Starting phenix.real_space_refine on Sun Mar 10 15:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohp_16883/03_2024/8ohp_16883_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1800 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2784 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 A 401 " pdbres="VAL A 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 B 401 " pdbres="VAL B 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 C 401 " pdbres="VAL C 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 D 401 " pdbres="VAL D 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 E 401 " pdbres="VAL E 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 F 401 " pdbres="VAL F 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 G 401 " pdbres="VAL G 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 H 401 " pdbres="VAL H 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 I 401 " pdbres="VAL I 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 J 401 " pdbres="VAL J 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 K 401 " pdbres="VAL K 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 L 401 " pdbres="VAL L 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 M 401 " pdbres="VAL M 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 N 401 " pdbres="VAL N 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 O 401 " pdbres="VAL O 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 P 401 " pdbres="VAL P 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 Q 401 " pdbres="VAL Q 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 R 401 " pdbres="VAL R 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 S 401 " pdbres="VAL S 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 T 401 " pdbres="VAL T 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 U 401 " pdbres="VAL U 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 V 401 " pdbres="VAL V 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 W 401 " pdbres="VAL W 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 116 Unusual residues: {'VP1': 1} Classifications: {'peptide': 13, 'undetermined': 1} Link IDs: {'TRANS': 12, None: 1} Not linked: pdbres="VP1 X 401 " pdbres="VAL X 350 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'VP1:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.77, per 1000 atoms: 0.64 Number of scatterers: 2784 At special positions: 0 Unit cell: (96.82, 109.98, 33.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 528 8.00 N 456 7.00 C 1800 6.00 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 583.7 milliseconds 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.26: 432 1.26 - 1.33: 338 1.33 - 1.40: 431 1.40 - 1.47: 455 1.47 - 1.54: 1176 Bond restraints: 2832 Sorted by residual: bond pdb=" C01 VP1 E 401 " pdb=" O03 VP1 E 401 " ideal model delta sigma weight residual 1.399 1.313 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C01 VP1 U 401 " pdb=" O03 VP1 U 401 " ideal model delta sigma weight residual 1.399 1.313 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C01 VP1 M 401 " pdb=" O03 VP1 M 401 " ideal model delta sigma weight residual 1.399 1.313 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C01 VP1 A 401 " pdb=" O03 VP1 A 401 " ideal model delta sigma weight residual 1.399 1.315 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C01 VP1 I 401 " pdb=" O03 VP1 I 401 " ideal model delta sigma weight residual 1.399 1.315 0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 2827 not shown) Histogram of bond angle deviations from ideal: 102.00 - 107.85: 112 107.85 - 113.70: 1694 113.70 - 119.54: 610 119.54 - 125.39: 1275 125.39 - 131.24: 125 Bond angle restraints: 3816 Sorted by residual: angle pdb=" C01 VP1 T 401 " pdb=" O03 VP1 T 401 " pdb=" C04 VP1 T 401 " ideal model delta sigma weight residual 113.89 126.51 -12.62 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C01 VP1 L 401 " pdb=" O03 VP1 L 401 " pdb=" C04 VP1 L 401 " ideal model delta sigma weight residual 113.89 126.44 -12.55 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C01 VP1 D 401 " pdb=" O03 VP1 D 401 " pdb=" C04 VP1 D 401 " ideal model delta sigma weight residual 113.89 126.43 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" C01 VP1 H 401 " pdb=" O03 VP1 H 401 " pdb=" C04 VP1 H 401 " ideal model delta sigma weight residual 113.89 123.61 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C01 VP1 X 401 " pdb=" O03 VP1 X 401 " pdb=" C04 VP1 X 401 " ideal model delta sigma weight residual 113.89 123.58 -9.69 3.00e+00 1.11e-01 1.04e+01 ... (remaining 3811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 1395 25.04 - 50.08: 54 50.08 - 75.12: 3 75.12 - 100.17: 12 100.17 - 125.21: 48 Dihedral angle restraints: 1512 sinusoidal: 648 harmonic: 864 Sorted by residual: dihedral pdb=" C04 VP1 E 401 " pdb=" C05 VP1 E 401 " pdb=" C06 VP1 E 401 " pdb=" C07 VP1 E 401 " ideal model delta sinusoidal sigma weight residual 63.85 -61.36 125.21 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C04 VP1 M 401 " pdb=" C05 VP1 M 401 " pdb=" C06 VP1 M 401 " pdb=" C07 VP1 M 401 " ideal model delta sinusoidal sigma weight residual 63.85 -61.33 125.18 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C04 VP1 U 401 " pdb=" C05 VP1 U 401 " pdb=" C06 VP1 U 401 " pdb=" C07 VP1 U 401 " ideal model delta sinusoidal sigma weight residual 63.85 -61.24 125.09 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 1509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.093: 408 1.093 - 2.186: 0 2.186 - 3.279: 0 3.279 - 4.373: 0 4.373 - 5.466: 24 Chirality restraints: 432 Sorted by residual: chirality pdb=" C05 VP1 E 401 " pdb=" C04 VP1 E 401 " pdb=" C06 VP1 E 401 " pdb=" C12 VP1 E 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.78 5.47 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C05 VP1 U 401 " pdb=" C04 VP1 U 401 " pdb=" C06 VP1 U 401 " pdb=" C12 VP1 U 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.78 5.46 2.00e-01 2.50e+01 7.46e+02 chirality pdb=" C05 VP1 M 401 " pdb=" C04 VP1 M 401 " pdb=" C06 VP1 M 401 " pdb=" C12 VP1 M 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.78 5.46 2.00e-01 2.50e+01 7.46e+02 ... (remaining 429 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 T 401 " 0.029 2.00e-02 2.50e+03 1.59e-02 8.21e+00 pdb=" C06 VP1 T 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 T 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 T 401 " -0.012 2.00e-02 2.50e+03 pdb=" C10 VP1 T 401 " 0.005 2.00e-02 2.50e+03 pdb=" C11 VP1 T 401 " 0.023 2.00e-02 2.50e+03 pdb=" C12 VP1 T 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 T 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 T 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 T 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 T 401 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 L 401 " 0.028 2.00e-02 2.50e+03 1.58e-02 8.09e+00 pdb=" C06 VP1 L 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 L 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 L 401 " -0.013 2.00e-02 2.50e+03 pdb=" C10 VP1 L 401 " 0.005 2.00e-02 2.50e+03 pdb=" C11 VP1 L 401 " 0.023 2.00e-02 2.50e+03 pdb=" C12 VP1 L 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 L 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 L 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 L 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 L 401 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 D 401 " 0.028 2.00e-02 2.50e+03 1.57e-02 7.99e+00 pdb=" C06 VP1 D 401 " 0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 D 401 " -0.020 2.00e-02 2.50e+03 pdb=" C09 VP1 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C10 VP1 D 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 D 401 " 0.022 2.00e-02 2.50e+03 pdb=" C12 VP1 D 401 " -0.010 2.00e-02 2.50e+03 pdb=" C13 VP1 D 401 " -0.012 2.00e-02 2.50e+03 pdb=" C14 VP1 D 401 " -0.019 2.00e-02 2.50e+03 pdb=" C15 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 D 401 " 0.009 2.00e-02 2.50e+03 pdb=" C17 VP1 D 401 " 0.022 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 683 2.81 - 3.33: 2014 3.33 - 3.85: 4598 3.85 - 4.38: 5138 4.38 - 4.90: 9250 Nonbonded interactions: 21683 Sorted by model distance: nonbonded pdb=" OG SER A 356 " pdb=" OD1 ASN A 359 " model vdw 2.283 2.440 nonbonded pdb=" OG SER I 356 " pdb=" OD1 ASN I 359 " model vdw 2.283 2.440 nonbonded pdb=" OG SER Q 356 " pdb=" OD1 ASN Q 359 " model vdw 2.284 2.440 nonbonded pdb=" OG SER M 356 " pdb=" OD1 ASN M 359 " model vdw 2.311 2.440 nonbonded pdb=" OG SER E 356 " pdb=" OD1 ASN E 359 " model vdw 2.312 2.440 ... (remaining 21678 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.000 Extract box with map and model: 5.360 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.015 0.086 2832 Z= 0.828 Angle : 1.281 12.625 3816 Z= 0.484 Chirality : 1.267 5.466 432 Planarity : 0.003 0.016 432 Dihedral : 31.061 125.208 936 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -3.72 (0.36), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.302 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.6581 time to fit residues: 57.5493 Evaluate side-chains 48 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN G 359 ASN H 351 GLN H 359 ASN N 351 GLN O 359 ASN P 351 GLN P 359 ASN V 351 GLN W 359 ASN X 351 GLN X 359 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2832 Z= 0.108 Angle : 0.502 6.608 3816 Z= 0.232 Chirality : 0.049 0.142 432 Planarity : 0.001 0.006 432 Dihedral : 24.852 89.494 432 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 21.97 % Favored : 76.52 % 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: -3.05 (0.39), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.30), residues: 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.312 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 73 average time/residue: 0.5261 time to fit residues: 40.4849 Evaluate side-chains 59 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2832 Z= 0.275 Angle : 0.573 7.400 3816 Z= 0.268 Chirality : 0.055 0.197 432 Planarity : 0.002 0.008 432 Dihedral : 22.765 89.918 432 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.65 % Allowed : 22.35 % Favored : 75.00 % 