Starting phenix.real_space_refine on Sun Dec 10 20:50:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/12_2023/7t9m_25762_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/12_2023/7t9m_25762.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/7t9m_25762/12_2023/7t9m_25762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/12_2023/7t9m_25762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/12_2023/7t9m_25762_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/12_2023/7t9m_25762_neut_trim.pdb" } 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= -0.001 sd= 0.023 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 C 5039 2.51 5 N 1255 2.21 5 O 1483 1.98 5 H 7719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R ASP 36": "OD1" <-> "OD2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 219": "OD1" <-> "OD2" Residue "R PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15546 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3219 Classifications: {'peptide': 217} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "L" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3186 Classifications: {'peptide': 213} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "R" Number of atoms: 9071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 9071 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.12, per 1000 atoms: 0.46 Number of scatterers: 15546 At special positions: 0 Unit cell: (66.332, 131.376, 148.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 O 1483 8.00 N 1255 7.00 C 5039 6.00 H 7719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 198 " " NAG R 801 " - " ASN R 177 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 113 " Time building additional restraints: 12.67 Conformation dependent library (CDL) restraints added in 1.6 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 30.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.663A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.761A pdb=" N THR H 139 " --> pdb=" O GLY H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.879A pdb=" N SER H 168 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 181 through 188 removed outlier: 4.077A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 removed outlier: 4.134A pdb=" N SER R 268 " --> pdb=" O PRO R 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 264 through 269' Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.467A pdb=" N CYS R 283 " --> pdb=" O TYR R 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 286 " --> pdb=" O HIS R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 442 Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 483 Processing helix chain 'R' and resid 484 through 491 Processing helix chain 'R' and resid 491 through 525 removed outlier: 3.684A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 555 removed outlier: 3.840A pdb=" N LEU R 555 " --> pdb=" O LEU R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 559 Processing helix chain 'R' and resid 576 through 610 Processing helix chain 'R' and resid 616 through 650 removed outlier: 3.974A pdb=" N ILE R 635 " --> pdb=" O PHE R 631 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS R 636 " --> pdb=" O THR R 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET R 637 " --> pdb=" O ASP R 633 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 682 removed outlier: 4.031A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) Proline residue: R 668 - end of helix removed outlier: 4.606A pdb=" N SER R 671 " --> pdb=" O TYR R 667 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS R 672 " --> pdb=" O PRO R 668 " (cutoff:3.500A) Proline residue: R 675 - end of helix removed outlier: 3.669A pdb=" N THR R 682 " --> pdb=" O TYR R 678 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 693 removed outlier: 4.391A pdb=" N GLN R 686 " --> pdb=" O THR R 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.686A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.698A pdb=" N VAL H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 158 through 160 removed outlier: 3.667A pdb=" N LYS H 215 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.566A pdb=" N THR L 73 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.605A pdb=" N ASN L 52 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 117 removed outlier: 4.013A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.631A pdb=" N ARG L 154 " --> pdb=" O TRP L 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP L 147 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 148 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 56 through 58 removed outlier: 6.467A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 66 through 67 removed outlier: 3.677A pdb=" N ILE R 67 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.188A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 166 through 167 removed outlier: 3.620A pdb=" N ILE R 167 " --> pdb=" O SER R 191 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 933 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: 6.08 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7705 1.02 - 1.22: 34 1.22 - 1.42: 3324 1.42 - 1.62: 4608 1.62 - 1.82: 68 Bond restraints: 15739 Sorted by residual: bond pdb=" ND2 ASN R 135 " pdb="HD21 ASN R 135 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" ND2 ASN R 135 " pdb="HD22 ASN R 135 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD22 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD21 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 1.463 1.504 -0.041 6.90e-03 2.10e+04 3.56e+01 ... (remaining 15734 not shown) Histogram of bond angle deviations from ideal: 95.06 - 104.29: 146 104.29 - 113.51: 18910 113.51 - 122.73: 7286 122.73 - 131.95: 2051 131.95 - 141.18: 19 Bond angle restraints: 28412 Sorted by residual: angle pdb=" N THR R 399 " pdb=" CA THR R 399 " pdb=" C THR R 399 " ideal model delta sigma weight residual 112.17 125.36 -13.19 1.36e+00 5.41e-01 9.40e+01 angle pdb=" C CYS R 398 " pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 119.83 128.18 -8.35 1.11e+00 