Starting phenix.real_space_refine on Thu Jul 18 21:01:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tdn_41171/07_2024/8tdn_41171.cif" } resolution = 3.1 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= 1.000 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 2330 2.51 5 N 600 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3620 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "B" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Chain: "E" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Time building chain proxies: 2.84, per 1000 atoms: 0.78 Number of scatterers: 3620 At special positions: 0 Unit cell: (70.55, 83.83, 40.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 685 8.00 N 600 7.00 C 2330 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: 1.34 Conformation dependent library (CDL) restraints added in 635.3 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 880 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.590A pdb=" N MET A 13 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL C 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LYS A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET C 13 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL E 16 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LYS C 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.255A pdb=" N VAL B 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 25 through 32 removed outlier: 6.349A pdb=" N ALA A 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL C 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN A 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL C 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL C 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N HIS A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL E 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN C 27 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL E 30 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 29 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL E 32 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 66 removed outlier: 6.375A pdb=" N THR B 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLU D 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU B 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE D 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLU B 63 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 10.236A pdb=" N GLU D 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N VAL B 65 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU A 63 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N GLU B 66 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL A 65 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE A 64 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 65 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A 66 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE C 64 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL E 65 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU C 66 " --> pdb=" O VAL E 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 69 through 75 removed outlier: 7.078A pdb=" N ASP B 74 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR D 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASP A 74 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR B 75 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 69 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU C 72 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 71 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE A 73 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR C 69 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU E 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 71 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ILE C 73 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 78 through 80 removed outlier: 6.904A pdb=" N LYS D 80 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR C 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 96 removed outlier: 3.501A pdb=" N ALA D 91 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL C 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR C 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE A 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA C 91 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL E 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR E 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE C 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 110 removed outlier: 6.643A pdb=" N ARG B 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE D 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR B 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA D 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA B 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU E 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 115 removed outlier: 7.031A pdb=" N TYR B 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 123 removed outlier: 6.878A pdb=" N THR B 119 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL D 122 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 119 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL B 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 121 " --> pdb=" O VAL B 122 