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: -2.52 (0.44), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.34), residues: 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 66 average time/residue: 0.5304 time to fit residues: 36.8768 Evaluate side-chains 57 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2832 Z= 0.243 Angle : 0.556 8.013 3816 Z= 0.257 Chirality : 0.054 0.190 432 Planarity : 0.002 0.007 432 Dihedral : 21.850 88.565 432 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 25.38 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.46), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.4432 time to fit residues: 29.2551 Evaluate side-chains 53 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain I residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2832 Z= 0.198 Angle : 0.524 8.557 3816 Z= 0.249 Chirality : 0.050 0.149 432 Planarity : 0.001 0.007 432 Dihedral : 21.084 87.451 432 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 25.38 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.47), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.36), residues: 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.4661 time to fit residues: 30.2957 Evaluate side-chains 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain G residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2832 Z= 0.128 Angle : 0.477 8.637 3816 Z= 0.229 Chirality : 0.047 0.117 432 Planarity : 0.001 0.006 432 Dihedral : 20.749 89.137 432 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.03 % Allowed : 25.76 % Favored : 71.21 % 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: -2.35 (0.48), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.36), residues: 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.4711 time to fit residues: 32.5449 Evaluate side-chains 63 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain Q residue 361 THR Chi-restraints excluded: chain U residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 2832 Z= 0.366 Angle : 0.654 8.778 3816 Z= 0.305 Chirality : 0.062 0.248 432 Planarity : 0.002 0.010 432 Dihedral : 21.798 89.961 432 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.65 % Allowed : 28.03 % Favored : 69.32 % 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: -2.36 (0.48), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.36), residues: 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 56 average time/residue: 0.4545 time to fit residues: 27.0934 Evaluate side-chains 52 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain L residue 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 2832 Z= 0.342 Angle : 0.637 8.560 3816 Z= 0.298 Chirality : 0.061 0.252 432 Planarity : 0.002 0.010 432 Dihedral : 21.578 89.794 432 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 28.79 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.47), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.36), residues: 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 LYS cc_start: 0.8203 (ptmt) cc_final: 0.7994 (ptmm) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.5297 time to fit residues: 31.5490 Evaluate side-chains 54 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain I residue 361 THR Chi-restraints excluded: chain L residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2832 Z= 0.189 Angle : 0.541 8.434 3816 Z= 0.259 Chirality : 0.050 0.144 432 Planarity : 0.001 0.006 432 Dihedral : 20.800 89.951 432 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 28.79 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.47), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.4786 time to fit residues: 29.4597 Evaluate side-chains 55 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain L residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 2832 Z= 0.444 Angle : 0.718 8.263 3816 Z= 0.333 Chirality : 0.069 0.312 432 Planarity : 0.002 0.011 432 Dihedral : 21.847 89.495 432 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.89 % Allowed : 28.41 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.47), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.36), residues: 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 480 Ramachandran restraints generated. 240 Oldfield, 0 Emsley, 240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.5140 time to fit residues: 30.5078 Evaluate side-chains 53 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain M residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.0060 chunk 19 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.107267 restraints weight = 5112.340| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.90 r_work: 0.3947 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2832 Z= 0.116 Angle : 0.508 8.157 3816 Z= 0.247 Chirality : 0.047 0.121 432 Planarity : 0.001 0.007 432 Dihedral : 20.629 89.237 432 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 29.55 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.48), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.76 seconds wall clock time: 25 minutes 10.77 seconds (1510.77 seconds total)