Starting phenix.real_space_refine on Mon Apr 28 19:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.map" model { file = "/net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9itz_60884/04_2025/9itz_60884.cif" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 10 5.16 5 C 5129 2.51 5 N 1416 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8039 Number of models: 1 Model: "" Number of chains: 16 Chain: "U" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 190 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "X" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 125 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "T" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1093 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 700 Unresolved non-hydrogen angles: 918 Unresolved non-hydrogen dihedrals: 588 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 31, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 369 Chain: "H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "J" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "N" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "O" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "P" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "Q" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 505 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "V" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 195 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 2, 'TRANS': 36} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 74 Chain: "Y" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 205 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 75 Chain: "Z" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1206 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 1011 Unresolved non-hydrogen dihedrals: 654 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 34, 'GLU:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 403 Time building chain proxies: 5.91, per 1000 atoms: 0.74 Number of scatterers: 8039 At special positions: 0 Unit cell: (79.98, 120.9, 79.98, 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 10 16.00 O 1484 8.00 N 1416 7.00 C 5129 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 - 3.00 Amino acid : True - 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 seconds 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'U' and resid 9 through 30 removed outlier: 3.872A pdb=" N ALA U 13 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 44 removed outlier: 4.129A pdb=" N ILE U 44 " --> pdb=" O ARG U 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 41 Proline residue: X 32 - end of helix Processing helix chain 'T' and resid 49 through 71 removed outlier: 3.671A pdb=" N ARG T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 87 Processing helix chain 'T' and resid 87 through 100 Processing helix chain 'T' and resid 101 through 106 Processing helix chain 'T' and resid 106 through 114 removed outlier: 3.506A pdb=" N VAL T 110 " --> pdb=" O ALA T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 125 Processing helix chain 'T' and resid 190 through 207 removed outlier: 3.552A pdb=" N ILE T 205 " --> pdb=" O SER T 201 " (cutoff:3.500A) Processing helix chain 'T' and resid 214 through 219 removed outlier: 4.400A pdb=" N TYR T 217 " --> pdb=" O GLY T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 230 removed outlier: 4.445A pdb=" N PHE T 230 " --> pdb=" O ILE T 227 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 252 Proline residue: T 243 - end of helix Processing helix chain 'T' and resid 253 through 267 Processing helix chain 'T' and resid 275 through 304 Processing helix chain 'H' and resid 3 through 38 removed outlier: 3.503A pdb=" N VAL H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Proline residue: H 20 - end of helix removed outlier: 4.110A pdb=" N ILE H 26 " --> pdb=" O VAL H 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 72 removed outlier: 3.706A pdb=" N ILE H 51 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY H 52 " --> pdb=" O TYR H 48 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU H 59 " --> pdb=" O PHE H 55 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 36 removed outlier: 4.403A pdb=" N GLY I 19 " --> pdb=" O LEU I 15 " (cutoff:3.500A) Proline residue: I 20 - end of helix removed outlier: 4.212A pdb=" N GLY I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE I 26 " --> pdb=" O VAL I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 41 through 72 Processing helix chain 'J' and resid 3 through 38 Proline residue: J 20 - end of helix removed outlier: 4.390A pdb=" N GLY J 23 " --> pdb=" O GLY J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 72 removed outlier: 3.625A pdb=" N PHE J 50 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE J 51 " --> pdb=" O THR J 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 18 through 38 Processing helix chain 'K' and resid 42 through 72 removed outlier: 3.930A pdb=" N TYR K 48 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 38 removed outlier: 4.110A pdb=" N VAL L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY L 19 " --> pdb=" O LEU L 15 " (cutoff:3.500A) Proline residue: L 20 - end of helix Processing helix chain 'L' and resid 41 through 72 removed outlier: 4.090A pdb=" N THR L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU L 57 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA L 58 " --> pdb=" O ALA L 54 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 38 removed outlier: 3.903A pdb=" N GLY M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix removed outlier: 4.023A pdb=" N GLY M 25 " --> pdb=" O GLY M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 72 removed outlier: 4.254A pdb=" N ILE M 66 " --> pdb=" O PHE M 62 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ALA M 67 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 15 Processing helix chain 'N' and resid 17 through 38 removed outlier: 3.755A pdb=" N VAL N 28 " --> pdb=" O ILE N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 70 removed outlier: 3.613A pdb=" N VAL N 46 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY N 52 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE N 66 " --> pdb=" O PHE N 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 19 through 38 Processing helix chain 'O' and resid 43 through 71 removed outlier: 4.361A pdb=" N LEU O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA O 60 " --> pdb=" O