Starting phenix.real_space_refine on Fri Apr 5 13:20:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi0_16886/04_2024/8oi0_16886_updated.pdb" } resolution = 2.9 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 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-5288/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: (105.28, 111.86, 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: 1.32 Conformation dependent library (CDL) restraints added in 353.0 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: 0.82 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: 1.42 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: 298 1.33 - 1.40: 483 1.40 - 1.47: 443 1.47 - 1.54: 1176 Bond restraints: 2832 Sorted by residual: bond pdb=" C01 VP1 Q 401 " pdb=" O03 VP1 Q 401 " ideal model delta sigma weight residual 1.399 1.309 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C01 VP1 I 401 " pdb=" O03 VP1 I 401 " ideal model delta sigma weight residual 1.399 1.309 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C01 VP1 A 401 " pdb=" O03 VP1 A 401 " ideal model delta sigma weight residual 1.399 1.309 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C01 VP1 G 401 " pdb=" O03 VP1 G 401 " ideal model delta sigma weight residual 1.399 1.312 0.087 2.00e-02 2.50e+03 1.89e+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 1.86e+01 ... (remaining 2827 not shown) Histogram of bond angle deviations from ideal: 102.07 - 107.91: 120 107.91 - 113.74: 1683 113.74 - 119.58: 610 119.58 - 125.41: 1277 125.41 - 131.25: 126 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 113.89 127.00 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C01 VP1 L 401 " pdb=" O03 VP1 L 401 " pdb=" C04 VP1 L 401 " ideal model delta sigma weight residual 113.89 126.96 -13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" C01 VP1 D 401 " pdb=" O03 VP1 D 401 " pdb=" C04 VP1 D 401 " ideal model delta sigma weight residual 113.89 126.92 -13.03 3.00e+00 1.11e-01 1.89e+01 angle pdb=" C01 VP1 X 401 " pdb=" O03 VP1 X 401 " pdb=" C04 VP1 X 401 " ideal model delta sigma weight residual 113.89 125.96 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C01 VP1 H 401 " pdb=" O03 VP1 H 401 " pdb=" C04 VP1 H 401 " ideal model delta sigma weight residual 113.89 125.95 -12.06 3.00e+00 1.11e-01 1.62e+01 ... (remaining 3811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 1422 24.87 - 49.74: 21 49.74 - 74.61: 9 74.61 - 99.48: 12 99.48 - 124.36: 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 -60.51 124.36 1 3.00e+01 1.11e-03 1.67e+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 -60.50 124.35 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C04 VP1 K 401 " pdb=" C05 VP1 K 401 " pdb=" C06 VP1 K 401 " pdb=" C07 VP1 K 401 " ideal model delta sinusoidal sigma weight residual 63.85 -60.48 124.33 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 1509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.093: 408 1.093 - 2.185: 0 2.185 - 3.278: 0 3.278 - 4.370: 0 4.370 - 5.463: 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 5.46 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 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 7.45e+02 ... (remaining 429 not shown) Planarity restraints: 432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 VP1 D 401 " 0.032 2.00e-02 2.50e+03 1.83e-02 1.09e+01 pdb=" C06 VP1 D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C07 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 D 401 " -0.023 2.00e-02 2.50e+03 pdb=" C09 VP1 D 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 D 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 D 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C13 VP1 D 401 " -0.014 2.00e-02 2.50e+03 pdb=" C14 VP1 D 401 " -0.022 2.00e-02 2.50e+03 pdb=" C15 VP1 D 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 D 401 " 0.012 2.00e-02 2.50e+03 pdb=" C17 VP1 D 401 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 L 401 " 0.032 2.00e-02 2.50e+03 1.83e-02 1.09e+01 pdb=" C06 VP1 L 401 " 0.005 2.00e-02 2.50e+03 pdb=" C07 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 L 401 " -0.024 2.00e-02 2.50e+03 pdb=" C09 VP1 L 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 L 401 " 0.006 2.00e-02 2.50e+03 pdb=" C11 VP1 L 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 L 401 " -0.012 2.00e-02 2.50e+03 pdb=" C13 VP1 L 401 " -0.015 2.00e-02 2.50e+03 pdb=" C14 VP1 L 401 " -0.023 2.00e-02 2.50e+03 pdb=" C15 VP1 L 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 L 401 " 0.012 2.00e-02 2.50e+03 pdb=" C17 VP1 L 401 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 VP1 T 401 " 0.032 2.00e-02 2.50e+03 1.82e-02 1.08e+01 