Starting phenix.real_space_refine on Sun Mar 10 15:31:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hzb_35087/03_2024/8hzb_35087.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1860 2.51 5 N 516 2.21 5 O 600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2976 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "E" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "F" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "A" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Chain: "B" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 496 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain breaks: 1 Time building chain proxies: 1.91, per 1000 atoms: 0.64 Number of scatterers: 2976 At special positions: 0 Unit cell: (96.28, 121.18, 36.52, 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 600 8.00 N 516 7.00 C 1860 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=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 622.1 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 50.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 21 removed outlier: 6.545A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 58 removed outlier: 6.799A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA D 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU C 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.526A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 69 through 80 removed outlier: 9.129A pdb=" N VAL D 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N GLY C 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR D 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR C 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL C 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA D 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N GLN C 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA D 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLY D 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA E 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN D 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.784A pdb=" N PHE C 94 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N THR D 92 " --> pdb=" O GLY E 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 97 through 98 removed outlier: 6.906A pdb=" N LYS D 97 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 21 removed outlier: 6.526A pdb=" N VAL F 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA B 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA F 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS B 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU F 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 46 through 58 removed outlier: 6.821A pdb=" N GLY A 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU A 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL F 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.572A pdb=" N VAL F 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL B 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN F 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 80 removed outlier: 9.115A pdb=" N VAL F 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.470A pdb=" N GLY A 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR F 72 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N THR A 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA F 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N GLN A 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL F 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR B 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN F 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS B 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.805A pdb=" N PHE A 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N THR F 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 97 through 98 removed outlier: 6.896A pdb=" N LYS F 97 " --> pdb=" O ASP B 98 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 162 hydrogen bond angles 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: 0.63 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 528 1.29 - 1.35: 460 1.35 - 1.42: 102 1.42 - 1.48: 501 1.48 - 1.55: 1391 Bond restraints: 2982 Sorted by residual: bond pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.16e+00 bond pdb=" CA LYS E 58 " pdb=" C LYS E 58 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.08e-02 8.57e+03 2.07e+00 bond pdb=" CA LYS C 58 " pdb=" C LYS C 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.95e+00 bond pdb=" CA LYS B 58 " pdb=" C LYS B 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.94e+00 bond pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 1.526 1.511 0.015 1.08e-02 8.57e+03 1.92e+00 ... (remaining 2977 not shown) Histogram of bond angle deviations from ideal: 104.38 - 109.75: 545 109.75 - 115.12: 1450 115.12 - 120.49: 942 120.49 - 125.86: 1083 125.86 - 131.24: 6 Bond angle restraints: 4026 Sorted by residual: angle pdb=" C GLY E 41 " pdb=" N SER E 42 " pdb=" CA SER E 42 " ideal model delta sigma weight residual 122.42 117.96 4.46 1.55e+00 4.16e-01 8.26e+00 angle pdb=" C GLY A 41 " pdb=" N SER A 42 " pdb=" CA SER A 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.24e+00 angle pdb=" C GLY B 41 " pdb=" N SER B 42 " pdb=" CA SER B 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY D 41 " pdb=" N SER D 42 " pdb=" CA SER D 42 " ideal model delta sigma weight residual 122.42 117.97 4.45 1.55e+00 4.16e-01 8.23e+00 angle pdb=" C GLY C 41 " pdb=" N SER C 42 " pdb=" CA SER C 42 " ideal model delta sigma weight residual 122.42 118.01 4.41 1.55e+00 4.16e-01 8.11e+00 ... (remaining 4021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1524 17.62 - 35.24: 186 35.24 - 52.85: 30 52.85 - 70.47: 0 70.47 - 88.09: 12 Dihedral angle restraints: 1752 sinusoidal: 582 harmonic: 1170 Sorted by residual: dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N GLY A 41 " pdb=" CA GLY A 41 " ideal model delta harmonic sigma weight residual 180.00 156.42 23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL D 40 " pdb=" C VAL D 40 " pdb=" N GLY D 41 " pdb=" CA GLY D 41 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA