Starting phenix.real_space_refine on Fri Mar 15 08:02:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cl3_16711/03_2024/8cl3_16711.pdb" } resolution = 3.14 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= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 774 atoms to isotropic. 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 72 5.16 5 C 6498 2.51 5 N 1770 2.21 5 O 1932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10272 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "C" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "E" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "G" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "I" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1633 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 79 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Time building chain proxies: 5.67, per 1000 atoms: 0.55 Number of scatterers: 10272 At special positions: 0 Unit cell: (112.53, 112.53, 70.68, 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 72 16.00 O 1932 8.00 N 1770 7.00 C 6498 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 66.7% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 160 through 173 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 100 through 105 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 160 through 173 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'I' and resid 16 through 31 Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 146 Processing helix chain 'I' and resid 160 through 173 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'K' and resid 16 through 31 Processing helix chain 'K' and resid 35 through 44 Processing helix chain 'K' and resid 48 through 58 Processing helix chain 'K' and resid 62 through 84 Processing helix chain 'K' and resid 100 through 105 Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 125 through 146 Processing helix chain 'K' and resid 160 through 173 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.665A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 206 Processing helix chain 'K' and resid 210 through 218 Processing sheet with id= 1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= 2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= 3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= 4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id= 5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id= 6, first strand: chain 'K' and resid 2 through 4 636 hydrogen bonds defined for protein. 1908 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: 2.88 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1752 1.32 - 1.44: 2538 1.44 - 1.56: 6078 1.56 - 1.68: 0 1.68 - 1.81: 132 Bond restraints: 10500 Sorted by residual: bond pdb=" C ARG G 143 " pdb=" O ARG G 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" C ARG A 143 " pdb=" O ARG A 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" C ARG I 143 " pdb=" O ARG I 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C ARG C 143 " pdb=" O ARG C 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" C ARG E 143 " pdb=" O ARG E 143 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 10495 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.85: 552 106.85 - 113.66: 5604 113.66 - 120.46: 4190 120.46 - 127.26: 3746 127.26 - 134.07: 188 Bond angle restraints: 14280 Sorted by residual: angle pdb=" CB LEU E 6 " pdb=" CG LEU E 6 " pdb=" CD1 LEU E 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU K 6 " pdb=" CG LEU K 6 " pdb=" CD1 LEU K 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU C 6 " pdb=" CG LEU C 6 " pdb=" CD1 LEU C 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU I 6 " pdb=" CG LEU I 6 " pdb=" CD1 LEU I 6 " ideal model delta sigma weight residual 110.70 123.29 -12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB LEU A 6 " pdb=" CG LEU A 6 " pdb=" CD1 LEU A 6 " ideal model delta sigma weight residual 110.70 123.27 -12.57 3.00e+00 1.11e-01 1.76e+01 ... (remaining 14275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5874 17.20 - 34.39: 420 34.39 - 51.59: 72 51.59 - 68.79: 12 68.79 - 85.98: 6 Dihedral angle restraints: 6384 sinusoidal: 2532 harmonic: 3852 Sorted by residual: dihedral pdb=" CA PHE C 32 " pdb=" C PHE C 32 " pdb=" N SER C 33 " pdb=" CA SER C 33 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE I 32 " pdb=" C PHE I 32 " pdb=" N SER I 33 " pdb=" CA SER I 33 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE G 32 " pdb=" C PHE G 32 " pdb=" N SER G 33 " pdb=" CA SER G 33 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.273: 1596 0.273 - 0.547: 0 0.547 - 0.820: 0 0.820 - 1.093: 0 1.093 - 1.367: 12 Chirality restraints: 1608 