Starting phenix.real_space_refine on Sat Mar 16 21:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/03_2024/6k1p_9719_updated.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9070 2.51 5 N 2911 2.21 5 O 3536 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 266": "NH1" <-> "NH2" Residue "K PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 308": "NH1" <-> "NH2" Residue "K ARG 341": "NH1" <-> "NH2" Residue "K PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "K GLU 495": "OE1" <-> "OE2" Residue "K TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 541": "NH1" <-> "NH2" Residue "K TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 611": "NH1" <-> "NH2" Residue "K ARG 614": "NH1" <-> "NH2" Residue "K ARG 639": "NH1" <-> "NH2" Residue "K ARG 645": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15841 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3826 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'peptide': 463, 'undetermined': 3} Link IDs: {'PTRANS': 17, 'TRANS': 445, None: 3} Not linked: pdbres="SER K 657 " pdbres="BEF K1201 " Not linked: pdbres="BEF K1201 " pdbres=" MG K1202 " Not linked: pdbres=" MG K1202 " pdbres="ADP K1203 " Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 8.37, per 1000 atoms: 0.53 Number of scatterers: 15841 At special positions: 0 Unit cell: (144.45, 129.47, 123.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3536 8.00 N 2911 7.00 C 9070 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 2 sheets defined 53.3% alpha, 2.0% beta 144 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 7.55 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.974A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 17 through 19 No H-bonds generated for 'chain 'B' and resid 17 through 19' Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 47 through 73 removed outlier: 3.959A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 80 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.554A pdb=" N ALA D 104 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 105 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 108 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 116 " --> pdb=" O LYS D 113 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 119 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER D 120 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.212A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.742A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.670A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 104 through 119 Processing helix chain 'K' and resid 200 through 210 removed outlier: 3.580A pdb=" N TRP K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU K 207 " --> pdb=" O GLY K 203 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER K 209 " --> pdb=" O ASN K 205 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU K 210 " --> pdb=" O TRP K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 240 Processing helix chain 'K' and resid 255 through 267 removed outlier: 4.093A pdb=" N ASN K 258 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU K 261 " --> pdb=" O ASN K 258 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG K 262 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE K 264 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG K 266 " --> pdb=" O GLU K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 287 No H-bonds generated for 'chain 'K' and resid 284 through 287' Processing helix chain 'K' and resid 328 through 330 No H-bonds generated for 'chain 'K' and resid 328 through 330' Processing helix chain 'K' and resid 335 through 341 removed outlier: 4.196A pdb=" N ARG K 341 " --> pdb=" O SER K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 370 removed outlier: 3.584A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 379 through 382 No H-bonds generated for 'chain 'K' and resid 379 through 382' Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.614A pdb=" N LEU K 401 " --> pdb=" O ILE K 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 397 through 401' Processing helix chain 'K' and