Starting phenix.real_space_refine on Wed Feb 14 15:43:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ucu_20728/02_2024/6ucu_20728_trim_updated.pdb" } resolution = 3.06 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= 0.002 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 5506 2.51 5 N 1246 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "I ARG 52": "NH1" <-> "NH2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 219": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 330": "NH1" <-> "NH2" Residue "I PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8198 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 227 Unusual residues: {'LMT': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 160 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 40 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 30 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Chain: "I" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 227 Unusual residues: {'LMT': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 592 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 160 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 40 Chain: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 20 Chain: "L" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'LMT': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 30 Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 40 Time building chain proxies: 5.15, per 1000 atoms: 0.63 Number of scatterers: 8198 At special positions: 0 Unit cell: (116.15, 141.45, 94.3, 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 22 16.00 O 1424 8.00 N 1246 7.00 C 5506 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 2 sheets defined 33.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.511A pdb=" N LEU A 55 " --> pdb=" O HIS A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.768A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 134 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 48 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'E' and resid 12 through 43 removed outlier: 5.820A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.512A pdb=" N LEU E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 50 through 54' Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.511A pdb=" N LEU I 55 " --> pdb=" O HIS I 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 51 through 55' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 365 through 372 removed outlier: 3.768A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 134 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 48 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 31 through 50 Processing helix chain 'L' and resid 52 through 56 Processing helix chain 'M' and resid 12 through 43 removed outlier: 5.820A pdb=" N ILE M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Proline residue: M 34 - end of helix Processing helix chain 'M' and resid 50 through 54 removed outlier: 3.512A pdb=" N LEU M 54 " --> pdb=" O PHE M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 50 through 54' Processing sheet with id= A, first strand: chain 'A' and resid 83 through 91 removed outlier: 4.140A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 93 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 100 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA A 91 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS A 102 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN A 89 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE A 104 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASP A 87 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 106 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG A 85 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 83 through 91 removed outlier: 4.140A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER I 93 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR I 100 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA I 91 " --> pdb=" O THR I 100 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS I 102 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASN I 89 " --> pdb=" O HIS I 102 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE I 104 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ASP I 87 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE I 106 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ARG I 85 " --> pdb=" O ILE I 106 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1452 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: 2.41 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1786 1.33 - 1.45: 1768 1.45 - 1.58: 4710 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 8302 Sorted by residual: bond pdb=" C7 LMT A 414 " pdb=" C8 LMT A 414 " ideal model delta sigma weight residual 1.529 1.479 0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C7 LMT I 401 " pdb=" C8 LMT I 401 " ideal model delta sigma weight residual 1.529 1.479 0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C ALA L 47 " pdb=" O ALA L 47 " ideal model delta sigma weight residual 1.236 1.206 0.030 1.26e-02 6.30e+03 5.61e+00 bond pdb=" C ALA D 47 " pdb=" O ALA D 47 " ideal model delta sigma weight residual 1.236 1.207 0.030 1.26e-02 6.30e+03 5.52e+00 bond pdb=" C7 LMT A 416 " pdb=" C8 LMT A 416 " ideal model delta sigma weight residual 1.529 1.483 0.046 2.00e-02 2.50e+03 5.25e+00 ... (remaining 8297 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.92: 240 106.92 - 113.75: 4694 113.75 - 120.57: 3133 120.57 - 127.40: 2830 127.40 - 134.23: 81 Bond angle restraints: 10978 Sorted by