Sorted by residual: chirality pdb=" CG LEU K 6 " pdb=" CB LEU K 6 " pdb=" CD1 LEU K 6 " pdb=" CD2 LEU K 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CG LEU E 6 " pdb=" CB LEU E 6 " pdb=" CD1 LEU E 6 " pdb=" CD2 LEU E 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 chirality pdb=" CG LEU G 6 " pdb=" CB LEU G 6 " pdb=" CD1 LEU G 6 " pdb=" CD2 LEU G 6 " both_signs ideal model delta sigma weight residual False -2.59 -1.22 -1.37 2.00e-01 2.50e+01 4.67e+01 ... (remaining 1605 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 136 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU A 136 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 136 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 137 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 136 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU G 136 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU G 136 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY G 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 136 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU E 136 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU E 136 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 137 " 0.016 2.00e-02 2.50e+03 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 6 1.77 - 2.55: 36 2.55 - 3.33: 13326 3.33 - 4.12: 25710 4.12 - 4.90: 47520 Warning: very small nonbonded interaction distances. Nonbonded interactions: 86598 Sorted by model distance: nonbonded pdb=" CD2 LEU E 6 " pdb=" CA GLY G 8 " model vdw 0.985 3.860 nonbonded pdb=" CA GLY A 8 " pdb=" CD2 LEU K 6 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU G 6 " pdb=" CA GLY I 8 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU A 6 " pdb=" CA GLY C 8 " model vdw 0.985 3.860 nonbonded pdb=" CD2 LEU C 6 " pdb=" CA GLY E 8 " model vdw 0.985 3.860 ... (remaining 86593 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' 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 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 12.030 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.710 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 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 0.068 10500 Z= 0.342 Angle : 0.974 12.594 14280 Z= 0.553 Chirality : 0.126 1.367 1608 Planarity : 0.009 0.056 1860 Dihedral : 12.731 85.982 3888 Min Nonbonded Distance : 0.985 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -1.02 (0.21), residues: 1314 helix: -0.88 (0.15), residues: 870 sheet: None (None), residues: 0 loop : 0.20 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 117 HIS 0.007 0.003 HIS E 62 PHE 0.013 0.003 PHE B 9 TYR 0.027 0.008 TYR K 164 ARG 0.014 0.002 ARG K 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.120 Fit side-chains REVERT: A 118 MET cc_start: 0.7654 (mtp) cc_final: 0.7411 (mtm) REVERT: C 143 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6837 (mtm-85) REVERT: E 118 MET cc_start: 0.7680 (mtp) cc_final: 0.7449 (mtp) REVERT: G 118 MET cc_start: 0.7651 (mtp) cc_final: 0.7409 (mtm) REVERT: K 118 MET cc_start: 0.7674 (mtp) cc_final: 0.7444 (mtp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2582 time to fit residues: 77.9028 Evaluate side-chains 160 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10500 Z= 0.282 Angle : 0.635 8.058 14280 Z= 0.310 Chirality : 0.045 0.151 1608 Planarity : 0.005 0.034 1860 Dihedral : 4.829 19.663 1410 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.94 % Allowed : 3.89 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.82 (0.22), residues: 1314 helix: 0.73 (0.17), residues: 870 sheet: None (None), residues: 0 loop : 0.44 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 117 HIS 0.002 0.001 HIS I 120 PHE 0.009 0.002 PHE A 161 TYR 0.009 0.001 TYR E 169 ARG 0.002 0.000 ARG I 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 4 residues processed: 157 average time/residue: 0.2157 time to fit residues: 48.5520 Evaluate side-chains 140 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.0050 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN F 7 GLN H 7 GLN J 7 GLN K 139 ASN L 7 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10500 Z= 0.286 Angle : 0.574 6.910 14280 Z= 0.284 Chirality : 0.044 0.137 1608 Planarity : 0.005 0.042 1860 Dihedral : 4.417 16.791 1410 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.76 % Allowed : 6.67 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.72 (0.23), residues: 1314 helix: 0.87 (0.17), residues: 870 sheet: -2.05 (0.49), residues: 54 loop : 0.25 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 117 HIS 0.002 0.001 HIS A 62 PHE 0.007 0.002 PHE C 32 TYR 0.008 0.001 TYR E 169 ARG 0.002 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.119 