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 231 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: 0.98 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1140 1.34 - 1.45: 536 1.45 - 1.57: 2019 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 3705 Sorted by residual: bond pdb=" CG PRO E 24 " pdb=" CD PRO E 24 " ideal model delta sigma weight residual 1.503 1.481 0.022 3.40e-02 8.65e+02 4.11e-01 bond pdb=" CG PRO C 24 " pdb=" CD PRO C 24 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.95e-01 bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.93e-01 bond pdb=" CG PRO D 24 " pdb=" CD PRO D 24 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.88e-01 bond pdb=" CG PRO B 24 " pdb=" CD PRO B 24 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.81e-01 ... (remaining 3700 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.15: 167 107.15 - 113.84: 2089 113.84 - 120.52: 1317 120.52 - 127.21: 1422 127.21 - 133.90: 45 Bond angle restraints: 5040 Sorted by residual: angle pdb=" CA TYR C 78 " pdb=" CB TYR C 78 " pdb=" CG TYR C 78 " ideal model delta sigma weight residual 113.90 116.91 -3.01 1.80e+00 3.09e-01 2.80e+00 angle pdb=" CA TYR D 78 " pdb=" CB TYR D 78 " pdb=" CG TYR D 78 " ideal model delta sigma weight residual 113.90 116.89 -2.99 1.80e+00 3.09e-01 2.76e+00 angle pdb=" CA TYR E 78 " pdb=" CB TYR E 78 " pdb=" CG TYR E 78 " ideal model delta sigma weight residual 113.90 116.88 -2.98 1.80e+00 3.09e-01 2.74e+00 angle pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " pdb=" CG TYR A 78 " ideal model delta sigma weight residual 113.90 116.86 -2.96 1.80e+00 3.09e-01 2.71e+00 angle pdb=" CA TYR B 78 " pdb=" CB TYR B 78 " pdb=" CG TYR B 78 " ideal model delta sigma weight residual 113.90 116.84 -2.94 1.80e+00 3.09e-01 2.68e+00 ... (remaining 5035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.74: 1801 13.74 - 27.48: 274 27.48 - 41.22: 85 41.22 - 54.96: 20 54.96 - 68.70: 5 Dihedral angle restraints: 2185 sinusoidal: 825 harmonic: 1360 Sorted by residual: dihedral pdb=" CA ALA C 25 " pdb=" C ALA C 25 " pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta harmonic sigma weight residual -180.00 -164.88 -15.12 0 5.00e+00 4.00e-02 9.15e+00 dihedral pdb=" CA ALA E 25 " pdb=" C ALA E 25 " pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta harmonic sigma weight residual -180.00 -164.90 -15.10 0 5.00e+00 4.00e-02 9.12e+00 dihedral pdb=" CA GLU E 62 " pdb=" CB GLU E 62 " pdb=" CG GLU E 62 " pdb=" CD GLU E 62 " ideal model delta sinusoidal sigma weight residual 180.00 127.60 52.40 3 1.50e+01 4.44e-03 9.11e+00 ... (remaining 2182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 262 0.025 - 0.049: 192 0.049 - 0.073: 51 0.073 - 0.098: 32 0.098 - 0.122: 53 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA VAL D 65 " pdb=" N VAL D 65 " pdb=" C VAL D 65 " pdb=" CB VAL D 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL A 65 " pdb=" N VAL A 65 " pdb=" C VAL A 65 " pdb=" CB VAL A 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 587 not shown) Planarity restraints: 625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.007 2.00e-02 2.50e+03 5.57e-03 6.20e-01 pdb=" CG TYR A 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 78 " 0.007 2.00e-02 2.50e+03 5.53e-03 6.12e-01 pdb=" CG TYR E 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR E 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 78 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 78 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 78 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " 0.007 2.00e-02 2.50e+03 5.53e-03 6.11e-01 pdb=" CG TYR B 78 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 622 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 739 2.80 - 3.32: 3073 3.32 - 3.85: 6288 3.85 - 4.37: 7035 4.37 - 4.90: 13646 Nonbonded interactions: 30781 Sorted by model distance: nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR B 119 " model vdw 2.270 2.440 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR C 119 " pdb=" OH TYR E 114 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR D 119 " model vdw 2.305 2.440 nonbonded pdb=" OD1 ASP A 99 " pdb=" NH1 ARG C 103 " model vdw 2.421 2.520 ... (remaining 30776 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' } 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: 0.940 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.130 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.004 0.022 3705 Z= 0.242 Angle : 0.540 4.368 5040 Z= 0.293 Chirality : 0.047 0.122 590 Planarity : 0.003 0.016 625 Dihedral : 15.568 68.705 1305 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 18.99 % Favored : 81.01 % 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 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 79 HIS 0.002 0.001 HIS B 31 PHE 0.013 0.002 PHE B 64 TYR 0.014 0.002 TYR A 78 ARG 0.001 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.400 Fit side-chains REVERT: A 61 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7747 (mp0) REVERT: B 62 GLU cc_start: 0.8148 (tt0) cc_final: 0.7578 (tt0) REVERT: C 61 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7455 (mp0) REVERT: D 62 GLU cc_start: 0.8140 (tt0) cc_final: 0.7896 (tt0) REVERT: E 61 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7789 (mp0) REVERT: E 66 GLU cc_start: 0.7819 (tt0) cc_final: 0.7388 (tt0) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2453 time to fit residues: 14.9399 Evaluate side-chains 50 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3705 Z= 0.282 Angle : 0.527 3.727 5040 Z= 0.286 Chirality : 0.047 0.126 590 Planarity : 0.003 0.017 625 Dihedral : 5.305 16.211 500 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.54 % Allowed : 14.68 % Favored : 81.77 % 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 (0.35), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 79 HIS 0.002 0.001 HIS E 31 PHE 0.011 0.002 PHE A 64 TYR 0.017 0.002 TYR A 78 ARG 0.001 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.417 Fit side-chains REVERT: A 61 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7812 (mp0) REVERT: D 62 GLU cc_start: 0.8158 (tt0) cc_final: 0.7619 (tt0) REVERT: E 66 GLU cc_start: 0.7890 (tt0) cc_final: 0.7394 (tt0) REVERT: E 80 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7847 (tttp) outliers start: 14 outliers final: 7 residues processed: 59 average time/residue: 0.2266 time to fit residues: 15.6967 Evaluate side-chains 56 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN C 27 ASN E 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3705 Z= 0.160 Angle : 0.474 3.605 5040 Z= 0.257 Chirality : 0.046 0.123 590 Planarity : 0.003 0.017 625 Dihedral : 4.994 15.939 500 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.78 % Allowed : 12.91 % Favored : 84.30 % 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: -2.85 (0.35), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 79 HIS 0.001 0.000 HIS A 31 PHE 0.010 0.001 PHE A 64 TYR 0.021 0.002 TYR C 114 ARG 0.001 0.000 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.399 Fit side-chains REVERT: A 61 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7932 (mp0) REVERT: D 62 GLU cc_start: 0.8198 (tt0) cc_final: 0.7678 (tt0) REVERT: E 66 GLU cc_start: 0.7900 (tt0) cc_final: 0.7424 (tt0) outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 0.2062 time to fit residues: 13.2017 Evaluate side-chains 52 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 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: 0.8342 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 3705 Z= 0.629 Angle : 0.676 4.066 5040 Z= 0.367 Chirality : 0.051 0.141 590 Planarity : 0.004 0.019 625 Dihedral : 5.824 18.782 500 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.32 % Allowed : 10.38 % Favored : 84.30 % 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: -3.12 (0.33), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.004 0.001 HIS E 31 PHE 0.011 0.002 PHE A 64 TYR 0.026 0.003 TYR C 114 ARG 0.002 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 46 time to evaluate : 0.427 Fit side-chains REVERT: A 61 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7857 (mp0) REVERT: B 62 GLU cc_start: 0.8189 (tt0) cc_final: 0.7725 (tt0) REVERT: C 66 GLU cc_start: 0.8106 (tt0) cc_final: 0.7540 (tt0) REVERT: D 62 GLU cc_start: 0.8171 (tt0) cc_final: 0.7651 (tt0) REVERT: E 66 GLU cc_start: 0.8044 (tt0) cc_final: 0.7476 (tt0) REVERT: E 78 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8673 (m-80) REVERT: E 80 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7857 (tttp) outliers start: 21 outliers final: 10 residues processed: 61 average time/residue: 0.1841 time to fit residues: 13.6145 Evaluate side-chains 57 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3705 Z= 0.210 Angle : 0.505 3.606 5040 Z= 0.274 Chirality : 0.046 0.123 590 Planarity : 0.003 0.018 625 Dihedral : 5.327 16.792 500 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.53 % Allowed : 11.39 % Favored : 86.08 % 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: -3.03 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 79 HIS 0.002 0.001 HIS A 31 PHE 0.010 0.002 PHE B 64 TYR 0.021 0.002 TYR C 114 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.419 Fit side-chains REVERT: A 61 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 62 GLU cc_start: 0.8183 (tt0) cc_final: 0.7776 (tt0) REVERT: C 66 GLU cc_start: 0.7961 (tt0) cc_final: 0.7637 (tt0) REVERT: D 62 GLU cc_start: 0.8164 (tt0) cc_final: 0.7652 (tt0) REVERT: E 66 GLU cc_start: 0.7932 (tt0) cc_final: 0.7475 (tt0) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1850 time to fit residues: 11.7349 Evaluate side-chains 55 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3705 Z= 0.319 Angle : 0.531 3.621 5040 Z= 0.287 Chirality : 0.047 0.129 590 Planarity : 0.003 0.016 625 Dihedral : 5.373 16.542 500 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.04 % Allowed : 11.90 % Favored : 85.06 % 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: -3.06 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.003 0.001 HIS A 31 PHE 0.010 0.002 PHE A 64 TYR 0.020 0.002 TYR B 78 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.413 Fit side-chains REVERT: A 61 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8007 (mp0) REVERT: B 62 GLU cc_start: 0.8151 (tt0) cc_final: 0.7754 (tt0) REVERT: C 66 GLU cc_start: 0.8018 (tt0) cc_final: 0.7725 (tt0) REVERT: D 62 GLU cc_start: 0.8171 (tt0) cc_final: 0.7671 (tt0) REVERT: E 66 GLU cc_start: 0.7936 (tt0) cc_final: 0.7434 (tt0) REVERT: E 80 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7875 (tttp) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 0.1961 