VAL F 40 " pdb=" C VAL F 40 " pdb=" N GLY F 41 " pdb=" CA GLY F 41 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 1749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 148 0.026 - 0.051: 160 0.051 - 0.077: 99 0.077 - 0.102: 71 0.102 - 0.128: 56 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 531 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL C 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL C 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 66 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.86e+00 pdb=" C VAL E 66 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL E 66 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY E 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 66 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C VAL B 66 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL B 66 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY B 67 " -0.008 2.00e-02 2.50e+03 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 154 2.71 - 3.26: 2853 3.26 - 3.80: 4388 3.80 - 4.35: 5053 4.35 - 4.90: 10336 Nonbonded interactions: 22784 Sorted by model distance: nonbonded pdb=" OE2 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.162 2.520 nonbonded pdb=" OE2 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.162 2.520 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.162 2.520 nonbonded pdb=" OE2 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.162 2.520 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.162 2.520 ... (remaining 22779 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' } 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: 1.930 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: 9.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.560 Find NCS groups from input model: 0.220 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.008 0.044 2982 Z= 0.575 Angle : 0.920 5.699 4026 Z= 0.518 Chirality : 0.059 0.128 534 Planarity : 0.004 0.014 498 Dihedral : 16.623 88.088 1008 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 20.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.28), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.22), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.019 0.006 PHE C 94 TYR 0.019 0.005 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.329 Fit side-chains REVERT: C 45 LYS cc_start: 0.7387 (tttt) cc_final: 0.7140 (tttm) REVERT: E 45 LYS cc_start: 0.7543 (tttt) cc_final: 0.7095 (tttm) REVERT: F 45 LYS cc_start: 0.7570 (tttt) cc_final: 0.7092 (tttm) REVERT: A 45 LYS cc_start: 0.7425 (tttt) cc_final: 0.7175 (tttm) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1820 time to fit residues: 5.2178 Evaluate side-chains 23 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7015 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2982 Z= 0.303 Angle : 0.707 5.494 4026 Z= 0.383 Chirality : 0.053 0.128 534 Planarity : 0.003 0.013 498 Dihedral : 6.922 22.580 426 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.33 % Allowed : 25.00 % Favored : 72.67 % 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: -3.63 (0.33), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 50 PHE 0.014 0.004 PHE B 94 TYR 0.014 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.296 Fit side-chains REVERT: E 45 LYS cc_start: 0.7657 (tttt) cc_final: 0.7146 (tttm) REVERT: B 45 LYS cc_start: 0.7607 (tttt) cc_final: 0.7164 (tttm) outliers start: 7 outliers final: 7 residues processed: 27 average time/residue: 0.1197 time to fit residues: 4.3453 Evaluate side-chains 28 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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: 0.7085 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2982 Z= 0.419 Angle : 0.801 7.237 4026 Z= 0.432 Chirality : 0.055 0.128 534 Planarity : 0.003 0.014 498 Dihedral : 7.471 22.711 426 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 8.67 % Allowed : 21.00 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.33), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 50 PHE 0.015 0.005 PHE B 94 TYR 0.017 0.005 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 22 time to evaluate : 0.316 Fit side-chains REVERT: D 44 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6825 (t) REVERT: D 45 LYS cc_start: 0.7465 (tttt) cc_final: 0.7031 (tttm) REVERT: C 44 THR cc_start: 0.6972 (OUTLIER) cc_final: 0.6677 (t) REVERT: E 44 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6805 (t) REVERT: E 45 LYS cc_start: 0.7810 (tttt) cc_final: 0.7346 (tttm) REVERT: F 39 TYR cc_start: 0.7136 (m-80) cc_final: 0.6936 (m-80) REVERT: F 44 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6726 (t) REVERT: A 44 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6661 (t) REVERT: B 44 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6616 (t) REVERT: B 45 LYS cc_start: 0.7699 (tttt) cc_final: 0.7301 (tttm) outliers start: 26 outliers final: 15 residues processed: 44 average time/residue: 0.1050 time to fit residues: 6.1502 Evaluate side-chains 43 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 22 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.0370 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 overall best weight: 1.2040 ------------------------------------------------------------------------------- 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: 0.6950 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2982 Z= 0.166 Angle : 0.569 4.636 4026 Z= 0.308 Chirality : 0.051 0.133 534 Planarity : 0.002 0.013 498 Dihedral : 6.000 21.623 426 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 7.00 % Allowed : 24.00 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 50 PHE 0.007 0.002 PHE B 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 18 time to evaluate : 0.333 Fit side-chains REVERT: C 44 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6430 (t) REVERT: E 45 LYS cc_start: 0.7792 (tttt) cc_final: 0.7313 (tttm) REVERT: F 44 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6627 (t) REVERT: A 39 TYR cc_start: 0.6824 (m-80) cc_final: 0.6616 (m-80) REVERT: A 44 THR cc_start: 0.6802 (OUTLIER) cc_final: 0.6552 (t) REVERT: B 45 LYS cc_start: 0.7638 (tttt) cc_final: 0.7244 (tttm) outliers start: 21 outliers final: 11 residues processed: 38 average time/residue: 0.0975 time to fit residues: 5.1364 Evaluate side-chains 31 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 17 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2982 Z= 0.251 Angle : 0.648 5.641 4026 Z= 0.349 Chirality : 0.054 0.250 534 Planarity : 0.002 0.013 498 Dihedral : 6.385 20.554 426 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 6.67 % Allowed : 23.