8.12e-01 5.66e+01 angle pdb=" C TYR L 139 " pdb=" N PRO L 140 " pdb=" CA PRO L 140 " ideal model delta sigma weight residual 119.98 111.67 8.31 1.16e+00 7.43e-01 5.13e+01 angle pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" C TYR L 93 " ideal model delta sigma weight residual 109.81 125.01 -15.20 2.21e+00 2.05e-01 4.73e+01 angle pdb=" N ASN L 137 " pdb=" CA ASN L 137 " pdb=" C ASN L 137 " ideal model delta sigma weight residual 111.24 120.27 -9.03 1.38e+00 5.25e-01 4.28e+01 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6769 17.71 - 35.43: 568 35.43 - 53.14: 121 53.14 - 70.86: 15 70.86 - 88.57: 12 Dihedral angle restraints: 7485 sinusoidal: 3960 harmonic: 3525 Sorted by residual: dihedral pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual 122.80 150.70 -27.90 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR L 93 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual -122.60 -150.02 27.42 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 7482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1282 0.256 - 0.513: 2 0.513 - 0.769: 2 0.769 - 1.025: 0 1.025 - 1.282: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA TYR L 93 " pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CB TYR L 93 " both_signs ideal model delta sigma weight residual False 2.51 1.23 1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" CA TYR L 139 " pdb=" N TYR L 139 " pdb=" C TYR L 139 " pdb=" CB TYR L 139 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CA THR R 399 " pdb=" N THR R 399 " pdb=" C THR R 399 " pdb=" CB THR R 399 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1284 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 137 " -0.297 2.00e-02 2.50e+03 4.19e-01 2.64e+03 pdb=" CG ASN L 137 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN L 137 " 0.317 2.00e-02 2.50e+03 pdb=" ND2 ASN L 137 " -0.017 2.00e-02 2.50e+03 pdb="HD21 ASN L 137 " -0.677 2.00e-02 2.50e+03 pdb="HD22 ASN L 137 " 0.638 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 135 " -0.270 2.00e-02 2.50e+03 2.85e-01 1.22e+03 pdb=" CG ASN R 135 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 135 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN R 135 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 135 " 0.410 2.00e-02 2.50e+03 pdb="HD22 ASN R 135 " -0.423 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 650 " -0.087 2.00e-02 2.50e+03 8.51e-02 1.09e+02 pdb=" CG ASN R 650 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN R 650 " 0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN R 650 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN R 650 " 0.119 2.00e-02 2.50e+03 pdb="HD22 ASN R 650 " -0.122 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1372 2.23 - 2.82: 33260 2.82 - 3.41: 39682 3.41 - 4.01: 53816 4.01 - 4.60: 82035 Nonbonded interactions: 210165 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 100 " model vdw 1.637 1.850 nonbonded pdb=" OE1 GLU L 184 " pdb="HH12 ARG L 187 " model vdw 1.682 1.850 nonbonded pdb=" HG3 PRO L 8 " pdb=" HE2 MET L 11 " model vdw 1.696 2.440 nonbonded pdb=" OD1 ASP R 232 " pdb=" HG SER R 234 " model vdw 1.729 1.850 nonbonded pdb=" HE2 HIS H 35 " pdb=" OE1 GLU H 99 " model vdw 1.729 1.850 ... (remaining 210160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.580 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: 0.220 Extract box with map and model: 18.940 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 51.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.005 0.066 8020 Z= 0.355 Angle : 0.878 15.204 10924 Z= 0.485 Chirality : 0.065 1.282 1287 Planarity : 0.005 0.065 1350 Dihedral : 12.803 88.199 2935 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.91 % Allowed : 0.79 % Favored : 98.30 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % 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: 0.15 (0.27), residues: 987 helix: 1.73 (0.31), residues: 258 sheet: -0.33 (0.35), residues: 253 loop : -0.51 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 546 HIS 0.002 0.001 HIS R 537 PHE 0.022 0.001 PHE R 434 TYR 0.044 0.002 TYR L 93 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.3939 time to fit residues: 49.3666 Evaluate side-chains 64 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1655 time to fit residues: 2.5090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8020 Z= 0.219 Angle : 0.560 8.643 10924 Z= 0.295 Chirality : 0.042 0.287 1287 Planarity : 0.004 0.058 1350 Dihedral : 5.423 51.677 1173 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.45 % Allowed : 4.99 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.48 (0.28), residues: 987 helix: 2.11 (0.32), residues: 257 sheet: -0.25 (0.34), residues: 261 loop : -0.28 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 546 HIS 0.003 0.001 HIS L 91 PHE 0.014 0.001 PHE R 434 TYR 0.036 0.001 TYR L 93 ARG 0.004 0.000 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.3519 time to fit residues: 33.3085 Evaluate side-chains 61 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2434 time to fit residues: 2.6814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8020 Z= 0.350 Angle : 0.564 9.490 10924 Z= 0.293 Chirality : 0.041 0.202 1287 Planarity : 0.004 0.035 1350 Dihedral : 5.210 48.517 1173 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.34 % Allowed : 6.12 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.44 (0.28), residues: 987 helix: 2.26 (0.32), residues: 262 sheet: -0.35 (0.35), residues: 249 loop : -0.41 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 546 HIS 0.003 0.001 HIS L 91 PHE 0.014 0.001 PHE R 434 TYR 0.021 0.001 TYR L 139 ARG 0.002 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 61 average time/residue: 0.3311 time to fit residues: 30.6429 Evaluate side-chains 58 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1605 time to fit residues: 2.3938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 78 optimal weight: 10.0000 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8020 Z= 0.169 Angle : 0.490 5.894 10924 Z= 0.254 Chirality : 0.041 0.152 