Starting phenix.real_space_refine (version: dev) on Tue Feb 21 16:18:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/02_2023/7lyt_23601_updated.pdb" } resolution = 2.9 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= 0.298 sd= 1.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 899 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A ARG 595": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 697": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 14354 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 11358 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 41, 'TRANS': 670} Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1259 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1045 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 689 Unusual residues: {' SC': 3} Classifications: {'DNA': 20, 'undetermined': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19, None: 3} Not linked: pdbres=" DA D 10 " pdbres=" SC D 11 " Not linked: pdbres=" SC D 11 " pdbres=" SC D 12 " Not linked: pdbres=" SC D 12 " pdbres=" SC D 13 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10645 SG CYS A 667 19.951 34.452 36.126 1.00 74.36 S ATOM 10691 SG CYS A 670 19.371 30.891 34.874 1.00 74.35 S ATOM 10893 SG CYS A 685 20.918 33.488 32.615 1.00 72.22 S ATOM 10933 SG CYS A 688 17.233 33.644 33.534 1.00 73.11 S Time building chain proxies: 7.50, per 1000 atoms: 0.52 Number of scatterers: 14354 At special positions: 0 Unit cell: (88.085, 98.12, 124.88, 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) Zn 1 29.99 S 24 16.00 P 94 15.00 Mg 2 11.99 O 1644 8.00 N 1392 7.00 C 4475 6.00 H 6722 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 685 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 670 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 667 " Number of angles added : 6 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 4 sheets defined 39.2% alpha, 7.7% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 6.37 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 126 through 168 removed outlier: 3.882A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.513A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 372 through 382 removed outlier: 3.513A pdb=" N THR A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.901A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 550 through 565 Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.751A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.686A pdb=" N ARG A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.583A pdb=" N HIS A 65 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 310 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS A 69 " --> pdb=" O TRP A 308 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP A 308 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.705A pdb=" N ALA A 261 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 388 through 395 removed outlier: 6.163A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 606 211 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 6711 1.09 - 1.35: 2334 1.35 - 1.61: 5600 1.61 - 1.86: 55 1.86 - 2.12: 3 Bond restraints: 14703 Sorted by residual: bond pdb=" P SC D 11 " pdb=" S2P SC D 11 " ideal model delta sigma weight residual 1.882 2.120 -0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" P SC D 13 " pdb=" S2P SC D 13 " ideal model delta sigma weight residual 1.882 2.119 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" P SC D 12 " pdb=" S2P SC D 12 " ideal model delta sigma weight residual 1.882 2.118 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C2 SC D 12 " pdb=" N3 SC D 12 " ideal model delta sigma weight residual 1.504 1.317 0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" C2 SC D 13 " pdb=" N3 SC D 13 " ideal model delta sigma weight residual 1.504 1.317 0.187 2.00e-02 2.50e+03 8.73e+01 ... (remaining 14698 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 805 106.92 - 113.70: 16705 113.70 - 120.48: 5273 120.48 - 127.25: 3564 127.25 - 134.03: 227 Bond angle restraints: 26574 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 104.87 -3.27 1.50e+00 4.44e-01 4.75e+00 angle pdb=" C3' DC C -6 " pdb=" C2' DC C -6 " pdb=" C1' DC C -6 " ideal model delta sigma weight residual 101.60 104.48 -2.88 1.50e+00 4.44e-01 3.69e+00 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 113.29 109.54 3.75 2.00e+00 2.50e-01 3.52e+00 angle pdb=" C LYS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 120.53 125.13 -4.60 2.52e+00 1.57e-01 3.33e+00 angle pdb=" N THR A 409 " pdb=" CA THR A 409 " pdb=" C THR A 409 " ideal model delta sigma weight residual 109.81 107.07 2.74 1.53e+00 4.27e-01 3.20e+00 ... (remaining 26569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 5426 34.33 - 68.65: 284 68.65 - 102.98: 27 102.98 - 137.30: 0 137.30 - 171.63: 2 Dihedral angle restraints: 5739 sinusoidal: 3352 harmonic: 2387 Sorted by residual: dihedral pdb=" O4' G B -20 " pdb=" C1' G B -20 " pdb=" N9 G B -20 " pdb=" C4 