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 50 PHE 0.010 0.003 PHE B 94 TYR 0.013 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 19 time to evaluate : 0.336 Fit side-chains REVERT: D 39 TYR cc_start: 0.6878 (m-80) cc_final: 0.6662 (m-80) REVERT: E 45 LYS cc_start: 0.7746 (tttt) cc_final: 0.7268 (tttm) REVERT: F 44 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6763 (t) REVERT: A 44 THR cc_start: 0.6912 (OUTLIER) cc_final: 0.6638 (t) REVERT: B 39 TYR cc_start: 0.7082 (m-80) cc_final: 0.6872 (m-80) REVERT: B 45 LYS cc_start: 0.7771 (tttt) cc_final: 0.7348 (tttm) outliers start: 20 outliers final: 14 residues processed: 38 average time/residue: 0.0984 time to fit residues: 5.1658 Evaluate side-chains 35 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 19 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2982 Z= 0.234 Angle : 0.629 5.535 4026 Z= 0.338 Chirality : 0.053 0.217 534 Planarity : 0.002 0.013 498 Dihedral : 6.231 20.660 426 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 6.67 % Allowed : 24.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.36), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.009 0.003 PHE B 94 TYR 0.010 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 18 time to evaluate : 0.328 Fit side-chains REVERT: E 45 LYS cc_start: 0.7851 (tttt) cc_final: 0.7381 (tttm) REVERT: F 44 THR cc_start: 0.7005 (OUTLIER) cc_final: 0.6771 (t) outliers start: 20 outliers final: 15 residues processed: 36 average time/residue: 0.1034 time to fit residues: 5.1741 Evaluate side-chains 33 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 17 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2982 Z= 0.171 Angle : 0.560 4.780 4026 Z= 0.302 Chirality : 0.052 0.188 534 Planarity : 0.002 0.013 498 Dihedral : 5.739 19.578 426 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 5.33 % Allowed : 24.33 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.37), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.006 0.002 PHE B 94 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.320 Fit side-chains REVERT: E 45 LYS cc_start: 0.7775 (tttt) cc_final: 0.7305 (tttm) REVERT: F 44 THR cc_start: 0.7030 (OUTLIER) cc_final: 0.6773 (t) outliers start: 16 outliers final: 15 residues processed: 29 average time/residue: 0.0781 time to fit residues: 3.4669 Evaluate side-chains 30 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN A 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2982 Z= 0.131 Angle : 0.514 4.593 4026 Z= 0.278 Chirality : 0.051 0.174 534 Planarity : 0.002 0.012 498 Dihedral : 5.319 17.829 426 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 5.00 % Allowed : 25.33 % Favored : 69.67 % 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 (0.39), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 50 PHE 0.004 0.001 PHE B 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 16 time to evaluate : 0.247 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 30 average time/residue: 0.0972 time to fit residues: 4.1341 Evaluate side-chains 26 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 13 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2982 Z= 0.132 Angle : 0.506 4.387 4026 Z= 0.274 Chirality : 0.051 0.168 534 Planarity : 0.002 0.012 498 Dihedral : 5.223 16.301 426 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.67 % Allowed : 26.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.40), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.004 0.001 PHE B 94 TYR 0.006 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 15 time to evaluate : 0.326 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 27 average time/residue: 0.1022 time to fit residues: 3.9817 Evaluate side-chains 26 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 14 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2982 Z= 0.253 Angle : 0.620 5.776 4026 Z= 0.332 Chirality : 0.052 0.154 534 Planarity : 0.002 0.014 498 Dihedral : 6.111 17.724 426 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 4.67 % Allowed : 25.33 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.39), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 50 PHE 0.010 0.003 PHE B 94 TYR 0.011 0.003 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 21 time to evaluate : 0.362 Fit side-chains REVERT: D 45 LYS cc_start: 0.7288 (tttt) cc_final: 0.6994 (tttm) REVERT: E 45 LYS cc_start: 0.7773 (tttt) cc_final: 0.7346 (tttm) REVERT: F 45 LYS cc_start: 0.7412 (tttt) cc_final: 0.7012 (tttm) REVERT: B 45 LYS cc_start: 0.7856 (tttt) cc_final: 0.7530 (tttm) outliers start: 14 outliers final: 13 residues processed: 32 average time/residue: 0.1285 time to fit residues: 5.3602 Evaluate side-chains 35 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 22 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 = 0.5038 r_free = 0.5038 target = 0.251723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.216101 restraints weight = 3332.736| |-----------------------------------------------------------------------------| r_work (start): 0.4653 rms_B_bonded: 2.72 r_work: 0.4571 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2982 Z= 0.216 Angle : 0.596 5.450 4026 Z= 0.319 Chirality : 0.051 0.155 534 Planarity : 0.002 0.013 498 Dihedral : 6.059 17.234 426 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 4.33 % Allowed : 25.33 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.39), residues: 408 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 50 PHE 0.008 0.002 PHE B 94 TYR 0.008 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1071.53 seconds wall clock time: 20 minutes 5.73 seconds (1205.73 seconds total)