Starting phenix.real_space_refine on Sun Mar 10 14:33:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohi_16881/03_2024/8ohi_16881_updated.pdb" } resolution = 2.8 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= 0.003 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 1350 2.51 5 N 342 2.21 5 O 396 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: 2088 Number of models: 1 Model: "" Number of chains: 18 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 Time building chain proxies: 1.37, per 1000 atoms: 0.66 Number of scatterers: 2088 At special positions: 0 Unit cell: (66.74, 89.3, 32.9, 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 396 8.00 N 342 7.00 C 1350 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 229.7 milliseconds 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 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: 0.33 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: 0.94 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: 324 1.26 - 1.33: 240 1.33 - 1.40: 354 1.40 - 1.47: 324 1.47 - 1.54: 882 Bond restraints: 2124 Sorted by residual: bond pdb=" C01 VP1 M 401 " pdb=" O03 VP1 M 401 " ideal model delta sigma weight residual 1.399 1.316 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C01 VP1 A 401 " pdb=" O03 VP1 A 401 " ideal model delta sigma weight residual 1.399 1.316 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C01 VP1 G 401 " pdb=" O03 VP1 G 401 " ideal model delta sigma weight residual 1.399 1.316 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C01 VP1 K 401 " pdb=" O03 VP1 K 401 " ideal model delta sigma weight residual 1.399 1.317 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C01 VP1 Q 401 " pdb=" O03 VP1 Q 401 " ideal model delta sigma weight residual 1.399 1.317 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 2119 not shown) Histogram of bond angle deviations from ideal: 102.03 - 107.90: 84 107.90 - 113.78: 1243 113.78 - 119.65: 479 119.65 - 125.52: 966 125.52 - 131.39: 90 Bond angle restraints: 2862 Sorted by residual: angle pdb=" C01 VP1 M 401 " pdb=" O03 VP1 M 401 " pdb=" C04 VP1 M 401 " ideal model delta sigma weight residual 113.89 119.99 -6.10 3.00e+00 1.11e-01 4.13e+00 angle pdb=" C01 VP1 G 401 " pdb=" O03 VP1 G 401 " pdb=" C04 VP1 G 401 " ideal model delta sigma weight residual 113.89 119.91 -6.02 3.00e+00 1.11e-01 4.03e+00 angle pdb=" C01 VP1 A 401 " pdb=" O03 VP1 A 401 " pdb=" C04 VP1 A 401 " ideal model delta sigma weight residual 113.89 119.89 -6.00 3.00e+00 1.11e-01 4.00e+00 angle pdb=" C06 VP1 L 401 " pdb=" C05 VP1 L 401 " pdb=" C12 VP1 L 401 " ideal model delta sigma weight residual 108.01 102.03 5.98 3.00e+00 1.11e-01 3.97e+00 angle pdb=" C06 VP1 R 401 " pdb=" C05 VP1 R 401 " pdb=" C12 VP1 R 401 " ideal model delta sigma weight residual 108.01 102.04 5.97 3.00e+00 1.11e-01 3.96e+00 ... (remaining 2857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 1050 25.41 - 50.82: 33 50.82 - 76.22: 0 76.22 - 101.63: 15 101.63 - 127.04: 36 Dihedral angle restraints: 1134 sinusoidal: 486 harmonic: 648 Sorted by residual: dihedral pdb=" C04 VP1 J 401 " pdb=" C05 VP1 J 401 " pdb=" C06 VP1 J 401 " pdb=" C07 VP1 J 401 " ideal model delta sinusoidal sigma weight residual 63.85 -63.19 127.04 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C04 VP1 D 401 " pdb=" C05 VP1 D 401 " pdb=" C06 VP1 D 401 " pdb=" C07 VP1 D 401 " ideal model delta sinusoidal sigma weight residual 63.85 -63.17 127.02 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" C04 VP1 P 401 " pdb=" C05 VP1 P 401 " pdb=" C06 VP1 P 401 " pdb=" C07 VP1 P 401 " ideal model delta sinusoidal sigma weight residual 63.85 -63.08 126.93 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 1131 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.104: 306 1.104 - 2.207: 0 2.207 - 3.311: 0 3.311 - 4.414: 0 4.414 - 5.517: 18 Chirality restraints: 324 Sorted by residual: chirality pdb=" C05 VP1 K 401 " pdb=" C04 VP1 K 401 " pdb=" C06 VP1 K 401 " pdb=" C12 VP1 K 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.84 5.52 2.00e-01 2.50e+01 7.61e+02 chirality pdb=" C05 VP1 Q 401 " pdb=" C04 VP1 Q 401 " pdb=" C06 VP1 Q 401 " pdb=" C12 VP1 Q 401 " both_signs ideal model delta sigma weight residual False 2.68 -2.83 5.51 2.00e-01 2.50e+01 7.60e+02 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 -2.83 5.51 2.00e-01 2.50e+01 7.60e+02 ... (remaining 321 not shown) Planarity restraints: 324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 M 401 " -0.010 2.00e-02 2.50e+03 5.78e-03 1.08e+00 pdb=" C06 VP1 M 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 M 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 M 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 M 401 " -0.002 2.00e-02 2.50e+03 pdb=" C11 VP1 M 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C13 VP1 M 401 " 0.005 2.00e-02 2.50e+03 pdb=" C14 VP1 M 401 " 0.007 2.00e-02 2.50e+03 pdb=" C15 VP1 M 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 M 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 M 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 G 401 " -0.010 2.00e-02 2.50e+03 5.77e-03 1.08e+00 pdb=" C06 VP1 G 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 G 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 G 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 G 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 G 401 " -0.001 2.00e-02 2.50e+03 pdb=" C11 VP1 G 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 G 401 " 0.002 2.00e-02 2.50e+03 pdb=" C13 VP1 G 401 " 0.005 2.00e-02 2.50e+03 pdb=" C14 VP1 G 401 " 0.008 2.00e-02 2.50e+03 pdb=" C15 VP1 G 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 G 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 G 401 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 A 401 " -0.009 2.00e-02 2.50e+03 5.71e-03 1.06e+00 pdb=" C06 VP1 A 401 " -0.002 2.00e-02 2.50e+03 pdb=" C07 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C08 VP1 A 401 " 0.007 2.00e-02 2.50e+03 pdb=" C09 VP1 A 401 " 0.005 2.00e-02 2.50e+03 pdb=" C10 VP1 A 401 " -0.001 2.00e-02 2.50e+03 pdb=" C11 VP1 A 401 " -0.008 2.00e-02 2.50e+03 pdb=" C12 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C13 VP1 A 401 " 0.004 2.00e-02 2.50e+03 pdb=" C14 VP1 A 401 " 0.008 2.00e-02 2.50e+03 pdb=" C15 VP1 A 401 " 0.003 2.00e-02 2.50e+03 pdb=" C16 VP1 A 401 " -0.005 2.00e-02 2.50e+03 pdb=" C17 VP1 A 401 " -0.008 2.00e-02 2.50e+03 ... (remaining 321 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 592 2.83 - 3.35: 1499 3.35 - 3.86: 3556 3.86 - 4.38: 3839 4.38 - 4.90: 6952 Nonbonded interactions: 16438 Sorted by model distance: nonbonded pdb=" OG SER B 352 " pdb=" O02 VP1 H 401 " model vdw 2.311 2.440 nonbonded pdb=" OG SER H 352 " pdb=" O02 VP1 N 401 " model vdw 2.316 2.440 nonbonded pdb=" NZ LYS Q 353 " pdb=" OD2 ASP Q 358 " model vdw 2.368 2.520 nonbonded pdb=" NZ LYS E 353 " pdb=" OD2 ASP E 358 " model vdw 2.368 2.520 nonbonded pdb=" NZ LYS K 353 " pdb=" OD2 ASP K 358 " model vdw 2.369 2.520 ... (remaining 16433 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' } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.360 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.014 0.083 2124 Z= 0.789 Angle : 1.164 6.096 2862 Z= 0.428 Chirality : 1.290 5.517 324 Planarity : 0.002 0.006 324 Dihedral : 32.527 127.039 702 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.52 % Allowed : 4.55 % Favored : 93.94 % 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: -2.86 (0.46), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.214 Fit side-chains REVERT: A 358 ASP cc_start: 0.7787 (m-30) cc_final: 0.7428 (m-30) REVERT: B 359 ASN