residual: angle pdb=" N MET A 94 " pdb=" CA MET A 94 " pdb=" C MET A 94 " ideal model delta sigma weight residual 114.56 119.46 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" N MET I 94 " pdb=" CA MET I 94 " pdb=" C MET I 94 " ideal model delta sigma weight residual 114.56 119.46 -4.90 1.27e+00 6.20e-01 1.49e+01 angle pdb=" CB LEU A 141 " pdb=" CG LEU A 141 " pdb=" CD2 LEU A 141 " ideal model delta sigma weight residual 110.70 122.17 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CB LEU I 141 " pdb=" CG LEU I 141 " pdb=" CD2 LEU I 141 " ideal model delta sigma weight residual 110.70 122.17 -11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.00e+00 1.00e+00 1.16e+01 ... (remaining 10973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 4757 21.39 - 42.77: 279 42.77 - 64.15: 60 64.15 - 85.54: 6 85.54 - 106.92: 16 Dihedral angle restraints: 5118 sinusoidal: 2352 harmonic: 2766 Sorted by residual: dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA HIS I 51 " pdb=" C HIS I 51 " pdb=" N ARG I 52 " pdb=" CA ARG I 52 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 5115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.334: 1192 0.334 - 0.668: 0 0.668 - 1.002: 0 1.002 - 1.336: 0 1.336 - 1.671: 2 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CG LEU A 141 " pdb=" CB LEU A 141 " pdb=" CD1 LEU A 141 " pdb=" CD2 LEU A 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CG LEU I 141 " pdb=" CB LEU I 141 " pdb=" CD1 LEU I 141 " pdb=" CD2 LEU I 141 " both_signs ideal model delta sigma weight residual False -2.59 -0.92 -1.67 2.00e-01 2.50e+01 6.98e+01 chirality pdb=" CA MET A 94 " pdb=" N MET A 94 " pdb=" C MET A 94 " pdb=" CB MET A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1191 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 114 " -0.049 2.00e-02 2.50e+03 4.88e-02 4.77e+01 pdb=" CG TYR I 114 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR I 114 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR I 114 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 114 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR I 114 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 114 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 114 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 114 " 0.049 2.00e-02 2.50e+03 4.88e-02 4.77e+01 pdb=" CG TYR A 114 " -0.116 2.00e-02 2.50e+03 pdb=" CD1 TYR A 114 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR A 114 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 114 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 114 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 114 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 171 " 0.041 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" CG TYR I 171 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TYR I 171 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR I 171 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 171 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR I 171 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR I 171 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR I 171 " 0.002 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 56 2.60 - 3.17: 6407 3.17 - 3.75: 11145 3.75 - 4.32: 15906 4.32 - 4.90: 28133 Nonbonded interactions: 61647 Sorted by model distance: nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.022 2.440 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.022 2.440 nonbonded pdb=" OG SER I 312 " pdb=" OG SER J 116 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 312 " pdb=" OG SER B 116 " model vdw 2.198 2.440 nonbonded pdb=" OG SER A 151 " pdb=" OE1 GLN A 169 " model vdw 2.205 2.440 ... (remaining 61642 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' and (resid 49 through 373 or (resid 401 through 417 and (name C1 or n \ ame C10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name C9 )))) selection = (chain 'I' and (resid 49 through 373 or (resid 401 through 417 and (name C1 or n \ ame C10 or name C11 or name C12 or name C2 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name C8 or name C9 )))) } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 26.160 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.012 0.064 8302 Z= 0.743 Angle : 1.545 11.469 10978 Z= 0.653 Chirality : 0.088 1.671 1194 Planarity : 0.007 0.068 1314 Dihedral : 15.160 106.923 3326 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.12 % Allowed : 3.24 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 934 helix: 0.36 (0.24), residues: 340 sheet: -0.72 (0.25), residues: 400 loop : -2.82 (0.35), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K 42 HIS 0.016 0.004 HIS M 29 PHE 0.017 0.002 PHE I 104 TYR 0.116 0.005 TYR I 114 ARG 0.009 0.002 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.864 Fit side-chains REVERT: A 239 LYS cc_start: 0.7859 (ttmp) cc_final: 0.7521 (mttp) REVERT: A 308 GLU cc_start: 0.7434 (pt0) cc_final: 0.7160 (pt0) REVERT: A 367 LEU cc_start: 0.7317 (mt) cc_final: 0.7061 (mt) REVERT: I 239 LYS cc_start: 0.7857 (ttmp) cc_final: 0.7518 (mttp) REVERT: I 308 GLU cc_start: 0.7426 (pt0) cc_final: 0.7148 (pt0) REVERT: I 367 LEU cc_start: 0.7319 (mt) cc_final: 0.7063 (mt) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2435 time to fit residues: 27.8556 Evaluate side-chains 38 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 99 GLN A 248 GLN E 29 HIS I 95 ASN I 99 GLN I 248 GLN M 29 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8302 Z= 0.214 Angle : 0.668 7.996 10978 Z= 0.328 Chirality : 0.045 0.286 1194 Planarity : 0.005 0.049 1314 Dihedral : 13.833 64.927 1638 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.75 % Allowed : 6.48 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 0.54 (0.28), residues: 934 helix: 2.51 (0.27), residues: 332 sheet: -0.29 (0.25), residues: 402 loop : -1.84 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 100 HIS 0.003 0.001 HIS A 346 PHE 0.015 0.001 PHE I 359 TYR 0.010 0.001 TYR A 79 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.865 Fit side-chains REVERT: A 369 MET cc_start: 0.6910 (mmp) cc_final: 0.6641 (mmm) REVERT: I 369 MET cc_start: 0.6927 (mmp) cc_final: 0.6661 (mmm) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.2219 time to fit residues: 16.5316 Evaluate side-chains 48 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain I residue 248 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN E 43 HIS I 248 GLN M 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8302 Z= 0.285 Angle : 0.659 6.557 10978 Z= 0.328 Chirality : 0.047 0.313 1194 Planarity : 0.005 0.044 1314 Dihedral : 12.855 57.828 1638 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.25 % Allowed : 7.73 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 934 helix: 2.84 (0.27), residues: 332 sheet: -0.41 (0.25), residues: 410 loop : -1.35 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.005 0.001 HIS I 346 PHE 0.016 0.001 PHE A 359 TYR 0.020 0.002 TYR A 79 ARG 0.003 0.000 ARG I 261 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.862 Fit side-chains REVERT: A 175 ASP cc_start: 0.8235 (p0) cc_final: 0.7968 (p0) REVERT: A 331 LYS cc_start: 0.8108 (tttt) cc_final: 0.7312 (mptt) REVERT: A 339 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7907 (pp) REVERT: I 175 ASP cc_start: 0.8234 (p0) cc_final: 0.7959 (p0) REVERT: I 331 LYS cc_start: 0.8111 (tttt) cc_final: 0.7313 (mptt) REVERT: I 339 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7898 (pp) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.2682 time to fit residues: 24.8135 Evaluate side-chains 56 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 365 GLN D 50 GLN I 248 GLN I 365 GLN L 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8302 Z= 0.271 Angle : 0.632 9.167 10978 Z= 0.313 Chirality : 0.045 0.314 1194 Planarity : 0.004 0.041 1314 Dihedral : 12.560 58.321 1638 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.75 % Allowed : 8.73 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 0.93 (0.29), residues: 934 helix: 2.91 (0.28), residues: 334 sheet: -0.44 (0.25), residues: 410 loop : -0.97 (0.47), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.004 0.001 HIS I 346 PHE 0.014 0.001 PHE A 359 TYR 0.012 0.002 TYR I 79 ARG 0.004 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.934 Fit side-chains REVERT: A 175 ASP cc_start: 0.8331 (p0) cc_final: 0.8026 (p0) REVERT: A 331 LYS cc_start: 0.8017 (tttt) cc_final: 0.7188 (mptt) REVERT: A 339 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7904 (pp) REVERT: I 175 ASP cc_start: 0.8291 (p0) cc_final: 0.7961 (p0) REVERT: I 331 LYS cc_start: 0.8021 (tttt) cc_final: 0.7186 (mptt) REVERT: I 339 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7896 (pp) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.2190 time to fit residues: 20.1126 Evaluate side-chains 58 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8302 Z= 0.225 Angle : 0.600 8.467 10978 Z= 0.298 Chirality : 0.044 0.290 1194 Planarity : 0.004 0.040 1314 Dihedral : 12.205 58.793 1638 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 11.10 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 1.06 (0.29), residues: 934 helix: 2.95 (0.28), residues: 338 sheet: -0.41 (0.25), residues: 408 loop : -0.72 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.003 0.001 HIS I 346 PHE 0.013 0.001 PHE A 359 TYR 0.012 0.001 TYR I 307 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.928 Fit side-chains REVERT: A 331 LYS cc_start: 0.8003 (tttt) cc_final: 0.7182 (mptt) REVERT: A 339 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7881 (pp) REVERT: A 360 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6406 (tp30) REVERT: I 331 LYS cc_start: 0.8009 (tttt) cc_final: 0.7182 (mptt) REVERT: I 339 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7874 (pp) REVERT: I 360 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6402 (tp30) outliers start: 16 outliers final: 8 residues processed: 58 average time/residue: 0.2240 time to fit residues: 18.2067 Evaluate side-chains 62 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain L residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8302 Z= 0.198 Angle : 0.580 7.905 10978 Z= 0.287 Chirality : 0.043 0.265 1194 Planarity : 0.004 0.039 1314 Dihedral : 11.835 59.417 1638 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.49 % Allowed : 11.35 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 1.23 (0.29), residues: 934 helix: 3.07 (0.28), residues: 338 sheet: -0.34 (0.25), residues: 408 loop : -0.51 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 36 HIS 0.002 0.001 HIS C 43 PHE 0.012 0.001 PHE A 359 TYR 0.013 0.001 TYR A 307 ARG 0.002 0.000 ARG I 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 0.891 Fit side-chains REVERT: A 331 LYS cc_start: 0.8016 (tttt) cc_final: 0.7173 (mptt) REVERT: A 360 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6408 (tp30) REVERT: I 331 LYS cc_start: 0.8017 (tttt) cc_final: 0.7171 (mptt) REVERT: I 360 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6411 (tp30) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.2217 time to fit residues: 19.9241 Evaluate side-chains 66 