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.643 44.386 1173 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.45 % Allowed : 6.69 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.60 (0.28), residues: 987 helix: 2.33 (0.31), residues: 262 sheet: -0.35 (0.34), residues: 260 loop : -0.20 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 161 HIS 0.001 0.000 HIS L 91 PHE 0.020 0.001 PHE R 416 TYR 0.016 0.001 TYR L 93 ARG 0.003 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 0.3662 time to fit residues: 32.8003 Evaluate side-chains 59 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1860 time to fit residues: 2.9428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8020 Z= 0.320 Angle : 0.538 8.106 10924 Z= 0.278 Chirality : 0.041 0.173 1287 Planarity : 0.003 0.035 1350 Dihedral : 4.825 46.064 1173 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.23 % Allowed : 7.48 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.44 (0.28), residues: 987 helix: 2.41 (0.32), residues: 257 sheet: -0.43 (0.34), residues: 250 loop : -0.44 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS L 91 PHE 0.011 0.001 PHE R 434 TYR 0.018 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 58 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.3831 time to fit residues: 33.1057 Evaluate side-chains 56 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2366 time to fit residues: 2.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8020 Z= 0.191 Angle : 0.492 7.326 10924 Z= 0.253 Chirality : 0.041 0.148 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.472 42.186 1173 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.34 % Allowed : 8.16 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.57 (0.28), residues: 987 helix: 2.49 (0.31), residues: 257 sheet: -0.39 (0.33), residues: 261 loop : -0.30 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.004 0.000 HIS R 32 PHE 0.010 0.001 PHE R 416 TYR 0.012 0.001 TYR L 93 ARG 0.003 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 0.3005 time to fit residues: 26.8893 Evaluate side-chains 57 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1969 time to fit residues: 2.6083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8020 Z= 0.190 Angle : 0.483 7.788 10924 Z= 0.248 Chirality : 0.040 0.141 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.321 41.774 1173 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.11 % Allowed : 8.50 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.67 (0.28), residues: 987 helix: 2.57 (0.31), residues: 257 sheet: -0.25 (0.33), residues: 256 loop : -0.30 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.012 0.001 PHE R 434 TYR 0.013 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.3377 time to fit residues: 29.6824 Evaluate side-chains 55 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2651 time to fit residues: 2.0866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8020 Z= 0.321 Angle : 0.529 8.318 10924 Z= 0.273 Chirality : 0.041 0.158 1287 Planarity : 0.003 0.034 1350 Dihedral : 4.601 43.639 1173 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.23 % Allowed : 8.73 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.50 (0.28), residues: 987 helix: 2.48 (0.31), residues: 260 sheet: -0.53 (0.32), residues: 266 loop : -0.32 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.003 0.001 HIS L 91 PHE 0.013 0.001 PHE R 666 TYR 0.016 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.3122 time to fit residues: 28.3842 Evaluate side-chains 57 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2575 time to fit residues: 2.3408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8020 Z= 0.465 Angle : 0.609 7.094 10924 Z= 0.320 Chirality : 0.042 0.202 1287 Planarity : 0.004 0.036 1350 Dihedral : 5.254 47.063 1173 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.11 % Allowed : 8.96 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.05 (0.27), residues: 987 helix: 2.26 (0.31), residues: 260 sheet: -0.85 (0.32), residues: 268 loop : -0.66 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 46 HIS 0.005 0.001 HIS L 91 PHE 0.016 0.002 PHE R 666 TYR 0.022 0.002 TYR L 139 ARG 0.004 0.001 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.3217 time to fit residues: 28.1134 Evaluate side-chains 56 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2410 time to fit residues: 1.8767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 20.0000 chunk 56 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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: 0.7803 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8020 Z= 0.153 Angle : 0.498 7.774 10924 Z= 0.256 Chirality : 0.041 0.142 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.573 40.423 1173 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.45 (0.28), residues: 987 helix: 2.39 (0.31), residues: 260 sheet: -0.52 (0.32), residues: 261 loop : -0.35 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.002 0.000 HIS R 32 PHE 0.016 0.001 PHE R 666 TYR 0.010 0.001 TYR L 139 ARG 0.003 0.000 ARG L 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3146 time to fit residues: 27.2086 Evaluate side-chains 53 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.079745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054655 restraints weight = 92126.216| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.79 r_work: 0.3013 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8020 Z= 0.193 Angle : 0.495 7.837 10924 Z= 0.256 Chirality : 0.041 0.158 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.453 41.305 1173 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.11 % Allowed : 9.30 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.50 (0.28), residues: 987 helix: 2.42 (0.31), residues: 261 sheet: -0.51 (0.32), residues: 264 loop : -0.30 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 46 HIS 0.002 0.000 HIS L 91 PHE 0.016 0.001 PHE R 666 TYR 0.014 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3716.67 seconds wall clock time: 66 minutes 49.90 seconds (4009.90 seconds total)