G B -20 " ideal model delta sinusoidal sigma weight residual 68.00 144.05 -76.05 1 1.70e+01 3.46e-03 2.52e+01 dihedral pdb=" CA GLN A 410 " pdb=" C GLN A 410 " pdb=" N GLU A 411 " pdb=" CA GLU A 411 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DC D -7 " ideal model delta sinusoidal sigma weight residual 220.00 48.37 171.63 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.051: 333 0.051 - 0.077: 101 0.077 - 0.102: 46 0.102 - 0.128: 23 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 351 " pdb=" N ILE A 351 " pdb=" C ILE A 351 " pdb=" CB ILE A 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL A 601 " pdb=" N VAL A 601 " pdb=" C VAL A 601 " pdb=" CB VAL A 601 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1257 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' SC D 11 " 0.174 2.00e-02 2.50e+03 5.96e-01 7.11e+03 pdb=" C2' SC D 11 " -1.038 2.00e-02 2.50e+03 pdb=" C3' SC D 11 " -0.424 2.00e-02 2.50e+03 pdb=" C4' SC D 11 " 0.418 2.00e-02 2.50e+03 pdb=" C5' SC D 11 " -0.352 2.00e-02 2.50e+03 pdb=" N1 SC D 11 " -0.159 2.00e-02 2.50e+03 pdb=" O3' SC D 11 " 0.314 2.00e-02 2.50e+03 pdb=" O4' SC D 11 " 1.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 13 " 0.291 2.00e-02 2.50e+03 5.42e-01 5.88e+03 pdb=" C2' SC D 13 " -0.901 2.00e-02 2.50e+03 pdb=" C3' SC D 13 " -0.390 2.00e-02 2.50e+03 pdb=" C4' SC D 13 " 0.366 2.00e-02 2.50e+03 pdb=" C5' SC D 13 " -0.448 2.00e-02 2.50e+03 pdb=" N1 SC D 13 " -0.206 2.00e-02 2.50e+03 pdb=" O3' SC D 13 " 0.426 2.00e-02 2.50e+03 pdb=" O4' SC D 13 " 0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 12 " 0.404 2.00e-02 2.50e+03 3.54e-01 2.51e+03 pdb=" C2' SC D 12 " -0.337 2.00e-02 2.50e+03 pdb=" C3' SC D 12 " -0.358 2.00e-02 2.50e+03 pdb=" C4' SC D 12 " 0.330 2.00e-02 2.50e+03 pdb=" C5' SC D 12 " -0.401 2.00e-02 2.50e+03 pdb=" N1 SC D 12 " -0.311 2.00e-02 2.50e+03 pdb=" O3' SC D 12 " 0.284 2.00e-02 2.50e+03 pdb=" O4' SC D 12 " 0.388 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 681 2.17 - 2.78: 26188 2.78 - 3.39: 38073 3.39 - 3.99: 50273 3.99 - 4.60: 76154 Nonbonded interactions: 191369 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 146 " pdb=" O2 DC C -5 " model vdw 1.565 1.850 nonbonded pdb="HH22 ARG A 542 " pdb=" O6 DG C -18 " model vdw 1.569 1.850 nonbonded pdb=" OE1 GLU A 7 " pdb=" H GLU A 7 " model vdw 1.604 1.850 nonbonded pdb=" HG1 THR A 340 " pdb=" OP2 DT C 0 " model vdw 1.607 1.850 nonbonded pdb=" O LEU A 14 " pdb=" H PHE A 18 " model vdw 1.625 1.850 ... (remaining 191364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 94 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4475 2.51 5 N 1392 2.21 5 O 1644 1.98 5 H 6722 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.200 Extract box with map and model: 3.110 Check model and map are aligned: 0.220 Process input model: 56.300 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.009 0.238 7981 Z= 0.453 Angle : 0.550 7.501 11217 Z= 0.312 Chirality : 0.036 0.128 1260 Planarity : 0.027 0.596 1116 Dihedral : 18.782 171.627 3222 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.33 % 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: -1.59 (0.29), residues: 710 helix: -0.04 (0.30), residues: 281 sheet: -1.48 (0.64), residues: 62 loop : -1.83 (0.28), residues: 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 2.2449 time to fit residues: 279.4148 Evaluate side-chains 84 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 7981 Z= 0.235 Angle : 0.862 19.738 11217 Z= 0.387 Chirality : 0.039 0.133 1260 Planarity : 0.004 0.037 1116 Dihedral : 19.427 172.183 1806 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.15 % 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: -0.82 (0.30), residues: 710 helix: 0.66 (0.30), residues: 288 sheet: -1.20 (0.67), residues: 62 loop : -1.45 (0.30), residues: 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 1.9916 time to fit residues: 190.4265 Evaluate side-chains 87 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.2107 time to fit residues: 2.1916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 7981 Z= 0.301 Angle : 0.848 18.401 11217 Z= 0.384 Chirality : 0.041 0.133 1260 Planarity : 0.004 0.036 1116 Dihedral : 19.592 171.238 1806 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 3.63 % 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: -0.91 (0.30), residues: 710 helix: 0.64 (0.30), residues: 289 sheet: -1.30 (0.65), residues: 62 loop : -1.53 (0.30), residues: 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 89 average time/residue: 1.9823 time to fit residues: 190.3394 Evaluate side-chains 85 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.6432 time to fit residues: 5.2640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.163 Angle : 0.801 16.677 11217 Z= 0.354 Chirality : 0.037 0.135 1260 Planarity : 0.004 0.035 1116 Dihedral : 19.433 170.256 1806 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 2.48 % 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: -0.38 (0.31), residues: 710 helix: 1.11 (0.31), residues: 290 sheet: -1.22 (0.66), residues: 60 loop : -1.24 (0.31), residues: 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 1.9277 time to fit residues: 193.9417 Evaluate side-chains 87 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.070 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.6842 time to fit residues: 4.