Number of atoms: 5618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5618 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 741} Chain breaks: 2 Unresolved non-hydrogen bonds: 504 Unresolved non-hydrogen angles: 634 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 10, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "C" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 920 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 922 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.18, per 1000 atoms: 0.55 Number of scatterers: 13100 At special positions: 0 Unit cell: (87.769, 121.099, 211.09, 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 104 16.00 O 2461 8.00 N 2247 7.00 C 8288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.5 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 20 sheets defined 38.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.798A pdb=" N GLU A 121 " --> pdb=" O ILE A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 224 through 236 Processing helix chain 'A' and resid 254 through 265 removed outlier: 3.689A pdb=" N PHE A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 258 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 259 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 335 through 343 removed outlier: 3.627A pdb=" N LEU A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 397 through 418 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.679A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 643 through 672 removed outlier: 3.592A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.673A pdb=" N SER A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 714 Processing helix chain 'A' and resid 737 through 760 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 766 through 793 removed outlier: 5.714A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) Proline residue: A 790 - end of helix removed outlier: 4.684A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 826 removed outlier: 4.313A pdb=" N VAL A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 102 through 117 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 224 through 236 Processing helix chain 'B' and resid 255 through 265 removed outlier: 4.037A pdb=" N LYS B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.617A pdb=" N LEU B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 397 through 418 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 434 through 443 removed outlier: 4.693A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 603 Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 643 through 672 Proline residue: B 655 - end of helix removed outlier: 3.573A pdb=" N SER B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 714 Processing helix chain 'B' and resid 737 through 760 Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 766 through 789 removed outlier: 5.706A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 826 removed outlier: 3.504A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL B 819 " --> pdb=" O GLY B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing sheet with id= A, first strand: chain 'A' and resid 28 through 31 Processing sheet with id= B, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.712A pdb=" N ALA A 275 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N CYS A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 302 " --> pdb=" O CYS A 276 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 325 through 329 Processing sheet with id= E, first strand: chain 'A' and resid 521 through 523 Processing sheet with id= F, first strand: chain 'A' and resid 541 through 543 Processing sheet with id= G, first strand: chain 'A' and resid 556 through 558 Processing sheet with id= H, first strand: chain 'A' and resid 718 through 722 removed outlier: 4.333A pdb=" N ASP A 718 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.389A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 169 through 171 Processing sheet with id= K, first strand: chain 'B' and resid 215 through 217 removed outlier: 3.691A pdb=" N ALA B 275 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 302 " --> pdb=" O CYS B 276 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 325 through 329 Processing sheet with id= M, first strand: chain 'B' and resid 521 through 523 Processing sheet with id= N, first strand: chain 'B' and resid 541 through 543 Processing sheet with id= O, first strand: chain 'B' and resid 556 through 558 Processing sheet with id= P, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= Q, first strand: chain 'C' and resid 6 through 9 Processing sheet with id= R, first strand: chain 'C' and resid 119 through 121 removed outlier: 5.481A pdb=" N ARG C 40 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 6 through 9 Processing sheet with id= T, first strand: chain 'D' and resid 119 through 121 removed outlier: 5.555A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2170 1.31 - 1.43: 3633 1.43 - 1.56: 7433 1.56 - 1.69: 0 1.69 - 1.82: 152 Bond restraints: 13388 Sorted by residual: bond pdb=" C04 QUS A 901 " pdb=" N14 QUS A 901 " ideal model delta sigma weight residual 1.324 1.438 -0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C04 