Fit side-chains REVERT: E 167 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7501 (ttp-110) REVERT: K 167 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7498 (ttp-110) outliers start: 19 outliers final: 8 residues processed: 149 average time/residue: 0.2388 time to fit residues: 49.4969 Evaluate side-chains 152 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain K residue 15 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 114 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 7 GLN E 139 ASN K 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10500 Z= 0.231 Angle : 0.529 6.802 14280 Z= 0.261 Chirality : 0.042 0.133 1608 Planarity : 0.005 0.048 1860 Dihedral : 4.160 16.930 1410 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.76 % Allowed : 6.57 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.05 (0.23), residues: 1314 helix: 1.14 (0.17), residues: 870 sheet: -1.61 (0.51), residues: 54 loop : 0.27 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 23 HIS 0.002 0.000 HIS C 62 PHE 0.009 0.001 PHE C 32 TYR 0.007 0.001 TYR K 169 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 118 MET cc_start: 0.7746 (mtp) cc_final: 0.7316 (mtm) REVERT: E 144 MET cc_start: 0.7490 (ttm) cc_final: 0.7215 (ttm) REVERT: E 167 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7482 (ttp-110) REVERT: K 118 MET cc_start: 0.7748 (mtp) cc_final: 0.7317 (mtm) REVERT: K 167 ARG cc_start: 0.7713 (mtp-110) cc_final: 0.7487 (ttp-110) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.2338 time to fit residues: 49.7783 Evaluate side-chains 153 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.6759 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10500 Z= 0.271 Angle : 0.544 6.647 14280 Z= 0.270 Chirality : 0.042 0.133 1608 Planarity : 0.005 0.050 1860 Dihedral : 4.126 17.299 1410 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.85 % Allowed : 7.78 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.15 (0.23), residues: 1314 helix: 1.21 (0.18), residues: 870 sheet: -1.40 (0.50), residues: 54 loop : 0.32 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 80 HIS 0.002 0.001 HIS I 62 PHE 0.009 0.001 PHE I 32 TYR 0.008 0.001 TYR K 169 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7557 (mtm) cc_final: 0.7350 (mtp) REVERT: E 144 MET cc_start: 0.7415 (ttm) cc_final: 0.7163 (ttm) REVERT: G 118 MET cc_start: 0.7548 (mtm) cc_final: 0.7348 (mtp) REVERT: K 167 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7447 (ttp-110) outliers start: 20 outliers final: 14 residues processed: 148 average time/residue: 0.2178 time to fit residues: 45.2430 Evaluate side-chains 155 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 74 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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: 0.6685 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10500 Z= 0.168 Angle : 0.483 6.645 14280 Z= 0.238 Chirality : 0.040 0.131 1608 Planarity : 0.005 0.050 1860 Dihedral : 3.802 16.048 1410 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.20 % Allowed : 8.70 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.50 (0.23), residues: 1314 helix: 1.46 (0.18), residues: 876 sheet: -1.15 (0.51), residues: 54 loop : 0.46 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 117 HIS 0.001 0.000 HIS I 62 PHE 0.009 0.001 PHE I 32 TYR 0.006 0.001 TYR I 169 ARG 0.001 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6301 (mt-10) REVERT: E 118 MET cc_start: 0.7805 (mtp) cc_final: 0.7453 (mtm) REVERT: E 144 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7148 (ttm) REVERT: K 118 MET cc_start: 0.7811 (mtp) cc_final: 0.7458 (mtm) outliers start: 13 outliers final: 6 residues processed: 161 average time/residue: 0.2391 time to fit residues: 54.5825 Evaluate side-chains 154 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain K residue 146 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 127 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 77 optimal weight: 0.0980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.6707 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10500 Z= 0.191 Angle : 0.490 6.287 14280 Z= 0.241 Chirality : 0.040 0.131 1608 Planarity : 0.005 0.051 1860 Dihedral : 3.741 14.431 1410 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.67 % Allowed : 8.89 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.59 (0.24), residues: 1314 helix: 1.56 (0.18), residues: 870 sheet: -1.08 (0.50), residues: 54 loop : 0.43 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 23 HIS 0.002 0.000 HIS K 62 PHE 0.009 0.001 PHE C 32 TYR 0.006 0.001 TYR A 169 ARG 0.001 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7829 (mtp) cc_final: 0.7628 (mtm) REVERT: E 144 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7130 (ttm) REVERT: G 118 MET cc_start: 0.7823 (mtp) cc_final: 0.7623 (mtm) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 0.2162 time to fit residues: 49.0735 Evaluate side-chains 150 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain I residue 13 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.0870 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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: 0.6702 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10500 Z= 0.188 Angle : 0.488 6.346 14280 Z= 0.241 Chirality : 0.040 0.131 1608 Planarity : 0.005 0.050 1860 Dihedral : 3.754 15.927 1410 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.85 % Allowed : 9.26 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.61 (0.24), residues: 1314 helix: 1.56 (0.18), residues: 870 sheet: -1.09 (0.51), residues: 54 loop : 0.47 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 23 HIS 0.002 0.000 HIS K 62 PHE 0.009 0.001 PHE I 32 TYR 0.006 0.001 TYR C 169 ARG 0.001 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 144 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7114 (ttm) outliers start: 20 outliers final: 17 residues processed: 157 average time/residue: 0.2266 time to fit residues: 50.6558 Evaluate side-chains 164 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.6739 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10500 Z= 0.246 Angle : 0.527 8.441 14280 Z= 0.261 Chirality : 0.042 0.133 1608 Planarity : 0.005 0.051 1860 Dihedral : 3.923 16.640 1410 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.78 % Allowed : 8.33 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.52 (0.24), residues: 1314 helix: 1.45 (0.18), residues: 870 sheet: -1.00 (0.51), residues: 54 loop : 0.52 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 80 HIS 0.002 0.000 HIS K 62 PHE 0.009 0.001 PHE K 32 TYR 0.007 0.001 TYR I 169 ARG 0.002 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 144 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7147 (ttm) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.2154 time to fit residues: 48.9249 Evaluate side-chains 169 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.0970 chunk 87 optimal weight: 0.3980 chunk 131 optimal weight: 0.0270 chunk 121 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 overall best weight: 0.2236 ------------------------------------------------------------------------------- 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: 0.6662 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10500 Z= 0.151 Angle : 0.485 6.627 14280 Z= 0.239 Chirality : 0.040 0.128 1608 Planarity : 0.005 0.050 1860 Dihedral : 3.619 14.365 1410 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.76 % Allowed : 9.17 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.67 (0.24), residues: 1314 helix: 1.57 (0.18), residues: 882 sheet: -0.95 (0.52), residues: 54 loop : 0.52 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 133 HIS 0.001 0.000 HIS E 120 PHE 0.010 0.001 PHE K 32 TYR 0.006 0.001 TYR K 145 ARG 0.001 0.000 ARG K 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 175 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6577 (mt-10) REVERT: E 144 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7098 (ttm) outliers start: 19 outliers final: 14 residues processed: 163 average time/residue: 0.2168 time to fit residues: 49.8549 Evaluate side-chains 161 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain I residue 13 GLN Chi-restraints excluded: chain I residue 191 VAL Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 191 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 107 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.204534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.158561 restraints weight = 9433.669| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.63 r_work: 0.3465 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10500 Z= 0.210 Angle : 0.512 6.191 14280 Z= 0.256 Chirality : 0.041 0.144 1608 Planarity : 0.005 0.051 1860 Dihedral : 3.766 15.836 1410 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.67 % Allowed : 9.72 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.64 (0.24), residues: 1314 helix: 1.50 (0.18), residues: 876 sheet: -1.05 (0.52), residues: 54 loop : 0.68 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 80 HIS 0.001 0.000 HIS C 62 PHE 0.009 0.001 PHE I 32 TYR 0.006 0.001 TYR C 169 ARG 0.003 0.000 ARG G 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.88 seconds wall clock time: 42 minutes 5.02 seconds (2525.02 seconds total)