Starting phenix.real_space_refine on Tue Feb 13 20:04:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcc_21148/02_2024/6vcc_21148.pdb" } resolution = 3.6 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= 0.011 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 24 5.16 5 C 4896 2.51 5 N 1236 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J GLU 36": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 23": "OE1" <-> "OE2" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "B" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "C" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "D" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "E" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "F" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "H" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "I" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "J" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "K" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "L" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 631 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Time building chain proxies: 4.67, per 1000 atoms: 0.62 Number of scatterers: 7572 At special positions: 0 Unit cell: (90, 92, 132, 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 24 16.00 O 1416 8.00 N 1236 7.00 C 4896 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: 4.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 15.7% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.620A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.655A pdb=" N GLY A 83 " --> pdb=" O CYS A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.636A pdb=" N PHE B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.765A pdb=" N GLY B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 46 removed outlier: 3.750A pdb=" N PHE C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.609A pdb=" N GLY C 83 " --> pdb=" O CYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.663A pdb=" N PHE D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.757A pdb=" N PHE E 43 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 46 removed outlier: 3.587A pdb=" N PHE F 43 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.598A pdb=" N GLY F 83 " --> pdb=" O CYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.867A pdb=" N VAL G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU G 47 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.800A pdb=" N GLY G 83 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.946A pdb=" N VAL H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU H 47 " --> pdb=" O PHE H 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.529A pdb=" N GLY H 83 " --> pdb=" O CYS H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 45 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.575A pdb=" N GLY I 83 " --> pdb=" O CYS I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.921A pdb=" N VAL J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN J 48 " --> pdb=" O LYS J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.527A pdb=" N GLY J 83 " --> pdb=" O CYS J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 45 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.559A pdb=" N GLY K 83 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.895A pdb=" N VAL L 46 " --> pdb=" O ASP L 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU L 47 " --> pdb=" O PHE L 43 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70 removed outlier: 5.164A pdb=" N VAL A 86 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER A 87 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 17 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 89 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 28 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 6.963A pdb=" N LEU B 28 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 16 removed outlier: 6.940A pdb=" N LEU C 28 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL D 86 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N SER D 87 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE D 17 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 18 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 28 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL E 86 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER E 87 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 17 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 18 " --> pdb=" O TYR E 27 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 28 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL F 86 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N SER F 87 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE F 17 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 14 through 18 removed outlier: 3.543A pdb=" N THR G 14 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL G 29 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89 removed outlier: 4.586A pdb=" N LYS H 30 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 17 through 18 removed outlier: 6.794A pdb=" N ILE H 17 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU H 89 " --> pdb=" O ILE H 17 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL H 86 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS I 30 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR I 18 " --> pdb=" O TYR I 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR I 14 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER I 87 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 17 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU I 89 " --> pdb=" O ILE I 17 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N VAL I 86 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS J 30 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 17 through 18 removed outlier: 6.863A pdb=" N ILE J 17 " --> pdb=" O SER J 87 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU J 89 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL J 86 " --> pdb=" O LYS J 58 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LYS K 30 " --> pdb=" O GLU J 70 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR K 18 " --> pdb=" O TYR K 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR K 14 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER K 87 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE K 17 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU K 89 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL K 86 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 30 " --> pdb=" O GLU K 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 14 " --> pdb=" O ILE L 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 18 removed outlier: 6.658A pdb=" N ILE L 17 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU L 89 " --> pdb=" O ILE L 17 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL L 86 " --> pdb=" O LYS L 58 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 489 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: 3.46 Time building geometry restraints manager: 4.62 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: 2431 1.34 - 1.46: 1687 1.46 - 1.58: 3598 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 7752 Sorted by residual: bond pdb=" N LYS L 54 " pdb=" CA LYS L 54 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.23e-02 6.61e+03 3.96e+00 bond pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.54e-02 4.22e+03 2.06e+00 bond pdb=" C VAL A 33 " pdb=" N PRO A 34 " ideal model delta sigma weight residual 1.326 1.345 -0.019 1.44e-02 4.82e+03 1.73e+00 bond pdb=" C VAL B 33 " pdb=" N PRO B 34 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.51e+00 bond pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.70e-02 3.46e+03 1.24e+00 ... (remaining 7747 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 320 107.28 - 113.95: 4183 113.95 - 120.63: 3075 120.63 - 127.30: 2853 127.30 - 133.98: 69 Bond angle restraints: 10500 Sorted by residual: angle pdb=" C LEU F 47 " pdb=" N GLN F 48 " pdb=" CA GLN F 48 " ideal model delta sigma weight residual 122.46 127.44 -4.98 1.41e+00 5.03e-01 1.25e+01 angle pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " pdb=" CG GLN F 48 " ideal model delta sigma weight residual 114.10 120.26 -6.16 2.00e+00 2.50e-01 9.50e+00 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 106.55 110.06 -3.51 1.45e+00 4.76e-01 5.86e+00 angle pdb=" C LEU H 89 " pdb=" N VAL H 90 " pdb=" CA VAL H 90 " ideal model delta sigma weight residual 121.70 125.73 -4.03 1.80e+00 3.09e-01 5.01e+00 angle pdb=" C LEU J 89 " pdb=" N VAL J 90 " pdb=" CA VAL J 90 " ideal model delta sigma weight residual 121.70 125.70 -4.00 1.80e+00 3.09e-01 4.94e+00 ... (remaining 10495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4277 17.65 - 35.30: 347 35.30 - 52.95: 47 52.95 - 70.60: 4 70.60 - 88.24: 5 Dihedral angle restraints: 4680 sinusoidal: 1944 harmonic: 2736 Sorted by residual: dihedral pdb=" CB GLU H 24 " pdb=" CG GLU H 24 " pdb=" CD GLU H 24 " pdb=" OE1 GLU H 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.24 -88.24 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU I 24 " pdb=" CG GLU I 24 " pdb=" CD GLU I 24 " pdb=" OE1 GLU I 24 " ideal model delta sinusoidal sigma weight residual 0.00 88.11 -88.11 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA ASP D 61 " pdb=" CB ASP D 61 " pdb=" CG ASP D 61 " pdb=" OD1 ASP D 61 " ideal model delta sinusoidal sigma weight residual -30.00 -80.47 50.47 1 2.00e+01 2.50e-03 8.72e+00 ... (remaining 4677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 684 0.039 - 0.078: 292 0.078 - 0.118: 135 0.118 - 0.157: 31 0.157 - 0.196: 10 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CB ILE F 38 " pdb=" CA ILE F 38 " pdb=" CG1 ILE F 38 " pdb=" CG2 ILE F 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CB ILE A 38 " pdb=" CA ILE A 38 " pdb=" CG1 ILE A 38 " pdb=" CG2 ILE A 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CB ILE E 38 " pdb=" CA ILE E 38 " pdb=" CG1 ILE E 38 " pdb=" CG2 ILE E 38 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 1149 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 33 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO C 34 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 33 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO H 34 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 34 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 34 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 77 " 0.108 9.50e-02 1.11e+02 5.00e-02 3.19e+00 pdb=" NE ARG H 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG H 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG H 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 77 " 0.012 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1573 2.78 - 3.31: 6085 3.31 - 3.84: 12354 3.84 - 4.37: 13207 4.37 - 4.90: 24311 Nonbonded interactions: 57530 Sorted by model distance: nonbonded pdb=" ND2 ASN D 82 " pdb=" OD1 ASP I 63 " model vdw 2.253 2.520 nonbonded pdb=" OD1 ASP E 63 " pdb=" ND2 ASN J 82 " model vdw 2.273 2.520 nonbonded pdb=" OD1 ASP D 63 " pdb=" ND2 ASN I 82 " model vdw 2.425 2.520 nonbonded pdb=" ND2 ASN E 82 " pdb=" OD1 ASP J 63 " model vdw 2.433 2.520 nonbonded pdb=" OD1 ASP B 63 " pdb=" ND2 ASN G 82 " model vdw 2.442 2.520 ... (remaining 57525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 0.280 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: 1.150 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.860 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 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 0.036 7752 Z= 0.236 Angle : 0.664 6.330 10500 Z= 0.376 Chirality : 0.054 0.196 1152 Planarity : 0.006 0.050 1356 Dihedral : 12.504 88.244 2904 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.24), residues: 912 helix: -3.99 (0.12), residues: 72 sheet: -3.22 (0.23), residues: 360 loop : -2.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 88 HIS 0.004 0.002 HIS J 19 PHE 0.008 0.001 PHE E 64 TYR 0.015 0.002 TYR D 18 ARG 0.023 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7152 (mtpp) cc_final: 0.6888 (mmtt) REVERT: B 70 GLU cc_start: 0.7086 (tt0) cc_final: 0.6733 (tt0) REVERT: C 23 GLU cc_start: 0.6398 (mt-10) cc_final: 0.6172 (mt-10) REVERT: D 15 LYS cc_start: 0.7854 (mttt) cc_final: 0.7217 (mmtt) REVERT: D 23 GLU cc_start: 0.6388 (mt-10) cc_final: 0.6174 (mt-10) REVERT: D 54 LYS cc_start: 0.7453 (mtpp) cc_final: 0.7117 (mtpt) REVERT: D 55 TYR cc_start: 0.7498 (m-80) cc_final: 0.7077 (m-80) REVERT: E 54 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6724 (mtmm) REVERT: F 66 VAL cc_start: 0.8090 (m) cc_final: 0.7838 (m) REVERT: H 20 LEU cc_start: 0.8541 (mp) cc_final: 0.8293 (mt) REVERT: H 54 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7695 (mmtm) REVERT: I 72 SER cc_start: 0.7102 (m) cc_final: 0.6847 (p) REVERT: J 60 MET cc_start: 0.8315 (tpp) cc_final: 0.8097 (tpp) REVERT: K 49 ARG cc_start: 0.6228 (mmm160) cc_final: 0.5993 (mmp80) REVERT: K 69 GLU cc_start: 0.6371 (pt0) cc_final: 0.5993 (pt0) REVERT: K 74 ASP cc_start: 0.6733 (m-30) cc_final: 0.6384 (p0) REVERT: L 34 PRO cc_start: 0.6822 (Cg_endo) cc_final: 0.6132 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2512 time to fit residues: 72.6345 Evaluate side-chains 184 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.0060 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN G 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7752 Z= 0.292 Angle : 0.620 8.458 10500 Z= 0.309 Chirality : 0.050 0.183 1152 Planarity : 0.005 0.051 1356 Dihedral : 4.165 12.375 1008 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.05 % Allowed : 14.76 % Favored : 81.19 % 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: -3.97 (0.25), residues: 912 helix: -1.44 (0.42), residues: 72 sheet: -3.13 (0.23), residues: 360 loop : -2.34 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 88 HIS 0.006 0.003 HIS B 19 PHE 0.017 0.002 PHE G 57 TYR 0.016 0.002 TYR A 27 ARG 0.005 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 195 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 LYS cc_start: 0.7221 (mtpp) cc_final: 0.6989 (mmtt) REVERT: B 58 LYS cc_start: 0.8149 (tttt) cc_final: 0.7762 (tttp) REVERT: B 70 GLU cc_start: 0.7162 (tt0) cc_final: 0.6828 (tt0) REVERT: C 23 GLU cc_start: 0.6519 (mt-10) cc_final: 0.6302 (mt-10) REVERT: D 54 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7351 (mtpt) REVERT: F 60 MET cc_start: 0.8176 (tpp) cc_final: 0.7976 (tpp) REVERT: H 54 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7610 (mmtm) REVERT: K 74 ASP cc_start: 0.6654 (m-30) cc_final: 0.6220 (p0) REVERT: L 44 LYS cc_start: 0.7745 (mtpp) cc_final: 0.7227 (ptpp) outliers start: 34 outliers final: 21 residues processed: 214 average time/residue: 0.2417 time to fit residues: 65.4203 Evaluate side-chains 201 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 180 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7752 Z= 0.285 Angle : 0.606 9.036 10500 Z= 0.296 Chirality : 0.050 0.146 1152 Planarity : 0.005 0.050 1356 Dihedral : 4.389 14.581 1008 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.05 % Allowed : 18.57 % Favored : 77.38 % 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: -3.42 (0.26), residues: 912 helix: 0.09 (0.56), residues: 84 sheet: -2.87 (0.24), residues: 360 loop : -2.13 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 88 HIS 0.006 0.002 HIS D 19 PHE 0.016 0.002 PHE L 64 TYR 0.014 0.002 TYR A 27 ARG 0.004 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8168 (tttt) cc_final: 0.7777 (tttp) REVERT: B 70 GLU cc_start: 0.7143 (tt0) cc_final: 0.6910 (tt0) REVERT: C 23 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6424 (mt-10) REVERT: D 36 GLU cc_start: 0.6090 (pm20) cc_final: 0.5882 (tt0) REVERT: D 54 LYS cc_start: 0.7668 (mtpp) cc_final: 0.7038 (mtpt) REVERT: D 70 GLU cc_start: 0.5789 (tt0) cc_final: 0.5446 (tt0) REVERT: F 64 PHE cc_start: 0.8187 (m-80) cc_final: 0.7986 (m-80) REVERT: G 44 LYS cc_start: 0.7411 (ttpt) cc_final: 0.7163 (ttmt) REVERT: H 54 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7743 (mmtm) REVERT: I 30 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7801 (tppt) REVERT: J 24 GLU cc_start: 0.5716 (mm-30) cc_final: 0.4860 (mm-30) REVERT: J 73 ASP cc_start: 0.6400 (m-30) cc_final: 0.5963 (p0) REVERT: K 54 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8051 (mmmt) REVERT: K 74 ASP cc_start: 0.6475 (m-30) cc_final: 0.6118 (p0) outliers start: 34 outliers final: 28 residues processed: 226 average time/residue: 0.2443 time to fit residues: 69.8483 Evaluate side-chains 227 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 19 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7752 Z= 0.134 Angle : 0.527 7.970 10500 Z= 0.258 Chirality : 0.048 0.169 1152 Planarity : 0.004 0.046 1356 Dihedral : 3.886 13.798 1008 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.10 % Allowed : 20.24 % Favored : 76.67 % 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: -2.88 (0.28), residues: 912 helix: 1.78 (0.65), residues: 72 sheet: -2.60 (0.25), residues: 360 loop : -1.86 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 88 HIS 0.002 0.001 HIS D 19 PHE 0.021 0.001 PHE L 64 TYR 0.010 0.001 TYR B 27 ARG 0.005 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 LYS cc_start: 0.7992 (tttt) cc_final: 0.7598 (ttmt) REVERT: C 23 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6249 (mt-10) REVERT: D 54 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7092 (mtpt) REVERT: D 70 GLU cc_start: 0.5785 (tt0) cc_final: 0.5267 (tt0) REVERT: E 69 GLU cc_start: 0.7444 (pt0) cc_final: 0.7213 (pt0) REVERT: G 44 LYS cc_start: 0.7488 (ttpt) cc_final: 0.7268 (ttmt) REVERT: H 54 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7819 (mmtm) REVERT: J 17 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8293 (mt) REVERT: J 24 GLU cc_start: 0.5435 (mm-30) cc_final: 0.4536 (mm-30) REVERT: J 73 ASP cc_start: 0.6378 (m-30) cc_final: 0.5975 (p0) REVERT: K 54 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7936 (mmmt) REVERT: K 74 ASP cc_start: 0.6271 (m-30) cc_final: 0.6020 (p0) REVERT: L 48 GLN cc_start: 0.6816 (pt0) cc_final: 0.6616 (pt0) outliers start: 26 outliers final: 21 residues processed: 210 average time/residue: 0.2430 time to fit residues: 64.8880 Evaluate side-chains 204 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 0.0000 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 2.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7752 Z= 0.270 Angle : 0.588 8.647 10500 Z= 0.285 Chirality : 0.049 0.162 1152 Planarity : 0.004 0.050 1356 Dihedral : 4.209 14.035 1008 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.52 % Allowed : 19.76 % Favored : 75.71 % 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: -2.78 (0.28), residues: 912 helix: 1.44 (0.67), residues: 84 sheet: -2.58 (0.25), residues: 360 loop : -1.75 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 88 HIS 0.005 0.002 HIS D 19 PHE 0.011 0.002 PHE I 64 TYR 0.013 0.002 TYR A 27 ARG 0.006 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8120 (tttt) cc_final: 0.7840 (tttp) REVERT: D 54 LYS cc_start: 0.7880 (mtpp) cc_final: 0.7238 (mtpt) REVERT: D 70 GLU cc_start: 0.5755 (tt0) cc_final: 0.5421 (tt0) REVERT: E 54 LYS cc_start: 0.7532 (mmmt) cc_final: 0.6774 (mptt) REVERT: F 60 MET cc_start: 0.7824 (tpp) cc_final: 0.6600 (tmm) REVERT: H 54 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8009 (mmtm) REVERT: I 30 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7831 (mttt) REVERT: J 24 GLU cc_start: 0.5665 (mm-30) cc_final: 0.4812 (mm-30) REVERT: J 61 ASP cc_start: 0.7157 (t70) cc_final: 0.6951 (t70) REVERT: J 73 ASP cc_start: 0.6516 (m-30) cc_final: 0.6048 (p0) REVERT: K 54 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7994 (mmmt) REVERT: K 74 ASP cc_start: 0.6421 (m-30) cc_final: 0.6128 (p0) REVERT: L 20 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (mp) outliers start: 38 outliers final: 31 residues processed: 223 average time/residue: 0.2310 time to fit residues: 65.8174 Evaluate side-chains 224 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 47 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7752 Z= 0.255 Angle : 0.570 8.399 10500 Z= 0.279 Chirality : 0.049 0.151 1152 Planarity : 0.004 0.049 1356 Dihedral : 4.150 17.165 1008 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.64 % Allowed : 19.76 % Favored : 75.60 % 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: -2.62 (0.28), residues: 912 helix: 1.66 (0.67), residues: 84 sheet: -2.52 (0.25), residues: 360 loop : -1.63 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 88 HIS 0.004 0.002 HIS L 19 PHE 0.026 0.002 PHE L 64 TYR 0.012 0.001 TYR A 27 ARG 0.005 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 58 LYS cc_start: 0.8136 (tttt) cc_final: 0.7878 (tttp) REVERT: D 15 LYS cc_start: 0.8388 (mttt) cc_final: 0.7804 (mttt) REVERT: D 54 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7387 (mtpt) REVERT: D 70 GLU cc_start: 0.5810 (tt0) cc_final: 0.5534 (tt0) REVERT: E 69 GLU cc_start: 0.7604 (pt0) cc_final: 0.7157 (pt0) REVERT: F 60 MET cc_start: 0.7852 (tpp) cc_final: 0.6455 (tmm) REVERT: H 54 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7882 (mmtm) REVERT: J 17 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8324 (mt) REVERT: J 24 GLU cc_start: 0.5701 (mm-30) cc_final: 0.4835 (mm-30) REVERT: J 73 ASP cc_start: 0.6542 (m-30) cc_final: 0.6084 (p0) REVERT: K 54 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7984 (mmmt) REVERT: K 74 ASP cc_start: 0.6465 (m-30) cc_final: 0.6049 (p0) outliers start: 39 outliers final: 33 residues processed: 218 average time/residue: 0.2237 time to fit residues: 62.8859 Evaluate side-chains 226 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 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: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7752 Z= 0.144 Angle : 0.535 8.988 10500 Z= 0.259 Chirality : 0.048 0.134 1152 Planarity : 0.004 0.049 1356 Dihedral : 3.805 14.908 1008 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.45 % Allowed : 22.14 % Favored : 74.40 % 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: -2.27 (0.29), residues: 912 helix: 1.89 (0.67), residues: 84 sheet: -2.16 (0.26), residues: 348 loop : -1.55 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 88 HIS 0.002 0.001 HIS I 19 PHE 0.030 0.001 PHE L 64 TYR 0.009 0.001 TYR A 27 ARG 0.009 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.913 Fit side-chains REVERT: B 58 LYS cc_start: 0.8051 (tttt) cc_final: 0.7673 (ttmt) REVERT: D 15 LYS cc_start: 0.8317 (mttt) cc_final: 0.7769 (mttt) REVERT: D 54 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7406 (mtpt) REVERT: D 70 GLU cc_start: 0.5782 (tt0) cc_final: 0.5523 (tt0) REVERT: E 69 GLU cc_start: 0.7609 (pt0) cc_final: 0.7194 (pt0) REVERT: F 60 MET cc_start: 0.7832 (tpp) cc_final: 0.6439 (tmm) REVERT: G 60 MET cc_start: 0.8156 (tpt) cc_final: 0.7947 (tpt) REVERT: J 17 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8319 (mt) REVERT: J 24 GLU cc_start: 0.5593 (mm-30) cc_final: 0.4730 (mm-30) REVERT: J 73 ASP cc_start: 0.6492 (m-30) cc_final: 0.6068 (p0) REVERT: K 54 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7903 (mmmt) REVERT: K 74 ASP cc_start: 0.6264 (m-30) cc_final: 0.5974 (p0) outliers start: 29 outliers final: 24 residues processed: 207 average time/residue: 0.2280 time to fit residues: 60.4428 Evaluate side-chains 210 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7752 Z= 0.368 Angle : 0.657 10.390 10500 Z= 0.318 Chirality : 0.051 0.160 1152 Planarity : 0.005 0.057 1356 Dihedral : 4.492 15.310 1008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.40 % Allowed : 21.79 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.29), residues: 912 helix: 1.50 (0.65), residues: 84 sheet: -2.10 (0.25), residues: 384 loop : -1.72 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 88 HIS 0.006 0.003 HIS F 19 PHE 0.030 0.002 PHE L 64 TYR 0.016 0.002 TYR A 27 ARG 0.007 0.001 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 0.928 Fit side-chains REVERT: B 58 LYS cc_start: 0.8154 (tttt) cc_final: 0.7915 (tttp) REVERT: C 60 MET cc_start: 0.8222 (tpp) cc_final: 0.7040 (ttm) REVERT: D 54 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7226 (mtpt) REVERT: D 70 GLU cc_start: 0.5859 (tt0) cc_final: 0.5387 (tt0) REVERT: F 60 MET cc_start: 0.7769 (tpp) cc_final: 0.6508 (tmm) REVERT: G 79 PRO cc_start: 0.7494 (Cg_endo) cc_final: 0.7015 (Cg_exo) REVERT: H 39 THR cc_start: 0.7517 (p) cc_final: 0.6553 (t) REVERT: J 24 GLU cc_start: 0.5782 (mm-30) cc_final: 0.4890 (mm-30) REVERT: J 73 ASP cc_start: 0.6590 (m-30) cc_final: 0.6164 (p0) REVERT: K 54 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8086 (mmmt) REVERT: K 74 ASP cc_start: 0.6571 (m-30) cc_final: 0.6183 (p0) outliers start: 37 outliers final: 35 residues processed: 221 average time/residue: 0.2398 time to fit residues: 67.4672 Evaluate side-chains 236 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 13 GLU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7752 Z= 0.214 Angle : 0.594 9.775 10500 Z= 0.284 Chirality : 0.049 0.135 1152 Planarity : 0.004 0.053 1356 Dihedral : 4.206 14.595 1008 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.81 % Allowed : 23.81 % Favored : 72.38 % 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: -2.25 (0.29), residues: 912 helix: 1.70 (0.66), residues: 84 sheet: -1.98 (0.26), residues: 384 loop : -1.56 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 88 HIS 0.003 0.001 HIS F 19 PHE 0.027 0.002 PHE L 64 TYR 0.011 