pdb=" C06 VP1 T 401 " 0.004 2.00e-02 2.50e+03 pdb=" C07 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C08 VP1 T 401 " -0.023 2.00e-02 2.50e+03 pdb=" C09 VP1 T 401 " -0.016 2.00e-02 2.50e+03 pdb=" C10 VP1 T 401 " 0.007 2.00e-02 2.50e+03 pdb=" C11 VP1 T 401 " 0.026 2.00e-02 2.50e+03 pdb=" C12 VP1 T 401 " -0.013 2.00e-02 2.50e+03 pdb=" C13 VP1 T 401 " -0.015 2.00e-02 2.50e+03 pdb=" C14 VP1 T 401 " -0.022 2.00e-02 2.50e+03 pdb=" C15 VP1 T 401 " -0.008 2.00e-02 2.50e+03 pdb=" C16 VP1 T 401 " 0.011 2.00e-02 2.50e+03 pdb=" C17 VP1 T 401 " 0.025 2.00e-02 2.50e+03 ... (remaining 429 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 27 2.61 - 3.18: 2205 3.18 - 3.75: 3824 3.75 - 4.33: 6148 4.33 - 4.90: 10220 Nonbonded interactions: 22424 Sorted by model distance: nonbonded pdb=" O02 VP1 L 401 " pdb=" OG SER T 352 " model vdw 2.037 2.440 nonbonded pdb=" O02 VP1 D 401 " pdb=" OG SER L 352 " model vdw 2.134 2.440 nonbonded pdb=" O02 VP1 H 401 " pdb=" OG SER P 352 " model vdw 2.217 2.440 nonbonded pdb=" OG SER I 356 " pdb=" OD1 ASN I 359 " model vdw 2.226 2.440 nonbonded pdb=" OG SER Q 356 " pdb=" OD1 ASN Q 359 " model vdw 2.227 2.440 ... (remaining 22419 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: 1.870 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: 5.400 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.630 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 0.090 2832 Z= 0.819 Angle : 1.315 13.112 3816 Z= 0.487 Chirality : 1.264 5.463 432 Planarity : 0.003 0.018 432 Dihedral : 30.751 124.356 936 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -3.25 (0.37), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.28), 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 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.255 Fit side-chains REVERT: C 353 LYS cc_start: 0.8231 (mttt) cc_final: 0.7878 (mtpp) REVERT: E 353 LYS cc_start: 0.8671 (tttt) cc_final: 0.8282 (ttmt) REVERT: K 353 LYS cc_start: 0.8205 (mttt) cc_final: 0.7786 (mtpp) REVERT: M 353 LYS cc_start: 0.8650 (tttt) cc_final: 0.8242 (ttmt) REVERT: O 353 LYS cc_start: 0.8162 (tttt) cc_final: 0.7670 (ttmm) REVERT: S 353 LYS cc_start: 0.8401 (mttt) cc_final: 0.7982 (mtpp) REVERT: U 353 LYS cc_start: 0.8583 (tttt) cc_final: 0.8120 (ttmt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.6909 time to fit residues: 41.7797 Evaluate side-chains 37 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B 359 ASN F 351 GLN H 351 GLN J 351 GLN L 351 GLN N 351 GLN O 359 ASN P 351 GLN R 351 GLN V 351 GLN X 351 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2832 Z= 0.140 Angle : 0.472 4.051 3816 Z= 0.217 Chirality : 0.053 0.238 432 Planarity : 0.001 0.007 432 Dihedral : 24.829 89.868 432 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 11.74 % Favored : 87.12 % 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 (0.40), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.31), 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 55 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.307 Fit side-chains REVERT: C 353 LYS cc_start: 0.8167 (mttt) cc_final: 0.7795 (mtpp) REVERT: E 353 LYS cc_start: 0.8641 (tttt) cc_final: 0.8269 (ttmt) REVERT: K 353 LYS cc_start: 0.8210 (mttt) cc_final: 0.7756 (mtpp) REVERT: K 359 ASN cc_start: 0.8735 (m-40) cc_final: 0.8503 (m-40) REVERT: M 353 LYS cc_start: 0.8616 (tttt) cc_final: 0.8216 (ttpt) REVERT: S 353 LYS cc_start: 0.8332 (mttt) cc_final: 0.7931 (mtpp) REVERT: U 353 LYS cc_start: 0.8591 (tttt) cc_final: 0.8175 (ttmt) outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 0.6055 time to fit residues: 34.2326 Evaluate side-chains 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 0.0060 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 359 ASN O 359 ASN T 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2832 Z= 0.322 Angle : 0.586 6.787 3816 Z= 0.264 Chirality : 0.067 0.325 432 Planarity : 0.002 0.011 432 Dihedral : 24.138 89.820 432 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.14 % Allowed : 16.29 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.41), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.31), 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 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.311 Fit side-chains REVERT: C 353 LYS cc_start: 0.8231 (mttt) cc_final: 0.7849 (mtpp) REVERT: E 353 LYS cc_start: 0.8668 (tttt) cc_final: 0.8318 (ttmt) REVERT: K 353 LYS cc_start: 0.8208 (mttt) cc_final: 0.7785 (mtpp) REVERT: K 359 ASN cc_start: 0.8774 (m-40) cc_final: 0.8514 (m-40) REVERT: M 353 LYS cc_start: 0.8656 (tttt) cc_final: 0.8247 (ttmt) REVERT: S 353 LYS cc_start: 0.8382 (mttt) cc_final: 0.7960 (mtpp) REVERT: U 353 LYS cc_start: 0.8610 (tttt) cc_final: 0.8161 (ttmt) outliers start: 3 outliers final: 1 residues processed: 47 average time/residue: 0.6201 time to fit residues: 30.5530 Evaluate side-chains 43 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J 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: 8.9990 chunk 19 optimal weight: 0.0030 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.0270 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 overall best weight: 0.9052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2832 Z= 0.099 Angle : 0.386 3.065 3816 Z= 0.194 Chirality : 0.047 0.114 432 Planarity : 0.001 0.006 432 Dihedral : 22.018 89.638 432 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % Favored : 81.06 % 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: -2.58 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.32), 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 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 43 time to evaluate : 0.250 Fit side-chains REVERT: E 353 LYS cc_start: 0.8605 (tttt) cc_final: 0.8243 (ttmt) REVERT: K 353 LYS cc_start: 0.8161 (mttt) cc_final: 0.7744 (mtpp) REVERT: K 359 ASN cc_start: 0.8752 (m-40) cc_final: 0.8438 (m-40) REVERT: M 353 LYS cc_start: 0.8593 (tttt) cc_final: 0.8229 (ttmt) REVERT: S 353 LYS cc_start: 0.8296 (mttt) cc_final: 0.7754 (mptt) REVERT: U 353 LYS cc_start: 0.8568 (tttt) cc_final: 0.8220 (ttpt) outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.8085 time to fit residues: 38.5740 Evaluate side-chains 38 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.0060 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 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 2832 Z= 0.167 Angle : 0.436 4.108 3816 Z= 0.211 Chirality : 0.051 0.180 432 Planarity : 0.001 0.006 432 Dihedral : 21.499 89.585 432 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 17.80 % Favored : 81.06 % 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: -2.59 (0.43), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.33), 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 43 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.286 Fit side-chains REVERT: E 353 LYS cc_start: 0.8630 (tttt) cc_final: 0.8276 (ttmt) REVERT: K 353 LYS cc_start: 0.8186 (mttt) cc_final: 0.7769 (mtpp) REVERT: K 359 ASN cc_start: 0.8780 (m-40) cc_final: 0.8456 (m-40) REVERT: M 353 LYS cc_start: 0.8636 (tttt) cc_final: 0.8252 (ttmt) REVERT: S 353 LYS cc_start: 0.8327 (mttt) cc_final: 0.7791 (mptt) REVERT: U 353 LYS cc_start: 0.8589 (tttt) cc_final: 0.8164 (ttmt) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.6315 time to fit residues: 27.8860 Evaluate side-chains 41 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.0060 chunk 23 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2832 Z= 0.245 Angle : 0.509 5.687 3816 Z= 0.237 Chirality : 0.059 0.271 432 Planarity : 0.002 0.009 432 Dihedral : 21.411 88.754 432 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 17.80 % Favored : 81.06 % 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: -2.74 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.32), 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 42 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.335 Fit side-chains REVERT: E 353 LYS cc_start: 0.8669 (tttt) cc_final: 0.8314 (ttmt) REVERT: K 353 LYS cc_start: 0.8185 (mttt) cc_final: 0.7777 (mtpp) REVERT: M 353 LYS cc_start: 0.8660 (tttt) cc_final: 0.8252 (ttmt) REVERT: S 353 LYS cc_start: 0.8391 (mttt) cc_final: 0.7975 (mtpp) REVERT: U 353 LYS cc_start: 0.8597 (tttt) cc_final: 0.8158 (ttmt) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.6377 time to fit residues: 27.5288 Evaluate side-chains 41 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE 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: 10.0000 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 0.0060 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.6802 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2832 Z= 0.233 Angle : 0.496 5.141 3816 Z= 0.232 Chirality : 0.058 0.259 432 Planarity : 0.002 0.009 432 Dihedral : 21.341 88.650 432 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.14 % Allowed : 18.18 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.41), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), 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 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.343 Fit side-chains REVERT: E 353 LYS cc_start: 0.8668 (tttt) cc_final: 0.8325 (ttmt) REVERT: G 353 LYS cc_start: 0.8355 (tttp) cc_final: 0.7793 (ttmm) REVERT: K 353 LYS cc_start: 0.8192 (mttt) cc_final: 0.7784 (mtpp) REVERT: M 353 LYS cc_start: 0.8664 (tttt) cc_final: 0.8245 (ttmt) REVERT: S 353 