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 142 ASN Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8302 Z= 0.295 Angle : 0.624 8.019 10978 Z= 0.311 Chirality : 0.045 0.272 1194 Planarity : 0.004 0.037 1314 Dihedral : 11.999 59.616 1638 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.24 % Allowed : 11.47 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 934 helix: 2.99 (0.28), residues: 338 sheet: -0.46 (0.26), residues: 410 loop : -0.50 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.004 0.001 HIS I 346 PHE 0.011 0.001 PHE A 126 TYR 0.013 0.002 TYR I 232 ARG 0.003 0.000 ARG I 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.888 Fit side-chains REVERT: A 331 LYS cc_start: 0.8140 (tttt) cc_final: 0.7454 (mttp) REVERT: A 360 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6488 (tp30) REVERT: I 331 LYS cc_start: 0.8143 (tttt) cc_final: 0.7455 (mttp) REVERT: I 360 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6486 (tp30) outliers start: 18 outliers final: 16 residues processed: 62 average time/residue: 0.2551 time to fit residues: 21.5525 Evaluate side-chains 68 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 248 GLN Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 142 ASN Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 248 GLN Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 360 GLU Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7042 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8302 Z= 0.190 Angle : 0.570 7.444 10978 Z= 0.284 Chirality : 0.042 0.234 1194 Planarity : 0.004 0.038 1314 Dihedral : 11.566 58.653 1638 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.24 % Allowed : 12.09 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 1.25 (0.29), residues: 934 helix: 3.12 (0.28), residues: 338 sheet: -0.40 (0.25), residues: 408 loop : -0.39 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.002 0.001 HIS C 43 PHE 0.012 0.001 PHE A 359 TYR 0.008 0.001 TYR A 79 ARG 0.002 0.000 ARG I 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.873 Fit side-chains REVERT: A 331 LYS cc_start: 0.8115 (tttt) cc_final: 0.7447 (mttp) REVERT: I 331 LYS cc_start: 0.8126 (tttt) cc_final: 0.7454 (mttp) outliers start: 18 outliers final: 12 residues processed: 62 average time/residue: 0.2467 time to fit residues: 20.7852 Evaluate side-chains 62 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 142 ASN Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8302 Z= 0.392 Angle : 0.682 8.335 10978 Z= 0.344 Chirality : 0.047 0.278 1194 Planarity : 0.005 0.037 1314 Dihedral : 12.411 57.479 1638 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.24 % Allowed : 11.85 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 934 helix: 3.02 (0.28), residues: 332 sheet: -0.59 (0.25), residues: 408 loop : -0.45 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 36 HIS 0.005 0.001 HIS I 346 PHE 0.014 0.002 PHE I 201 TYR 0.015 0.002 TYR A 232 ARG 0.006 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 1.137 Fit side-chains REVERT: A 79 TYR cc_start: 0.8733 (m-80) cc_final: 0.8487 (m-80) REVERT: A 331 LYS cc_start: 0.8181 (tttt) cc_final: 0.7295 (mttt) REVERT: I 79 TYR cc_start: 0.8714 (m-80) cc_final: 0.8467 (m-80) REVERT: I 331 LYS cc_start: 0.8221 (tttt) cc_final: 0.7326 (mttt) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 0.2560 time to fit residues: 23.3183 Evaluate side-chains 64 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 142 ASN Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 0.0770 chunk 72 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8302 Z= 0.196 Angle : 0.566 7.106 10978 Z= 0.285 Chirality : 0.042 0.219 1194 Planarity : 0.004 0.036 1314 Dihedral : 11.568 59.306 1638 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.00 % Allowed : 12.84 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 1.20 (0.29), residues: 934 helix: 3.11 (0.28), residues: 338 sheet: -0.50 (0.26), residues: 408 loop : -0.31 (0.48), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 36 HIS 0.002 0.001 HIS A 346 PHE 0.012 0.001 PHE I 126 TYR 0.008 0.001 TYR E 38 ARG 0.001 0.000 ARG I 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.932 Fit side-chains REVERT: A 331 LYS cc_start: 0.8165 (tttt) cc_final: 0.7319 (mttt) REVERT: I 331 LYS cc_start: 0.8151 (tttt) cc_final: 0.7331 (mttt) outliers start: 16 outliers final: 14 residues processed: 63 average time/residue: 0.2395 time to fit residues: 20.6027 Evaluate side-chains 64 residues out of total 820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain I residue 101 SER Chi-restraints excluded: chain I residue 142 ASN Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 368 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.166565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120529 restraints weight = 7868.337| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.83 r_work: 0.3434 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8302 Z= 0.190 Angle : 0.556 7.016 10978 Z= 0.281 Chirality : 0.042 0.216 1194 Planarity : 0.004 0.038 1314 Dihedral : 10.908 59.771 1638 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 12.97 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: 1.32 (0.29), residues: 934 helix: 3.17 (0.28), residues: 338 sheet: -0.43 (0.26), residues: 406 loop : -0.18 (0.48), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 36 HIS 0.002 0.001 HIS K 43 PHE 0.011 0.001 PHE A 126 TYR 0.007 0.001 TYR M 38 ARG 0.002 0.000 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1806.90 seconds wall clock time: 33 minutes 44.96 seconds (2024.96 seconds total)