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7981 Z= 0.247 Angle : 0.819 17.125 11217 Z= 0.366 Chirality : 0.039 0.131 1260 Planarity : 0.004 0.035 1116 Dihedral : 19.452 169.370 1806 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 2.81 % 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: -0.46 (0.31), residues: 710 helix: 1.05 (0.30), residues: 292 sheet: -1.14 (0.66), residues: 60 loop : -1.33 (0.32), residues: 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 1.8656 time to fit residues: 190.6701 Evaluate side-chains 89 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.5790 time to fit residues: 4.7760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7981 Z= 0.225 Angle : 0.813 16.829 11217 Z= 0.362 Chirality : 0.039 0.130 1260 Planarity : 0.004 0.037 1116 Dihedral : 19.394 168.855 1806 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.97 % 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: -0.40 (0.31), residues: 710 helix: 1.09 (0.31), residues: 293 sheet: -1.10 (0.65), residues: 60 loop : -1.28 (0.32), residues: 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 1.9665 time to fit residues: 200.9672 Evaluate side-chains 93 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.5164 time to fit residues: 5.0711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.156 Angle : 0.795 16.313 11217 Z= 0.351 Chirality : 0.037 0.127 1260 Planarity : 0.003 0.036 1116 Dihedral : 19.269 169.292 1806 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 2.15 % 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: -0.10 (0.32), residues: 710 helix: 1.43 (0.31), residues: 292 sheet: -1.27 (0.64), residues: 62 loop : -1.14 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 2.0626 time to fit residues: 214.1022 Evaluate side-chains 88 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1664 time to fit residues: 1.5361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.0170 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 7981 Z= 0.148 Angle : 0.788 16.010 11217 Z= 0.346 Chirality : 0.036 0.126 1260 Planarity : 0.003 0.037 1116 Dihedral : 19.170 169.216 1806 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 1.98 % 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: 0.14 (0.32), residues: 710 helix: 1.71 (0.32), residues: 290 sheet: -1.24 (0.59), residues: 71 loop : -1.03 (0.33), residues: 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 93 average time/residue: 1.8619 time to fit residues: 187.0749 Evaluate side-chains 93 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 2.2273 time to fit residues: 3.6449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 7981 Z= 0.223 Angle : 0.806 16.609 11217 Z= 0.358 Chirality : 0.038 0.127 1260 Planarity : 0.004 0.036 1116 Dihedral : 19.228 168.186 1806 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.98 % 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 (0.32), residues: 710 helix: 1.44 (0.31), residues: 292 sheet: -1.13 (0.64), residues: 62 loop : -1.09 (0.33), residues: 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 1.7992 time to fit residues: 185.6422 Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.9577 time to fit residues: 4.6347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.180 Angle : 0.798 16.361 11217 Z= 0.352 Chirality : 0.037 0.125 1260 Planarity : 0.004 0.036 1116 Dihedral : 19.211 168.465 1806 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.32 % 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 (0.32), residues: 710 helix: 1.55 (0.31), residues: 291 sheet: -1.27 (0.62), residues: 66 loop : -1.02 (0.34), residues: 353 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 94 average time/residue: 1.8560 time to fit residues: 188.7880 Evaluate side-chains 92 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.091331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.082931 restraints weight = 46782.375| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.60 r_work: 0.3167 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 7981 Z= 0.241 Angle : 0.813 16.655 11217 Z= 0.362 Chirality : 0.039 0.127 1260 Planarity : 0.004 0.035 1116 Dihedral : 19.287 167.914 1806 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.82 % 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: -0.15 (0.32), residues: 710 helix: 1.28 (0.31), residues: 297 sheet: -1.20 (0.63), residues: 66 loop : -1.11 (0.34), residues: 347 =============================================================================== Job complete usr+sys time: 5174.85 seconds wall clock time: 91 minutes 9.11 seconds (5469.11 seconds total)