resid 414 through 417 No H-bonds generated for 'chain 'K' and resid 414 through 417' Processing helix chain 'K' and resid 435 through 445 removed outlier: 3.524A pdb=" N LYS K 443 " --> pdb=" O LYS K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 475 removed outlier: 3.717A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 removed outlier: 3.793A pdb=" N PHE K 482 " --> pdb=" O PRO K 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 479 through 482' Processing helix chain 'K' and resid 495 through 500 removed outlier: 3.567A pdb=" N VAL K 498 " --> pdb=" O GLU K 495 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN K 500 " --> pdb=" O LEU K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 517 removed outlier: 3.563A pdb=" N LYS K 509 " --> pdb=" O GLN K 505 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 538 removed outlier: 3.865A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 555 through 564 removed outlier: 3.724A pdb=" N GLN K 559 " --> pdb=" O GLU K 555 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE K 561 " --> pdb=" O ARG K 557 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP K 562 " --> pdb=" O ILE K 558 " (cutoff:3.500A) Processing helix chain 'K' and resid 578 through 581 No H-bonds generated for 'chain 'K' and resid 578 through 581' Processing helix chain 'K' and resid 602 through 609 removed outlier: 3.624A pdb=" N LEU K 606 " --> pdb=" O PRO K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 655 removed outlier: 3.610A pdb=" N ALA K 640 " --> pdb=" O ILE K 636 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN K 642 " --> pdb=" O GLU K 638 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU K 644 " --> pdb=" O ALA K 640 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN K 652 " --> pdb=" O GLN K 648 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 321 through 323 removed outlier: 7.245A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA K 252 " --> pdb=" O ALA K 301 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 425 through 431 removed outlier: 3.533A pdb=" N VAL K 623 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 593 " --> pdb=" O PHE K 624 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU K 626 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU K 595 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR K 628 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE K 524 " --> pdb=" O VAL K 594 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2929 1.33 - 1.45: 5243 1.45 - 1.57: 7919 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 16722 Sorted by residual: bond pdb=" BE BEF K1201 " pdb=" F2 BEF K1201 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" BE BEF K1201 " pdb=" F1 BEF K1201 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" BE BEF K1201 " pdb=" F3 BEF K1201 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.508 -0.086 3.00e-02 1.11e+03 8.25e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.15e+00 ... (remaining 16717 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.19: 1391 105.19 - 112.88: 9421 112.88 - 120.58: 7788 120.58 - 128.27: 4895 128.27 - 135.96: 362 Bond angle restraints: 23857 Sorted by residual: angle pdb=" F1 BEF K1201 " pdb=" BE BEF K1201 " pdb=" F3 BEF K1201 " ideal model delta sigma weight residual 120.12 98.83 21.29 3.00e+00 1.11e-01 5.04e+01 angle pdb=" N PHE K 248 " pdb=" CA PHE K 248 " pdb=" C PHE K 248 " ideal model delta sigma weight residual 111.02 118.82 -7.80 1.25e+00 6.40e-01 3.89e+01 angle pdb=" N ILE K 275 " pdb=" CA ILE K 275 " pdb=" C ILE K 275 " ideal model delta sigma weight residual 109.34 98.85 10.49 2.08e+00 2.31e-01 2.54e+01 angle pdb=" N ALA K 273 " pdb=" CA ALA K 273 " pdb=" C ALA K 273 " ideal model delta sigma weight residual 108.38 115.06 -6.68 1.35e+00 5.49e-01 2.45e+01 angle pdb=" F2 BEF K1201 " pdb=" BE BEF K1201 " pdb=" F3 BEF K1201 " ideal model delta sigma weight residual 119.96 105.14 14.82 3.00e+00 1.11e-01 2.44e+01 ... (remaining 23852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 7787 32.67 - 65.33: 1519 65.33 - 98.00: 16 98.00 - 130.67: 