time to fit residues: 12.9963 Evaluate side-chains 58 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3705 Z= 0.192 Angle : 0.485 3.495 5040 Z= 0.263 Chirality : 0.046 0.123 590 Planarity : 0.003 0.020 625 Dihedral : 5.152 16.041 500 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.53 % Allowed : 12.41 % Favored : 85.06 % 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: -3.04 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 79 HIS 0.002 0.000 HIS A 31 PHE 0.010 0.001 PHE B 64 TYR 0.019 0.002 TYR C 114 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.405 Fit side-chains REVERT: A 61 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7942 (mp0) REVERT: B 62 GLU cc_start: 0.8177 (tt0) cc_final: 0.7803 (tt0) REVERT: C 66 GLU cc_start: 0.7943 (tt0) cc_final: 0.7671 (tt0) REVERT: D 62 GLU cc_start: 0.8186 (tt0) cc_final: 0.7731 (tt0) REVERT: E 66 GLU cc_start: 0.7934 (tt0) cc_final: 0.7464 (tt0) REVERT: E 80 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7846 (tttp) outliers start: 10 outliers final: 9 residues processed: 51 average time/residue: 0.1998 time to fit residues: 12.3419 Evaluate side-chains 56 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8345 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3705 Z= 0.486 Angle : 0.606 3.838 5040 Z= 0.328 Chirality : 0.049 0.136 590 Planarity : 0.003 0.019 625 Dihedral : 5.590 17.693 500 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.78 % Allowed : 12.66 % Favored : 84.56 % 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: -3.16 (0.33), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.003 0.001 HIS A 31 PHE 0.011 0.002 PHE A 64 TYR 0.025 0.003 TYR C 78 ARG 0.001 0.000 ARG E 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.417 Fit side-chains REVERT: A 61 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7519 (mp0) REVERT: B 62 GLU cc_start: 0.8155 (tt0) cc_final: 0.7838 (tt0) REVERT: D 62 GLU cc_start: 0.8150 (tt0) cc_final: 0.7673 (tt0) REVERT: E 66 GLU cc_start: 0.8022 (tt0) cc_final: 0.7382 (tt0) REVERT: E 80 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7886 (tttp) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1934 time to fit residues: 13.3201 Evaluate side-chains 61 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3705 Z= 0.212 Angle : 0.497 3.588 5040 Z= 0.270 Chirality : 0.047 0.121 590 Planarity : 0.003 0.019 625 Dihedral : 5.249 16.429 500 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.53 % Allowed : 12.41 % Favored : 85.06 % 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: -3.10 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 79 HIS 0.002 0.001 HIS A 31 PHE 0.011 0.001 PHE B 64 TYR 0.019 0.002 TYR C 114 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.422 Fit side-chains REVERT: A 61 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7501 (mp0) REVERT: B 62 GLU cc_start: 0.8166 (tt0) cc_final: 0.7862 (tt0) REVERT: C 66 GLU cc_start: 0.7983 (tt0) cc_final: 0.7710 (tt0) REVERT: D 62 GLU cc_start: 0.8177 (tt0) cc_final: 0.7574 (tt0) REVERT: E 66 GLU cc_start: 0.7974 (tt0) cc_final: 0.7505 (tt0) REVERT: E 80 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7900 (tttp) outliers start: 10 outliers final: 8 residues processed: 51 average time/residue: 0.2030 time to fit residues: 12.7226 Evaluate side-chains 55 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3705 Z= 0.244 Angle : 0.508 3.739 5040 Z= 0.274 Chirality : 0.047 0.126 590 Planarity : 0.003 0.019 625 Dihedral : 5.218 15.826 500 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.78 % Allowed : 12.15 % Favored : 85.06 % 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: -3.06 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 79 HIS 0.002 0.001 HIS A 31 PHE 0.011 0.002 PHE B 64 TYR 0.018 0.002 TYR C 114 ARG 0.001 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.408 Fit side-chains REVERT: A 61 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7506 (mp0) REVERT: B 62 GLU cc_start: 0.8182 (tt0) cc_final: 0.7888 (tt0) REVERT: C 66 GLU cc_start: 0.7963 (tt0) cc_final: 0.7698 (tt0) REVERT: D 62 GLU cc_start: 0.8173 (tt0) cc_final: 0.7605 (tt0) REVERT: E 66 GLU cc_start: 0.7986 (tt0) cc_final: 0.7500 (tt0) REVERT: E 80 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7872 (tttp) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.1929 time to fit residues: 12.6070 Evaluate side-chains 58 residues out of total 395 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 117 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.139850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.118666 restraints weight = 4199.319| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.88 r_work: 0.3766 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3705 Z= 0.206 Angle : 0.494 4.051 5040 Z= 0.266 Chirality : 0.047 0.123 590 Planarity : 0.003 0.020 625 Dihedral : 5.129 17.303 500 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.53 % Allowed : 11.90 % Favored : 85.57 % 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: -3.06 (0.34), residues: 445 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 79 HIS 0.002 0.000 HIS A 31 PHE 0.011 0.001 PHE B 64 TYR 0.018 0.002 TYR C 114 ARG 0.001 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1420.41 seconds wall clock time: 25 minutes 58.99 seconds (1558.99 seconds total)