LYS cc_start: 0.8414 (mttt) cc_final: 0.7988 (mtpp) REVERT: U 353 LYS cc_start: 0.8586 (tttt) cc_final: 0.8150 (ttmt) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.6433 time to fit residues: 29.0788 Evaluate side-chains 43 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain J 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: 0.8980 chunk 6 optimal weight: 0.0670 chunk 19 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2832 Z= 0.165 Angle : 0.434 3.845 3816 Z= 0.212 Chirality : 0.052 0.189 432 Planarity : 0.001 0.007 432 Dihedral : 20.806 88.789 432 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 18.56 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.42), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.32), 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 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.310 Fit side-chains REVERT: E 353 LYS cc_start: 0.8635 (tttt) cc_final: 0.8293 (ttmt) REVERT: K 353 LYS cc_start: 0.8192 (mttt) cc_final: 0.7784 (mtpp) REVERT: M 353 LYS cc_start: 0.8645 (tttt) cc_final: 0.8251 (ttmt) REVERT: S 353 LYS cc_start: 0.8396 (mttt) cc_final: 0.7877 (mptt) REVERT: U 353 LYS cc_start: 0.8589 (tttt) cc_final: 0.8162 (ttmt) outliers start: 2 outliers final: 3 residues processed: 43 average time/residue: 0.6504 time to fit residues: 29.4316 Evaluate side-chains 45 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.0870 chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.9762 ------------------------------------------------------------------------------- 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: 0.8162 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2832 Z= 0.182 Angle : 0.452 4.246 3816 Z= 0.219 Chirality : 0.053 0.200 432 Planarity : 0.002 0.007 432 Dihedral : 20.782 88.403 432 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 18.94 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.41), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.32), 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 43 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.270 Fit side-chains REVERT: E 353 LYS cc_start: 0.8641 (tttt) cc_final: 0.8300 (ttmt) REVERT: G 353 LYS cc_start: 0.8383 (tttp) cc_final: 0.7804 (ttmm) REVERT: K 353 LYS cc_start: 0.8196 (mttt) cc_final: 0.7788 (mtpp) REVERT: M 353 LYS cc_start: 0.8655 (tttt) cc_final: 0.8249 (ttmt) REVERT: S 353 LYS cc_start: 0.8398 (mttt) cc_final: 0.7880 (mptt) REVERT: U 353 LYS cc_start: 0.8591 (tttt) cc_final: 0.8165 (ttmt) outliers start: 1 outliers final: 2 residues processed: 43 average time/residue: 0.6564 time to fit residues: 29.5501 Evaluate side-chains 44 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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: 0.8259 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 2832 Z= 0.492 Angle : 0.759 9.176 3816 Z= 0.330 Chirality : 0.088 0.492 432 Planarity : 0.003 0.016 432 Dihedral : 22.943 87.858 432 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.14 % Allowed : 17.80 % Favored : 81.06 % 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: -3.23 (0.39), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.30), 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 47 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.302 Fit side-chains REVERT: C 353 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7916 (mtpp) REVERT: E 353 LYS cc_start: 0.8711 (tttt) cc_final: 0.8352 (ttmt) REVERT: G 353 LYS cc_start: 0.8388 (tttp) cc_final: 0.7854 (ttmm) REVERT: K 353 LYS cc_start: 0.8217 (mttt) cc_final: 0.7803 (mtpp) REVERT: M 353 LYS cc_start: 0.8682 (tttt) cc_final: 0.8267 (ttmt) REVERT: S 353 LYS cc_start: 0.8418 (mttt) cc_final: 0.7982 (mtpp) REVERT: U 353 LYS cc_start: 0.8614 (tttt) cc_final: 0.8163 (ttmt) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.6015 time to fit residues: 29.1079 Evaluate side-chains 46 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain Q residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.112760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092083 restraints weight = 4224.003| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.39 r_work: 0.3355 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2832 Z= 0.255 Angle : 0.534 5.604 3816 Z= 0.247 Chirality : 0.062 0.285 432 Planarity : 0.002 0.010 432 Dihedral : 22.007 89.028 432 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 18.94 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.40), residues: 240 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.31), residues: 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.82 seconds wall clock time: 25 minutes 22.68 seconds (1522.68 seconds total)