QUS B 901 " pdb=" N14 QUS B 901 " ideal model delta sigma weight residual 1.324 1.437 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C05 QUS A 901 " pdb=" N15 QUS A 901 " ideal model delta sigma weight residual 1.331 1.438 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C05 QUS B 901 " pdb=" N15 QUS B 901 " ideal model delta sigma weight residual 1.331 1.437 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C05 QUS A 901 " pdb=" O20 QUS A 901 " ideal model delta sigma weight residual 1.331 1.420 -0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 13383 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 381 106.80 - 113.61: 7289 113.61 - 120.43: 4962 120.43 - 127.24: 5455 127.24 - 134.06: 156 Bond angle restraints: 18243 Sorted by residual: angle pdb=" C LEU B 711 " pdb=" N PHE B 712 " pdb=" CA PHE B 712 " ideal model delta sigma weight residual 122.06 116.38 5.68 1.86e+00 2.89e-01 9.32e+00 angle pdb=" CB MET A 802 " pdb=" CG MET A 802 " pdb=" SD MET A 802 " ideal model delta sigma weight residual 112.70 121.08 -8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" N GLN A 360 " pdb=" CA GLN A 360 " pdb=" CB GLN A 360 " ideal model delta sigma weight residual 110.28 114.58 -4.30 1.55e+00 4.16e-01 7.68e+00 angle pdb=" N GLN B 360 " pdb=" CA GLN B 360 " pdb=" CB GLN B 360 " ideal model delta sigma weight residual 110.28 114.53 -4.25 1.55e+00 4.16e-01 7.52e+00 angle pdb=" N TRP B 532 " pdb=" CA TRP B 532 " pdb=" C TRP B 532 " ideal model delta sigma weight residual 108.34 111.91 -3.57 1.31e+00 5.83e-01 7.42e+00 ... (remaining 18238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7188 17.93 - 35.86: 625 35.86 - 53.80: 107 53.80 - 71.73: 13 71.73 - 89.66: 8 Dihedral angle restraints: 7941 sinusoidal: 2751 harmonic: 5190 Sorted by residual: dihedral pdb=" CB CYS B 515 " pdb=" SG CYS B 515 " pdb=" SG CYS B 534 " pdb=" CB CYS B 534 " ideal model delta sinusoidal sigma weight residual 93.00 -177.69 -89.31 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS A 515 " pdb=" SG CYS A 515 " pdb=" SG CYS A 534 " pdb=" CB CYS A 534 " ideal model delta sinusoidal sigma weight residual 93.00 175.16 -82.16 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " pdb=" SG CYS A 531 " pdb=" CB CYS A 531 " ideal model delta sinusoidal sigma weight residual 93.00 25.10 67.90 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 7938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1206 0.033 - 0.065: 595 0.065 - 0.098: 188 0.098 - 0.131: 72 0.131 - 0.163: 6 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA THR A 742 " pdb=" N THR A 742 " pdb=" C THR A 742 " pdb=" CB THR A 742 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA THR B 742 " pdb=" N THR B 742 " pdb=" C THR B 742 " pdb=" CB THR B 742 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 2064 not shown) Planarity restraints: 2356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 307 " 0.019 2.00e-02 2.50e+03 1.53e-02 5.81e+00 pdb=" CG TRP A 307 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 307 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 307 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 307 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 307 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 307 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 307 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 107 " 0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO C 108 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 108 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 108 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 107 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D 108 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 108 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 108 " -0.027 5.00e-02 4.00e+02 ... (remaining 2353 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1740 2.75 - 3.29: 12732 3.29 - 3.83: 21252 3.83 - 4.36: 23253 4.36 - 4.90: 41589 Nonbonded interactions: 100566 Sorted by model distance: nonbonded pdb=" O SER B 116 " pdb=" OG SER B 120 " model vdw 2.217 2.440 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.219 2.440 nonbonded pdb=" O TYR B 629 " pdb=" OG1 THR B 632 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR B 311 " pdb=" OD1 ASP B 480 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 311 " pdb=" OD1 ASP A 480 " model vdw 2.257 2.440 ... (remaining 100561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 538 or (resid 539 and (name N or name CA or nam \ e C or name O or name CB )) or resid 540 through 827 or resid 901)) selection = (chain 'B' and (resid 25 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 540 or (resid 541 and (name N o \ r name CA or name C or name O or name CB )) or resid 542 through 827 or resid 90 \ 1)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 92 or (resid 93 through 94 and (name N or name C \ A or name C or name O or name CB )) or resid 95 through 125)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 8.880 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 37.820 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 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 : 0.004 0.114 13388 Z= 0.258 Angle : 0.588 8.385 18243 Z= 0.307 Chirality : 0.043 0.163 2067 Planarity : 0.004 0.055 2356 Dihedral : 13.372 89.659 4553 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.31 (0.21), residues: 1778 helix: 1.80 (0.20), residues: 700 sheet: -0.69 (0.31), residues: 298 loop : -0.90 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 307 HIS 0.005 0.001 HIS A 45 PHE 0.017 0.001 PHE B 456 TYR 0.016 0.001 TYR D 103 ARG 0.008 0.001 ARG A 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.378 Fit side-chains REVERT: B 307 TRP cc_start: 0.6663 (p-90) cc_final: 0.5934 (p-90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2854 time to fit residues: 71.5234 Evaluate side-chains 152 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 72 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13388 Z= 0.255 Angle : 0.567 10.500 18243 Z= 0.286 Chirality : 0.044 0.230 2067 Planarity : 0.004 0.039 2356 Dihedral : 4.497 60.316 1930 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.63 % Allowed : 7.12 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1778 helix: 1.85 (0.20), residues: 698 sheet: -0.89 (0.31), residues: 298 loop : -0.85 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 307 HIS 0.005 0.001 HIS A 45 PHE 0.030 0.002 PHE A 712 TYR 0.015 0.001 TYR A 481 ARG 0.007 0.001 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.502 Fit side-chains revert: symmetry clash REVERT: B 307 TRP cc_start: 0.6877 (p-90) cc_final: 0.6136 (p-90) outliers start: 8 outliers final: 5 residues processed: 164 average time/residue: 0.2913 time to fit residues: 67.8326 Evaluate side-chains 158 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 547 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 134 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 129 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13388 Z= 0.296 Angle : 0.579 8.809 18243 Z= 0.294 Chirality : 0.045 0.186 2067 Planarity : 0.004 0.038 2356 Dihedral : 4.568 61.480 1930 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.34 % Allowed : 11.31 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.27 (0.21), residues: 1778 helix: 1.87 (0.20), residues: 698 sheet: -0.95 (0.30), residues: 318 loop : -0.89 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 307 HIS 0.006 0.001 HIS A 44 PHE 0.027 0.002 PHE A 712 TYR 0.017 0.001 TYR B 481 ARG 0.009 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.451 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 14 residues processed: 164 average time/residue: 0.2880 time to fit residues: 67.0092 Evaluate side-chains 166 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13388 Z= 0.284 Angle : 0.569 8.391 18243 Z= 0.289 Chirality : 0.044 0.147 2067 Planarity : 0.004 0.038 2356 Dihedral : 4.556 61.302 1930 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.58 % Allowed : 13.84 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.27 (0.21), residues: 1778 helix: 1.83 (0.20), residues: 702 sheet: -0.97 (0.30), residues: 318 loop : -0.84 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 307 HIS 0.006 0.001 HIS A 44 PHE 0.025 0.002 PHE A 712 TYR 0.017 0.001 TYR B 481 ARG 0.008 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 1.397 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 170 average time/residue: 0.2675 time to fit residues: 65.3714 Evaluate side-chains 170 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 13388 Z= 0.471 Angle : 0.666 11.154 18243 Z= 0.342 Chirality : 0.048 0.278 2067 Planarity : 0.005 0.049 2356 Dihedral : 4.896 61.792 1930 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.01 % Allowed : 15.11 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.04 (0.21), residues: 1778 helix: 1.72 (0.20), residues: 698 sheet: -1.23 (0.29), residues: 318 loop : -0.99 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 307 HIS 0.010 0.001 HIS A 44 PHE 0.042 0.003 PHE B 456 TYR 0.022 0.002 TYR A 481 ARG 0.007 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 158 time to evaluate : 1.564 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 188 average time/residue: 0.2726 time to fit residues: 75.1601 Evaluate side-chains 179 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 172 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13388 Z= 0.332 Angle : 0.599 9.885 18243 Z= 0.308 Chirality : 0.046 0.368 2067 Planarity : 0.004 0.038 2356 Dihedral : 4.799 61.431 1930 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.53 % Allowed : 16.06 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.11 (0.21), residues: 1778 helix: 1.76 (0.20), residues: 696 sheet: -1.11 (0.30), residues: 318 loop : -0.96 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 307 HIS 0.008 0.001 HIS A 44 PHE 0.058 0.002 PHE A 544 TYR 0.020 0.002 TYR B 481 ARG 0.008 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.495 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 30 residues processed: 178 average time/residue: 0.2679 time to fit residues: 69.3497 Evaluate side-chains 183 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 0.0370 chunk 97 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 171 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13388 Z= 0.183 Angle : 0.546 12.045 18243 Z= 0.276 Chirality : 0.044 0.370 2067 Planarity : 0.004 0.041 2356 Dihedral : 4.514 60.588 1930 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.77 % Allowed : 16.77 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % 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: 0.27 (0.21), residues: 1778 helix: 1.85 (0.20), residues: 690 sheet: -0.99 (0.30), residues: 318 loop : -0.81 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 38 HIS 0.004 0.001 HIS A 44 PHE 0.018 0.001 PHE A 712 TYR 0.019 0.001 TYR A 547 ARG 0.010 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 155 time to evaluate : 1.368 Fit side-chains revert: symmetry clash REVERT: A 360 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: B 360 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8115 (mt0) outliers start: 35 outliers final: 26 residues processed: 180 average time/residue: 0.2633 time to fit residues: 69.0666 Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 360 GLN Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.0270 chunk 156 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13388 Z= 0.168 Angle : 0.549 11.387 18243 Z= 0.274 Chirality : 0.045 0.373 2067 Planarity : 0.004 0.039 2356 Dihedral : 4.399 60.282 1930 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.22 % Allowed : 17.88 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1778 helix: 1.89 (0.20), residues: 692 sheet: -0.94 (0.30), residues: 318 loop : -0.73 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 38 HIS 0.003 0.001 HIS A 218 PHE 0.020 0.001 PHE A 544 TYR 0.018 0.001 TYR A 547 ARG 0.010 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.514 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 176 average time/residue: 0.2668 time to fit residues: 68.7360 Evaluate side-chains 179 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 151 optimal weight: 0.0070 chunk 104 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13388 Z= 0.224 Angle : 0.566 12.176 18243 Z= 0.284 Chirality : 0.046 0.404 2067 Planarity : 0.004 0.038 2356 Dihedral : 4.442 60.852 1930 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.37 % Allowed : 17.64 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1778 helix: 1.83 (0.20), residues: 698 sheet: -0.94 (0.30), residues: 318 loop : -0.73 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 38 HIS 0.004 0.001 HIS A 218 PHE 0.024 0.002 PHE A 544 TYR 0.016 0.001 TYR A 547 ARG 0.010 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.342 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 29 residues processed: 174 average time/residue: 0.2711 time to fit residues: 68.3752 Evaluate side-chains 180 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13388 Z= 0.222 Angle : 0.573 13.013 18243 Z= 0.285 Chirality : 0.046 0.388 2067 Planarity : 0.004 0.038 2356 Dihedral : 4.436 60.861 1930 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.37 % Allowed : 17.88 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1778 helix: 1.82 (0.20), residues: 698 sheet: -0.91 (0.30), residues: 318 loop : -0.70 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 38 HIS 0.004 0.001 HIS A 44 PHE 0.018 0.001 PHE B 456 TYR 0.015 0.001 TYR A 481 ARG 0.010 0.001 ARG B 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 234 MET cc_start: 0.7898 (ptm) cc_final: 0.7698 (ptp) REVERT: A 393 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7101 (tp40) REVERT: A 429 MET cc_start: 0.6020 (mmm) cc_final: 0.5788 (mtp) REVERT: B 229 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7103 (mt-10) REVERT: B 393 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7023 (tp40) REVERT: B 429 MET cc_start: 0.6044 (mmm) cc_final: 0.5833 (mtp) REVERT: C 103 TYR cc_start: 0.7491 (m-80) cc_final: 0.6887 (m-80) outliers start: 30 outliers final: 28 residues processed: 174 average time/residue: 0.2745 time to fit residues: 69.2557 Evaluate side-chains 182 residues out of total 1542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 393 GLN Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 336 TRP Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 409 TYR Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 531 CYS Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 735 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.3980 chunk 130 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 59 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.143486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111688 restraints weight = 30351.178| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.94 r_work: 0.3602 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13388 Z= 0.286 Angle : 0.602 13.740 18243 Z= 0.301 Chirality : 0.047 0.402 2067 Planarity : 0.004 0.037 2356 Dihedral : 4.555 61.403 1930 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 17.96 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1778 helix: 1.75 (0.20), residues: 702 sheet: -0.95 (0.30), residues: 318 loop : -0.78 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 38 HIS 0.004 0.001 HIS A 44 PHE 0.024 0.002 PHE B 456 TYR 0.016 0.001 TYR B 481 ARG 0.010 0.001 ARG A 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.40 seconds wall clock time: 54 minutes 17.21 seconds (3257.21 seconds total)