2 130.67 - 163.34: 4 Dihedral angle restraints: 9328 sinusoidal: 5735 harmonic: 3593 Sorted by residual: dihedral pdb=" C5' ADP K1203 " pdb=" O5' ADP K1203 " pdb=" PA ADP K1203 " pdb=" O2A ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 80.71 -140.70 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O2A ADP K1203 " pdb=" O3A ADP K1203 " pdb=" PA ADP K1203 " pdb=" PB ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 71.04 -131.04 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP K1203 " pdb=" O3A ADP K1203 " pdb=" PB ADP K1203 " pdb=" PA ADP K1203 " ideal model delta sinusoidal sigma weight residual -60.00 63.66 -123.66 1 2.00e+01 2.50e-03 3.73e+01 ... (remaining 9325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2086 0.065 - 0.129: 548 0.129 - 0.194: 64 0.194 - 0.258: 10 0.258 - 0.323: 4 Chirality restraints: 2712 Sorted by residual: chirality pdb=" CA ILE K 275 " pdb=" N ILE K 275 " pdb=" C ILE K 275 " pdb=" CB ILE K 275 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASN K 542 " pdb=" N ASN K 542 " pdb=" C ASN K 542 " pdb=" CB ASN K 542 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASP K 494 " pdb=" N ASP K 494 " pdb=" C ASP K 494 " pdb=" CB ASP K 494 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 2709 not shown) Planarity restraints: 2012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " 0.034 2.00e-02 2.50e+03 1.44e-02 5.74e+00 pdb=" N9 DA I 91 " -0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO D 100 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.032 2.00e-02 2.50e+03 1.49e-02 5.56e+00 pdb=" N1 DT I 88 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " -0.017 2.00e-02 2.50e+03 ... (remaining 2009 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 35 2.45 - 3.06: 9124 3.06 - 3.68: 24819 3.68 - 4.29: 37579 4.29 - 4.90: 54822 Nonbonded interactions: 126379 Sorted by model distance: nonbonded pdb=" O SER D 33 " pdb=" CD1 TYR D 34 " model vdw 1.838 3.340 nonbonded pdb=" O GLY K 584 " pdb=" F2 BEF K1201 " model vdw 2.196 2.390 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.283 2.440 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.287 2.520 nonbonded pdb=" OD1 ASP K 494 " pdb=" N HIS K 496 " model vdw 2.309 2.520 ... (remaining 126374 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.160 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 49.450 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.010 0.232 16722 Z= 0.591 Angle : 1.035 21.289 23857 Z= 0.578 Chirality : 0.057 0.323 2712 Planarity : 0.007 0.060 2012 Dihedral : 24.900 163.335 7002 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.51 % Favored : 90.91 % Rotamer: Outliers : 0.10 % Allowed : 1.34 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.18), residues: 1210 helix: -2.64 (0.14), residues: 687 sheet: -2.80 (0.71), residues: 49 loop : -3.29 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K 267 HIS 0.010 0.002 HIS K 327 PHE 0.033 0.004 PHE F 100 TYR 0.039 0.004 TYR H 37 ARG 0.011 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8661 (m-10) cc_final: 0.8229 (m-80) REVERT: C 74 LYS cc_start: 0.8910 (mttt) cc_final: 0.8505 (pttm) REVERT: D 80 TYR cc_start: 0.8056 (m-10) cc_final: 0.7772 (m-10) REVERT: E 122 LYS cc_start: 0.8305 (pttt) cc_final: 0.8105 (pttp) REVERT: F 88 TYR cc_start: 0.8739 (m-10) cc_final: 0.7965 (m-80) REVERT: G 90 ASP cc_start: 0.8537 (t70) cc_final: 0.7581 (t0) REVERT: G 95 LYS cc_start: 0.8618 (tptm) cc_final: 0.8347 (mtpp) REVERT: H 80 TYR cc_start: 0.7648 (m-10) cc_final: 0.6920 (m-10) REVERT: K 350 LEU cc_start: 0.8984 (tp) cc_final: 0.8704 (tp) REVERT: K 351 ILE cc_start: 0.8521 (mt) cc_final: 0.8300 (pt) REVERT: K 362 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7231 (mt-10) REVERT: K 470 MET cc_start: 0.8401 (tpt) cc_final: 0.8085 (tpp) REVERT: K 511 LEU cc_start: 0.8520 (mt) cc_final: 0.8199 (tt) REVERT: K 527 MET cc_start: 0.7930 (mtm) cc_final: 0.7709 (mtp) REVERT: K 586 ASN cc_start: 0.8210 (t0) cc_final: 0.6590 (p0) REVERT: K 599 ASP cc_start: 0.7596 (t0) cc_final: 0.6923 (t0) REVERT: K 635 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7776 (mtmm) REVERT: K 648 GLN cc_start: 0.7559 (tp-100) cc_final: 0.7003 (tm-30) outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.3651 time to fit residues: 135.9363 Evaluate side-chains 165 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 492 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 0.0870 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 46 HIS E 68 GLN G 38 ASN G 89 ASN H 81 ASN K 205 ASN ** K 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 GLN K 477 ASN K 526 GLN ** K 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16722 Z= 0.197 Angle : 0.661 7.641 23857 Z= 0.372 Chirality : 0.039 0.173 2712 Planarity : 0.005 0.072 2012 Dihedral : 29.141 163.104 4560 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.72 % Allowed : 10.14 % Favored : 88.13 % 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: -2.69 (0.22), residues: 1210 helix: -0.98 (0.18), residues: 711 sheet: -2.59 (0.69), residues: 56 loop : -2.93 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.004 0.001 HIS K 361 PHE 0.018 0.002 PHE K 185 TYR 0.021 0.002 TYR D 37 ARG 0.008 0.001 ARG K 655 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.7972 (pp30) cc_final: 0.7532 (pp30) REVERT: E 77 ASP cc_start: 0.8332 (m-30) cc_final: 0.7392 (t0) REVERT: H 30 ARG cc_start: 0.7669 (ptp90) cc_final: 0.7291 (ptp-170) REVERT: K 219 LEU cc_start: 0.8153 (tt) cc_final: 0.7931 (tt) REVERT: K 350 LEU cc_start: 0.8869 (tp) cc_final: 0.8376 (tt) REVERT: K 351 ILE cc_start: 0.8583 (mt) cc_final: 0.8198 (mt) REVERT: K 470 MET cc_start: 0.8193 (tpt) cc_final: 0.7918 (tpp) REVERT: K 586 ASN cc_start: 0.8064 (t0) cc_final: 0.6627 (p0) REVERT: K 599 ASP cc_start: 0.7546 (t0) cc_final: 0.7006 (t0) outliers start: 18 outliers final: 10 residues processed: 194 average time/residue: 0.2726 time to fit residues: 78.1545 Evaluate side-chains 166 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 425 LYS Chi-restraints excluded: chain K residue 532 ASP Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 0.0870 overall best weight: 3.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN D 81 ASN F 25 ASN G 89 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16722 Z= 0.318 Angle : 0.670 8.140 23857 Z= 0.376 Chirality : 0.040 0.249 2712 Planarity : 0.005 0.049 2012 Dihedral : 28.921 161.342 4559 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.35 % Allowed : 11.20 % Favored : 85.45 % 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: -1.84 (0.24), residues: 1210 helix: -0.21 (0.19), residues: 711 sheet: -2.25 (0.72), residues: 56 loop : -2.73 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 260 HIS 0.004 0.001 HIS K 554 PHE 0.019 0.002 PHE K 375 TYR 0.016 0.002 TYR C 57 ARG 0.005 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8876 (m-80) cc_final: 0.8641 (m-80) REVERT: A 76 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8203 (tm-30) REVERT: D 49 THR cc_start: 0.8775 (m) cc_final: 0.8559 (p) REVERT: E 77 ASP cc_start: 0.8422 (m-30) cc_final: 0.7308 (t0) REVERT: H 30 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7436 (ptp-170) REVERT: K 276 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8459 (tt) REVERT: K 335 MET cc_start: 0.8429 (tpp) cc_final: 0.8082 (tpp) REVERT: K 350 LEU cc_start: 0.8763 (tp) cc_final: 0.8432 (tp) REVERT: K 470 MET cc_start: 0.8276 (tpt) cc_final: 0.7927 (tpp) REVERT: K 599 ASP cc_start: 0.7677 (t0) cc_final: 0.7057 (t0) outliers start: 35 outliers final: 25 residues processed: 188 average time/residue: 0.2766 time to fit residues: 77.2596 Evaluate side-chains 173 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 chunk 141 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 25 ASN K 586 ASN K 613 HIS ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16722 Z= 0.150 Angle : 0.565 11.684 23857 Z= 0.321 Chirality : 0.035 0.170 2712 Planarity : 0.004 0.040 2012 Dihedral : 28.539 162.159 4559 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % 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: -0.90 (0.25), residues: 1210 helix: 0.56 (0.20), residues: 709 sheet: -1.98 (0.76), residues: 50 loop : -2.35 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 384 HIS 0.005 0.001 HIS B 75 PHE 0.021 0.001 PHE K 375 TYR 0.017 0.001 TYR D 80 ARG 0.003 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 GLN cc_start: 0.9385 (tp40) cc_final: 0.9035 (tp40) REVERT: E 76 GLN cc_start: 0.8205 (pp30) cc_final: 0.7854 (tm-30) REVERT: E 77 ASP cc_start: 0.8232 (m-30) cc_final: 0.7352 (t0) REVERT: G 95 LYS cc_start: 0.8611 (tptm) cc_final: 0.8350 (mtpp) REVERT: H 30 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7403 (ptp-170) REVERT: K 276 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8578 (tt) REVERT: K 335 MET cc_start: 0.8310 (tpp) cc_final: 0.7974 (tpp) REVERT: K 350 LEU cc_start: 0.8702 (tp) cc_final: 0.8396 (tp) REVERT: K 469 MET cc_start: 0.7361 (mmp) cc_final: 0.7059 (mtt) REVERT: K 559 GLN cc_start: 0.8065 (mt0) cc_final: 0.7618 (tm-30) REVERT: K 599 ASP cc_start: 0.7665 (t0) cc_final: 0.7101 (t0) outliers start: 21 outliers final: 8 residues processed: 188 average time/residue: 0.2601 time to fit residues: 73.2814 Evaluate side-chains 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 overall best weight: 2.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 93 GLN F 25 ASN K 601 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16722 Z= 0.243 Angle : 0.597 7.370 23857 Z= 0.337 Chirality : 0.037 0.239 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.561 161.744 4559 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.16 % Allowed : 14.16 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.25), residues: 1210 helix: 0.69 (0.21), residues: 709 sheet: -1.99 (0.76), residues: 50 loop : -2.33 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 384 HIS 0.008 0.001 HIS B 75 PHE 0.018 0.001 PHE K 375 TYR 0.029 0.002 TYR D 80 ARG 0.005 0.000 ARG K 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8549 (mm) REVERT: E 76 GLN cc_start: 0.8367 (pp30) cc_final: 0.7968 (tm-30) REVERT: E 77 ASP cc_start: 0.8388 (m-30) cc_final: 0.7242 (t0) REVERT: G 95 LYS cc_start: 0.8664 (tptm) cc_final: 0.8378 (mtpp) REVERT: H 30 ARG cc_start: 0.7801 (ptp90) cc_final: 0.7498 (ptp-170) REVERT: H 98 LEU cc_start: 0.9035 (tt) cc_final: 0.8753 (tt) REVERT: K 225 LEU cc_start: 0.8650 (mm) cc_final: 0.8290 (mm) REVERT: K 276 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8706 (tt) REVERT: K 335 MET cc_start: 0.8393 (tpp) cc_final: 0.8104 (tpp) REVERT: K 350 LEU cc_start: 0.8689 (tp) cc_final: 0.8343 (tp) REVERT: K 599 ASP cc_start: 0.7753 (t0) cc_final: 0.7150 (t0) outliers start: 33 outliers final: 23 residues processed: 170 average time/residue: 0.2643 time to fit residues: 67.3149 Evaluate side-chains 165 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 93 GLN F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16722 Z= 0.201 Angle : 0.571 8.465 23857 Z= 0.324 Chirality : 0.036 0.229 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.479 161.727 4559 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.87 % Allowed : 15.02 % Favored : 82.11 % 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: -0.54 (0.25), residues: 1210 helix: 0.89 (0.21), residues: 709 sheet: -1.83 (0.77), residues: 50 loop : -2.27 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 384 HIS 0.008 0.001 HIS B 75 PHE 0.019 0.001 PHE K 375 TYR 0.021 0.002 TYR K 537 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 147 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8365 (pp30) cc_final: 0.8012 (tm-30) REVERT: E 77 ASP cc_start: 0.8333 (m-30) cc_final: 0.7293 (t0) REVERT: G 95 LYS cc_start: 0.8670 (tptm) cc_final: 0.8384 (mtpp) REVERT: H 30 ARG cc_start: 0.7846 (ptp90) cc_final: 0.7527 (ptp-170) REVERT: H 98 LEU cc_start: 0.9013 (tt) cc_final: 0.8766 (tt) REVERT: K 225 LEU cc_start: 0.8594 (mm) cc_final: 0.8283 (mm) REVERT: K 276 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8751 (tt) REVERT: K 335 MET cc_start: 0.8383 (tpp) cc_final: 0.8092 (tpp) REVERT: K 350 LEU cc_start: 0.8702 (tp) cc_final: 0.8356 (tp) REVERT: K 599 ASP cc_start: 0.7753 (t0) cc_final: 0.7143 (t0) outliers start: 30 outliers final: 21 