0.001 TYR A 27 ARG 0.006 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 0.899 Fit side-chains REVERT: B 84 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7201 (mmm160) REVERT: C 60 MET cc_start: 0.8049 (tpp) cc_final: 0.6896 (ttm) REVERT: D 15 LYS cc_start: 0.8279 (mttt) cc_final: 0.7706 (mttt) REVERT: D 54 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7222 (mtpt) REVERT: D 70 GLU cc_start: 0.5782 (tt0) cc_final: 0.5314 (tt0) REVERT: E 54 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7475 (mmmt) REVERT: E 69 GLU cc_start: 0.7675 (pt0) cc_final: 0.7254 (pt0) REVERT: F 60 MET cc_start: 0.7739 (tpp) cc_final: 0.6545 (tmm) REVERT: G 79 PRO cc_start: 0.7452 (Cg_endo) cc_final: 0.6965 (Cg_exo) REVERT: H 54 LYS cc_start: 0.8393 (mmmm) cc_final: 0.7800 (mmmt) REVERT: J 17 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8471 (mt) REVERT: J 24 GLU cc_start: 0.5780 (mm-30) cc_final: 0.4828 (mm-30) REVERT: J 73 ASP cc_start: 0.6623 (m-30) cc_final: 0.6169 (p0) REVERT: K 54 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7958 (mmmt) REVERT: K 74 ASP cc_start: 0.6486 (m-30) cc_final: 0.6134 (p0) outliers start: 32 outliers final: 29 residues processed: 212 average time/residue: 0.2333 time to fit residues: 63.7177 Evaluate side-chains 220 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 83 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7752 Z= 0.175 Angle : 0.594 10.580 10500 Z= 0.282 Chirality : 0.049 0.136 1152 Planarity : 0.004 0.055 1356 Dihedral : 4.047 14.319 1008 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.33 % Allowed : 24.64 % Favored : 72.02 % 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: -2.08 (0.29), residues: 912 helix: 1.91 (0.66), residues: 84 sheet: -1.89 (0.26), residues: 384 loop : -1.44 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 88 HIS 0.002 0.001 HIS F 19 PHE 0.026 0.002 PHE L 64 TYR 0.010 0.001 TYR A 27 ARG 0.006 0.000 ARG K 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 0.834 Fit side-chains REVERT: C 60 MET cc_start: 0.8032 (tpp) cc_final: 0.6846 (ttm) REVERT: D 15 LYS cc_start: 0.8253 (mttt) cc_final: 0.7702 (mttt) REVERT: D 54 LYS cc_start: 0.7986 (mtpp) cc_final: 0.7212 (mtpt) REVERT: D 70 GLU cc_start: 0.5767 (tt0) cc_final: 0.5294 (tt0) REVERT: E 54 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7521 (mmmt) REVERT: E 69 GLU cc_start: 0.7669 (pt0) cc_final: 0.7267 (pt0) REVERT: F 60 MET cc_start: 0.7669 (tpp) cc_final: 0.6303 (tmm) REVERT: G 79 PRO cc_start: 0.7410 (Cg_endo) cc_final: 0.6905 (Cg_exo) REVERT: H 54 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8203 (mmmm) REVERT: J 17 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8446 (mt) REVERT: J 24 GLU cc_start: 0.5633 (mm-30) cc_final: 0.4684 (mm-30) REVERT: J 73 ASP cc_start: 0.6684 (m-30) cc_final: 0.6228 (p0) REVERT: K 54 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7924 (mmmt) REVERT: K 74 ASP cc_start: 0.6596 (m-30) cc_final: 0.6159 (p0) outliers start: 28 outliers final: 27 residues processed: 207 average time/residue: 0.2348 time to fit residues: 62.1351 Evaluate side-chains 218 residues out of total 840 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain G residue 89 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.219080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.186753 restraints weight = 7348.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.191717 restraints weight = 5328.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.195254 restraints weight = 4204.557| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7752 Z= 0.134 Angle : 0.562 10.223 10500 Z= 0.267 Chirality : 0.048 0.134 1152 Planarity : 0.004 0.051 1356 Dihedral : 3.753 13.478 1008 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.33 % Allowed : 24.52 % Favored : 72.14 % 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: -1.85 (0.30), residues: 912 helix: 2.06 (0.65), residues: 84 sheet: -1.74 (0.26), residues: 384 loop : -1.28 (0.33), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 88 HIS 0.001 0.001 HIS F 19 PHE 0.024 0.001 PHE L 64 TYR 0.008 0.001 TYR A 27 ARG 0.006 0.000 ARG K 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.87 seconds wall clock time: 34 minutes 47.99 seconds (2087.99 seconds total)