cc_start: 0.8323 (t0) cc_final: 0.8115 (t0) REVERT: C 353 LYS cc_start: 0.8168 (mttt) cc_final: 0.7953 (mtpt) REVERT: C 359 ASN cc_start: 0.7986 (p0) cc_final: 0.7399 (p0) REVERT: D 356 SER cc_start: 0.9157 (p) cc_final: 0.8902 (t) REVERT: E 358 ASP cc_start: 0.7930 (m-30) cc_final: 0.7712 (m-30) REVERT: I 353 LYS cc_start: 0.8360 (mttt) cc_final: 0.8029 (mtpt) REVERT: L 359 ASN cc_start: 0.8141 (m-40) cc_final: 0.7929 (m-40) REVERT: P 356 SER cc_start: 0.9207 (p) cc_final: 0.8807 (t) REVERT: R 359 ASN cc_start: 0.8382 (m-40) cc_final: 0.7979 (m-40) outliers start: 3 outliers final: 4 residues processed: 43 average time/residue: 0.8878 time to fit residues: 39.2673 Evaluate side-chains 43 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 351 GLN ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2124 Z= 0.114 Angle : 0.497 4.456 2862 Z= 0.215 Chirality : 0.062 0.241 324 Planarity : 0.001 0.007 324 Dihedral : 28.119 89.843 329 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 13.64 % Favored : 84.85 % 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 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.38), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.233 Fit side-chains REVERT: A 358 ASP cc_start: 0.7659 (m-30) cc_final: 0.7273 (m-30) REVERT: B 359 ASN cc_start: 0.8103 (t0) cc_final: 0.7874 (t0) REVERT: C 353 LYS cc_start: 0.8256 (mttt) cc_final: 0.8022 (mtpt) REVERT: C 359 ASN cc_start: 0.7800 (p0) cc_final: 0.7339 (p0) REVERT: E 358 ASP cc_start: 0.7926 (m-30) cc_final: 0.7636 (m-30) REVERT: F 353 LYS cc_start: 0.8179 (mttt) cc_final: 0.7905 (mtmt) REVERT: I 353 LYS cc_start: 0.8285 (mttt) cc_final: 0.8011 (mtpt) REVERT: J 356 SER cc_start: 0.8972 (t) cc_final: 0.8722 (t) REVERT: O 353 LYS cc_start: 0.8330 (mtmm) cc_final: 0.7958 (mtpt) outliers start: 3 outliers final: 0 residues processed: 46 average time/residue: 0.8366 time to fit residues: 39.6239 Evaluate side-chains 40 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2124 Z= 0.260 Angle : 0.690 6.298 2862 Z= 0.280 Chirality : 0.088 0.375 324 Planarity : 0.003 0.012 324 Dihedral : 25.210 89.733 324 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.56 % Allowed : 12.12 % Favored : 82.32 % 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: -2.38 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.38), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: A 358 ASP cc_start: 0.7563 (m-30) cc_final: 0.7210 (m-30) REVERT: C 353 LYS cc_start: 0.8363 (mttt) cc_final: 0.8121 (mtpt) REVERT: E 358 ASP cc_start: 0.7946 (m-30) cc_final: 0.7614 (m-30) REVERT: F 353 LYS cc_start: 0.8249 (mttt) cc_final: 0.7962 (mtmt) REVERT: I 353 LYS cc_start: 0.8301 (mttt) cc_final: 0.8036 (mtpt) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 0.9496 time to fit residues: 43.8504 Evaluate side-chains 43 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain P residue 357 LEU Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN K 351 GLN ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2124 Z= 0.229 Angle : 0.637 5.810 2862 Z= 0.264 Chirality : 0.080 0.358 324 Planarity : 0.003 0.011 324 Dihedral : 24.477 89.793 324 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 12.63 % Favored : 82.83 % 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: -2.33 (0.50), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.38), residues: 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: A 353 LYS cc_start: 0.7894 (mttm) cc_final: 0.7541 (mttm) REVERT: A 358 ASP cc_start: 0.7512 (m-30) cc_final: 0.7127 (m-30) REVERT: C 353 LYS cc_start: 0.8349 (mttt) cc_final: 0.8084 (mtpt) REVERT: C 359 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7143 (p0) REVERT: E 353 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8683 (mttp) REVERT: E 358 ASP cc_start: 0.7931 (m-30) cc_final: 0.7593 (m-30) REVERT: F 353 LYS cc_start: 0.8270 (mttt) cc_final: 0.7985 (mtmt) REVERT: I 353 LYS cc_start: 0.8296 (mttt) cc_final: 0.8039 (mtpt) REVERT: M 358 ASP cc_start: 0.7906 (m-30) cc_final: 0.7693 (m-30) outliers start: 9 outliers final: 4 residues processed: 42 average time/residue: 0.8937 time to fit residues: 38.5780 Evaluate side-chains 41 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2124 Z= 0.164 Angle : 0.529 4.645 2862 Z= 0.228 Chirality : 0.066 0.267 324 Planarity : 0.002 0.009 324 Dihedral : 23.959 89.134 324 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 13.64 % Favored : 81.82 % 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: -2.22 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.39), residues: 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.209 Fit side-chains REVERT: A 353 LYS cc_start: 0.7886 (mttm) cc_final: 0.7507 (mttm) REVERT: A 358 ASP cc_start: 0.7489 (m-30) cc_final: 0.7088 (m-30) REVERT: C 353 LYS cc_start: 0.8358 (mttt) cc_final: 0.8076 (mtpt) REVERT: E 358 ASP cc_start: 0.7881 (m-30) cc_final: 0.7535 (m-30) REVERT: F 353 LYS cc_start: 0.8286 (mttt) cc_final: 0.8012 (mtmt) REVERT: I 353 LYS cc_start: 0.8278 (mttt) cc_final: 0.8028 (mtpt) REVERT: M 358 ASP cc_start: 0.7877 (m-30) cc_final: 0.7666 (m-30) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.8967 time to fit residues: 37.7409 Evaluate side-chains 39 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2124 Z= 0.159 Angle : 0.514 5.015 2862 Z= 0.222 Chirality : 0.064 0.252 324 Planarity : 0.002 0.008 324 Dihedral : 23.759 88.932 324 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.06 % Allowed : 12.12 % Favored : 81.82 % 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: -2.18 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.235 Fit side-chains REVERT: A 353 LYS cc_start: 0.7865 (mttm) cc_final: 0.7501 (mttm) REVERT: A 358 ASP cc_start: 0.7534 (m-30) cc_final: 0.7139 (m-30) REVERT: C 353 LYS cc_start: 0.8380 (mttt) cc_final: 0.8120 (mtpt) REVERT: E 353 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8663 (mttp) REVERT: E 358 ASP cc_start: 0.7874 (m-30) cc_final: 0.7513 (m-30) REVERT: F 353 LYS cc_start: 0.8280 (mttt) cc_final: 0.8007 (mtmt) REVERT: I 353 LYS cc_start: 0.8229 (mttt) cc_final: 0.7976 (mtpt) outliers start: 12 outliers final: 6 residues processed: 43 average time/residue: 1.0167 time to fit residues: 44.7722 Evaluate side-chains 41 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain L residue 353 LYS Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN E 351 GLN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 2124 Z= 0.302 Angle : 0.732 7.065 2862 Z= 0.297 Chirality : 0.094 0.431 324 Planarity : 0.003 0.014 324 Dihedral : 24.293 89.652 324 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 13.13 % Favored : 82.32 % 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: -2.20 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.228 Fit side-chains REVERT: A 358 ASP cc_start: 0.7517 (m-30) cc_final: 0.7112 (m-30) REVERT: C 353 LYS cc_start: 0.8366 (mttt) cc_final: 0.8100 (mtpt) REVERT: E 353 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: E 358 ASP cc_start: 0.7852 (m-30) cc_final: 0.7494 (m-30) REVERT: F 353 LYS cc_start: 0.8253 (mttt) cc_final: 0.7967 (mtmt) REVERT: I 353 LYS cc_start: 0.8295 (mttt) cc_final: 0.8033 (mtpt) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 1.0231 time to fit residues: 40.8762 Evaluate side-chains 39 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2124 Z= 0.229 Angle : 0.629 5.819 2862 Z= 0.260 Chirality : 0.078 0.347 324 Planarity : 0.002 0.011 324 Dihedral : 24.017 89.000 324 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 13.64 % Favored : 81.82 % 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: -2.20 