residues processed: 163 average time/residue: 0.2443 time to fit residues: 61.3219 Evaluate side-chains 164 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 0.5980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16722 Z= 0.189 Angle : 0.560 8.164 23857 Z= 0.319 Chirality : 0.036 0.208 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.441 161.741 4559 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.25 % Allowed : 14.55 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1210 helix: 1.09 (0.21), residues: 703 sheet: -1.72 (0.78), residues: 50 loop : -2.21 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 384 HIS 0.008 0.001 HIS B 75 PHE 0.018 0.001 PHE K 375 TYR 0.020 0.001 TYR K 537 ARG 0.003 0.000 ARG K 411 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8378 (pp30) cc_final: 0.8020 (tm-30) REVERT: E 77 ASP cc_start: 0.8303 (m-30) cc_final: 0.7295 (t0) REVERT: G 95 LYS cc_start: 0.8658 (tptm) cc_final: 0.8376 (mtpp) REVERT: H 30 ARG cc_start: 0.7806 (ptp90) cc_final: 0.7477 (ptp-170) REVERT: H 98 LEU cc_start: 0.8982 (tt) cc_final: 0.8744 (tt) REVERT: K 276 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8785 (tt) REVERT: K 335 MET cc_start: 0.8365 (tpp) cc_final: 0.8073 (tpp) REVERT: K 350 LEU cc_start: 0.8708 (tp) cc_final: 0.8373 (tp) REVERT: K 599 ASP cc_start: 0.7719 (t0) cc_final: 0.7119 (t0) outliers start: 34 outliers final: 25 residues processed: 173 average time/residue: 0.2493 time to fit residues: 65.8183 Evaluate side-chains 173 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 534 LEU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16722 Z= 0.310 Angle : 0.639 9.086 23857 Z= 0.356 Chirality : 0.039 0.263 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.615 160.748 4559 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.16 % Allowed : 14.74 % Favored : 82.11 % 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: -0.56 (0.25), residues: 1210 helix: 0.85 (0.21), residues: 696 sheet: -1.79 (0.79), residues: 50 loop : -2.14 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 260 HIS 0.007 0.001 HIS B 75 PHE 0.016 0.002 PHE K 375 TYR 0.021 0.002 TYR K 537 ARG 0.003 0.000 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 147 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8537 (mm) REVERT: E 76 GLN cc_start: 0.8438 (pp30) cc_final: 0.8036 (tm-30) REVERT: E 77 ASP cc_start: 0.8418 (m-30) cc_final: 0.7149 (t0) REVERT: E 90 MET cc_start: 0.8010 (mmp) cc_final: 0.7573 (mmm) REVERT: F 79 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9125 (mmmt) REVERT: G 95 LYS cc_start: 0.8681 (tptm) cc_final: 0.8479 (mtpt) REVERT: H 30 ARG cc_start: 0.7820 (ptp90) cc_final: 0.7513 (ptp-170) REVERT: H 98 LEU cc_start: 0.9204 (tt) cc_final: 0.8963 (tt) REVERT: K 225 LEU cc_start: 0.8489 (mm) cc_final: 0.8163 (mm) REVERT: K 276 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8809 (tt) REVERT: K 335 MET cc_start: 0.8483 (tpp) cc_final: 0.8097 (tpp) REVERT: K 350 LEU cc_start: 0.8786 (tp) cc_final: 0.8452 (tp) REVERT: K 599 ASP cc_start: 0.7829 (t0) cc_final: 0.7145 (t0) outliers start: 33 outliers final: 26 residues processed: 169 average time/residue: 0.2488 time to fit residues: 65.1650 Evaluate side-chains 166 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16722 Z= 0.239 Angle : 0.600 9.156 23857 Z= 0.337 Chirality : 0.037 0.251 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.550 160.728 4559 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.06 % Allowed : 15.41 % Favored : 81.53 % 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 (0.25), residues: 1210 helix: 1.00 (0.21), residues: 692 sheet: -1.73 (0.79), residues: 50 loop : -2.06 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 384 HIS 0.007 0.001 HIS B 75 PHE 0.016 0.001 PHE K 375 TYR 0.020 0.002 TYR K 537 ARG 0.004 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 142 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 76 GLN cc_start: 0.8434 (pp30) cc_final: 0.8025 (tm-30) REVERT: E 77 ASP cc_start: 0.8409 (m-30) cc_final: 0.7194 (t0) REVERT: E 90 MET cc_start: 0.8016 (mmp) cc_final: 0.7570 (mmm) REVERT: F 79 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9091 (mmmt) REVERT: G 95 LYS cc_start: 0.8682 (tptm) cc_final: 0.8385 (mtpp) REVERT: H 30 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7526 (ptp-170) REVERT: H 98 LEU cc_start: 0.9139 (tt) cc_final: 0.8896 (tt) REVERT: K 225 LEU cc_start: 0.8436 (mm) cc_final: 0.8099 (mm) REVERT: K 276 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8827 (tt) REVERT: K 335 MET cc_start: 0.8455 (tpp) cc_final: 0.8115 (tpp) REVERT: K 350 LEU cc_start: 0.8765 (tp) cc_final: 0.8427 (tp) REVERT: K 469 MET cc_start: 0.7389 (mmp) cc_final: 0.7113 (mtt) REVERT: K 599 ASP cc_start: 0.7798 (t0) cc_final: 0.7120 (t0) outliers start: 32 outliers final: 26 residues processed: 164 average time/residue: 0.2514 time to fit residues: 64.0963 Evaluate side-chains 165 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 336 LEU Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 506 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 0.0010 chunk 115 optimal weight: 0.2980 chunk 12 optimal weight: 0.0010 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 1.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16722 Z= 0.177 Angle : 0.577 17.043 23857 Z= 0.322 Chirality : 0.035 0.236 2712 Planarity : 0.004 0.036 2012 Dihedral : 28.413 160.890 4559 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.30 % Allowed : 16.56 % Favored : 81.15 % 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: -0.04 (0.26), residues: 1210 helix: 1.31 (0.21), residues: 686 sheet: -1.57 (0.81), residues: 50 loop : -1.93 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 384 HIS 0.008 0.001 HIS B 75 PHE 0.015 0.001 PHE K 375 TYR 0.018 0.001 TYR K 537 ARG 0.004 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 98 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8507 (mm) REVERT: D 102 GLU cc_start: 0.7025 (tp30) cc_final: 0.6316 (tp30) REVERT: E 76 GLN cc_start: 0.8444 (pp30) cc_final: 0.8035 (tm-30) REVERT: E 77 ASP cc_start: 0.8354 (m-30) cc_final: 0.7310 (t0) REVERT: F 79 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9052 (mmtt) REVERT: G 95 LYS cc_start: 0.8696 (tptm) cc_final: 0.8406 (mtpp) REVERT: H 30 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7491 (ptp-170) REVERT: H 98 LEU cc_start: 0.9096 (tt) cc_final: 0.8853 (tt) REVERT: K 225 LEU cc_start: 0.8322 (mm) cc_final: 0.7954 (mm) REVERT: K 276 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8793 (tt) REVERT: K 335 MET cc_start: 0.8410 (tpp) cc_final: 0.8134 (tpp) REVERT: K 350 LEU cc_start: 0.8704 (tp) cc_final: 0.8360 (tp) REVERT: K 599 ASP cc_start: 0.7761 (t0) cc_final: 0.7065 (t0) outliers start: 24 outliers final: 19 residues processed: 165 average time/residue: 0.2491 time to fit residues: 63.1126 Evaluate side-chains 168 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 238 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 359 ASN Chi-restraints excluded: chain K residue 417 VAL Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 25 ASN ** K 617 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 = 0.3878 r_free = 0.3878 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.099347 restraints weight = 31122.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.100682 restraints weight = 21025.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101184 restraints weight = 16272.845| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16722 Z= 0.188 Angle : 0.571 9.390 23857 Z= 0.322 Chirality : 0.036 0.234 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.403 160.922 4559 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.87 % Allowed : 16.56 % Favored : 80.57 % 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: -0.03 (0.26), residues: 1210 helix: 1.30 (0.21), residues: 690 sheet: -1.49 (0.81), residues: 50 loop : -1.93 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 384 HIS 0.008 0.001 HIS B 75 PHE 0.015 0.001 PHE K 375 TYR 0.023 0.002 TYR K 537 ARG 0.004 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.30 seconds wall clock time: 45 minutes 33.86 seconds (2733.86 seconds total)