Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 19:59:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/04_2023/6k1p_9719_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/04_2023/6k1p_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_9719/04_2023/6k1p_9719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/04_2023/6k1p_9719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/04_2023/6k1p_9719_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k1p_9719/04_2023/6k1p_9719_updated.pdb" } resolution = 3.87 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 8.45, 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: 7.39 Conformation dependent library (CDL) restraints added in 1.6 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: 6.02 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: 6.87 Time building geometry restraints manager: 7.89 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: 7612 32.67 - 65.33: 1438 65.33 - 98.00: 16 98.00 - 130.67: 2 130.67 - 163.34: 4 Dihedral angle restraints: 9072 sinusoidal: 5479 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 9069 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: 0.020 Extract box with map and model: 3.860 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 47.010 Find NCS groups from input model: 0.510 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.910 ------------------------------------------------------------------------------- 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 : 24.716 163.335 6746 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 % 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 *********************** 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 : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.3684 time to fit residues: 136.2915 Evaluate side-chains 158 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1294 time to fit residues: 1.8732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 125 GLN C 38 ASN D 46 HIS E 68 GLN G 38 ASN K 205 ASN K 230 GLN K 437 GLN K 477 ASN K 526 GLN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 16722 Z= 0.286 Angle : 0.682 8.699 23857 Z= 0.384 Chirality : 0.040 0.222 2712 Planarity : 0.005 0.070 2012 Dihedral : 29.339 163.380 4303 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 2.58 % 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: -2.56 (0.22), residues: 1210 helix: -0.86 (0.18), residues: 699 sheet: -2.39 (0.74), residues: 51 loop : -2.89 (0.26), residues: 460 *********************** 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 200 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 183 average time/residue: 0.2806 time to fit residues: 76.2352 Evaluate side-chains 157 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1362 time to fit residues: 4.8569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 110 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 132 optimal weight: 0.0270 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 overall best weight: 2.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 81 ASN F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 16722 Z= 0.252 Angle : 0.629 8.036 23857 Z= 0.356 Chirality : 0.038 0.281 2712 Planarity : 0.005 0.052 2012 Dihedral : 29.200 161.213 4303 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.24), residues: 1210 helix: -0.07 (0.20), residues: 711 sheet: -2.00 (0.77), residues: 51 loop : -2.72 (0.27), residues: 448 *********************** 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 190 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 179 average time/residue: 0.2955 time to fit residues: 77.3399 Evaluate side-chains 153 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1377 time to fit residues: 5.4178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 586 ASN K 601 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2873 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= 0.196 Angle : 0.583 7.567 23857 Z= 0.332 Chirality : 0.036 0.269 2712 Planarity : 0.004 0.038 2012 Dihedral : 29.007 161.596 4303 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 1.15 % 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: -1.02 (0.25), residues: 1210 helix: 0.47 (0.20), residues: 710 sheet: -2.27 (0.73), residues: 51 loop : -2.38 (0.28), residues: 449 *********************** 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 175 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 1.468 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 172 average time/residue: 0.2695 time to fit residues: 70.2303 Evaluate side-chains 148 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 141 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1500 time to fit residues: 3.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 0.0970 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: 0.7980 overall best weight: 2.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN F 25 ASN ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3048 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= 0.251 Angle : 0.609 8.585 23857 Z= 0.342 Chirality : 0.037 0.192 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.994 161.405 4303 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 2.49 % 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: 0.70 (0.21), residues: 699 sheet: -1.94 (0.78), residues: 50 loop : -2.28 (0.28), residues: 461 *********************** 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 173 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 160 average time/residue: 0.2645 time to fit residues: 64.5643 Evaluate side-chains 152 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1327 time to fit residues: 5.1908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 0.0670 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 0.0670 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 613 HIS ** 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: 0.7970 moved from start: 0.3315 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= 0.174 Angle : 0.561 7.436 23857 Z= 0.318 Chirality : 0.035 0.205 2712 Planarity : 0.004 0.038 2012 Dihedral : 28.820 161.773 4303 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.44 % 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: -0.37 (0.26), residues: 1210 helix: 1.09 (0.21), residues: 700 sheet: -1.83 (0.74), residues: 52 loop : -2.23 (0.28), residues: 458 *********************** 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 174 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.246 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 167 average time/residue: 0.2655 time to fit residues: 67.0744 Evaluate side-chains 153 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1539 time to fit residues: 4.1225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 140 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 0.0870 overall best weight: 3.9164 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 16722 Z= 0.340 Angle : 0.649 8.290 23857 Z= 0.361 Chirality : 0.039 0.203 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.982 160.735 4303 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 1.63 % 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: -0.61 (0.25), residues: 1210 helix: 0.86 (0.21), residues: 687 sheet: -1.98 (0.77), residues: 50 loop : -2.16 (0.29), residues: 473 *********************** 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 164 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.592 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 155 average time/residue: 0.2541 time to fit residues: 60.2747 Evaluate side-chains 146 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.400 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1331 time to fit residues: 4.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3562 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= 0.169 Angle : 0.569 7.507 23857 Z= 0.320 Chirality : 0.036 0.172 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.792 161.088 4303 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.57 % 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: -0.13 (0.26), residues: 1210 helix: 1.29 (0.21), residues: 682 sheet: -1.77 (0.77), residues: 50 loop : -2.00 (0.29), residues: 478 *********************** 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 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 1.383 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 159 average time/residue: 0.2570 time to fit residues: 62.4486 Evaluate side-chains 146 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1438 time to fit residues: 2.5493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 0.0030 chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 64 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** 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: 0.7915 moved from start: 0.3928 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= 0.149 Angle : 0.551 7.429 23857 Z= 0.310 Chirality : 0.035 0.237 2712 Planarity : 0.004 0.038 2012 Dihedral : 28.646 161.285 4303 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.29 % 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: 0.05 (0.26), residues: 1210 helix: 1.46 (0.21), residues: 686 sheet: -1.59 (0.77), residues: 52 loop : -2.02 (0.28), residues: 472 *********************** 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 161 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.595 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 160 average time/residue: 0.3017 time to fit residues: 71.3796 Evaluate side-chains 142 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2103 time to fit residues: 2.1896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** K 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3884 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 : 0.581 8.673 23857 Z= 0.324 Chirality : 0.036 0.240 2712 Planarity : 0.004 0.034 2012 Dihedral : 28.684 160.614 4303 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.19 % 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: -0.01 (0.25), residues: 1210 helix: 1.39 (0.21), residues: 688 sheet: -1.54 (0.76), residues: 52 loop : -2.02 (0.28), residues: 470 ********************** 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 155 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.283 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 154 average time/residue: 0.2742 time to fit residues: 63.5950 Evaluate side-chains 145 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1356 time to fit residues: 1.9673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 617 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 = 0.3896 r_free = 0.3896 target = 0.138514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.100769 restraints weight = 31133.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.101466 restraints weight = 19472.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102106 restraints weight = 14523.708| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3971 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 : 0.573 7.996 23857 Z= 0.320 Chirality : 0.036 0.234 2712 Planarity : 0.004 0.035 2012 Dihedral : 28.661 160.316 4303 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.48 % 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: 0.10 (0.25), residues: 1210 helix: 1.47 (0.21), residues: 685 sheet: -1.43 (0.77), residues: 52 loop : -1.95 (0.28), residues: 473 =============================================================================== Job complete usr+sys time: 2274.80 seconds wall clock time: 42 minutes 39.22 seconds (2559.22 seconds total)