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.39), residues: 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.243 Fit side-chains REVERT: A 358 ASP cc_start: 0.7504 (m-30) cc_final: 0.7094 (m-30) REVERT: C 353 LYS cc_start: 0.8356 (mttt) cc_final: 0.8086 (mtpt) REVERT: C 359 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7118 (p0) REVERT: E 353 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8645 (mttp) REVERT: E 358 ASP cc_start: 0.7894 (m-30) cc_final: 0.7544 (m-30) REVERT: F 353 LYS cc_start: 0.8287 (mttt) cc_final: 0.8013 (mtmt) REVERT: I 353 LYS cc_start: 0.8288 (mttt) cc_final: 0.8028 (mtpt) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 0.9822 time to fit residues: 39.3075 Evaluate side-chains 40 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain L residue 353 LYS Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2124 Z= 0.175 Angle : 0.537 4.721 2862 Z= 0.230 Chirality : 0.067 0.276 324 Planarity : 0.002 0.009 324 Dihedral : 23.721 89.726 324 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 13.13 % Favored : 82.32 % 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: -2.16 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.39), residues: 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.244 Fit side-chains REVERT: A 358 ASP cc_start: 0.7514 (m-30) cc_final: 0.7105 (m-30) REVERT: C 353 LYS cc_start: 0.8358 (mttt) cc_final: 0.8083 (mtpt) REVERT: E 353 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8665 (mttp) REVERT: E 358 ASP cc_start: 0.7899 (m-30) cc_final: 0.7570 (m-30) REVERT: F 353 LYS cc_start: 0.8286 (mttt) cc_final: 0.8017 (mtmt) REVERT: I 353 LYS cc_start: 0.8263 (mttt) cc_final: 0.7964 (mtpt) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.9125 time to fit residues: 37.5326 Evaluate side-chains 40 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain L residue 353 LYS Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2124 Z= 0.138 Angle : 0.481 5.347 2862 Z= 0.211 Chirality : 0.060 0.224 324 Planarity : 0.002 0.007 324 Dihedral : 23.452 89.136 324 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.55 % Allowed : 13.64 % Favored : 81.82 % 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: -2.14 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.39), residues: 180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 360 Ramachandran restraints generated. 180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.233 Fit side-chains REVERT: A 358 ASP cc_start: 0.7507 (m-30) cc_final: 0.7099 (m-30) REVERT: C 353 LYS cc_start: 0.8387 (mttt) cc_final: 0.8148 (mtpt) REVERT: E 353 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (mttp) REVERT: E 358 ASP cc_start: 0.7905 (m-30) cc_final: 0.7554 (m-30) REVERT: F 353 LYS cc_start: 0.8268 (mttt) cc_final: 0.7983 (mtmt) REVERT: I 353 LYS cc_start: 0.8183 (mttt) cc_final: 0.7915 (mtpt) REVERT: O 353 LYS cc_start: 0.8274 (mttm) cc_final: 0.7928 (mtpt) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 1.0795 time to fit residues: 42.0437 Evaluate side-chains 38 residues out of total 198 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain Q residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN ** H 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.099158 restraints weight = 2817.452| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.89 r_work: 0.3292 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2124 Z= 0.263 Angle : 0.672 6.325 2862 Z= 0.275 Chirality : 0.085 0.380 324 Planarity : 0.003 0.012 324 Dihedral : 23.860 88.442 324 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.54 % Allowed : 14.65 % Favored : 81.82 % 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: -2.15 (0.51), residues: 180 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1277.13 seconds wall clock time: 23 minutes 56.94 seconds (1436.94 seconds total)