THR O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 15 Processing helix chain 'P' and resid 17 through 38 removed outlier: 3.860A pdb=" N GLY P 25 " --> pdb=" O GLY P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 72 removed outlier: 3.821A pdb=" N PHE P 50 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE P 51 " --> pdb=" O THR P 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE P 66 " --> pdb=" O PHE P 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA P 67 " --> pdb=" O GLY P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 38 removed outlier: 4.612A pdb=" N GLY Q 19 " --> pdb=" O LEU Q 15 " (cutoff:3.500A) Proline residue: Q 20 - end of helix removed outlier: 3.534A pdb=" N ASN Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 71 removed outlier: 3.771A pdb=" N LEU Q 59 " --> pdb=" O PHE Q 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 28 Processing helix chain 'V' and resid 30 through 44 Processing helix chain 'Y' and resid 9 through 48 removed outlier: 3.721A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ARG Y 31 " --> pdb=" O ALA Y 27 " (cutoff:3.500A) Proline residue: Y 32 - end of helix Processing helix chain 'Z' and resid 49 through 71 Processing helix chain 'Z' and resid 80 through 99 removed outlier: 3.535A pdb=" N MET Z 84 " --> pdb=" O LEU Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 105 through 114 removed outlier: 4.569A pdb=" N LEU Z 109 " --> pdb=" O THR Z 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE Z 113 " --> pdb=" O LEU Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 122 Processing helix chain 'Z' and resid 190 through 219 removed outlier: 3.548A pdb=" N THR Z 194 " --> pdb=" O ASP Z 190 " (cutoff:3.500A) Proline residue: Z 215 - end of helix Processing helix chain 'Z' and resid 234 through 264 Proline residue: Z 243 - end of helix removed outlier: 3.660A pdb=" N LEU Z 250 " --> pdb=" O LEU Z 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE Z 254 " --> pdb=" O LEU Z 250 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE Z 255 " --> pdb=" O PHE Z 251 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLY Z 257 " --> pdb=" O ASN Z 253 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 304 removed outlier: 3.520A pdb=" N PHE Z 276 " --> pdb=" O LEU Z 272 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR Z 296 " --> pdb=" O ALA Z 292 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2469 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: 2.09 Time building geometry restraints manager: 2.76 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: 1677 1.33 - 1.45: 1610 1.45 - 1.57: 4794 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 8101 Sorted by residual: bond pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.04e-02 9.25e+03 1.42e+01 bond pdb=" N VAL Z 38 " pdb=" CA VAL Z 38 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.18e-02 7.18e+03 9.68e+00 bond pdb=" N VAL O 22 " pdb=" CA VAL O 22 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.21e-02 6.83e+03 9.43e+00 bond pdb=" N ILE Z 48 " pdb=" CA ILE Z 48 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 9.01e+00 bond pdb=" N ILE O 18 " pdb=" CA ILE O 18 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 8096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 10246 1.52 - 3.03: 735 3.03 - 4.55: 91 4.55 - 6.06: 21 6.06 - 7.58: 9 Bond angle restraints: 11102 Sorted by residual: angle pdb=" N ILE M 41 " pdb=" CA ILE M 41 " pdb=" C ILE M 41 " ideal model delta sigma weight residual 111.91 105.39 6.52 8.90e-01 1.26e+00 5.36e+01 angle pdb=" N ILE Q 41 " pdb=" CA ILE Q 41 " pdb=" C ILE Q 41 " ideal model delta sigma weight residual 112.43 106.02 6.41 9.20e-01 1.18e+00 4.86e+01 angle pdb=" N VAL Z 231 " pdb=" CA VAL Z 231 " pdb=" C VAL Z 231 " ideal model delta sigma weight residual 113.00 105.42 7.58 1.30e+00 5.92e-01 3.40e+01 angle pdb=" N ILE N 41 " pdb=" CA ILE N 41 " pdb=" C ILE N 41 " ideal model delta sigma weight residual 111.91 106.86 5.05 8.90e-01 1.26e+00 3.21e+01 angle pdb=" C GLU H 42 " pdb=" CA GLU H 42 " pdb=" CB GLU H 42 " ideal model delta sigma weight residual 116.54 110.66 5.88 1.15e+00 7.56e-01 2.61e+01 ... (remaining 11097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 4403 17.60 - 35.20: 190 35.20 - 52.79: 24 52.79 - 70.39: 2 70.39 - 87.99: 3 Dihedral angle restraints: 4622 sinusoidal: 982 harmonic: 3640 Sorted by residual: dihedral pdb=" CA MET H 49 " pdb=" C MET H 49 " pdb=" N PHE H 50 " pdb=" CA PHE H 50 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU L 15 " pdb=" C LEU L 15 " pdb=" N GLY L 16 " pdb=" CA GLY L 16 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU H 64 " pdb=" C LEU H 64 " pdb=" N VAL H 65 " pdb=" CA VAL H 65 " ideal model delta harmonic sigma weight residual 180.00 -163.61 -16.39 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1017 0.052 - 0.104: 319 0.104 - 0.156: 72 0.156 - 0.209: 41 0.209 - 0.261: 2 Chirality restraints: 1451 Sorted by residual: chirality pdb=" CB ILE P 18 " pdb=" CA ILE P 18 " pdb=" CG1 ILE P 18 " pdb=" CG2 ILE P 18 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE H 18 " pdb=" CA ILE H 18 " pdb=" CG1 ILE H 18 " pdb=" CG2 ILE H 18 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ILE Q 41 " pdb=" N ILE Q 41 " pdb=" C ILE Q 41 " pdb=" CB ILE Q 41 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1448 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Q 38 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO Q 39 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO Q 39 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO Q 39 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE N 53 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ILE N 53 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE N 53 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA N 54 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 19 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO Q 20 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO Q 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 20 " 0.025 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 829 2.74 - 3.28: 9778 3.28 - 3.82: 14154 3.82 - 4.36: 15235 4.36 - 4.90: 24544 Nonbonded interactions: 64540 Sorted by model distance: nonbonded pdb=" O LEU N 6 " pdb=" OG1 THR N 9 " model vdw 2.204 3.040 nonbonded pdb=" O ILE I 53 " pdb=" OG1 THR I 56 " model vdw 2.204 3.040 nonbonded pdb=" O ARG P 44 " pdb=" OG1 THR P 47 " model vdw 2.240 3.040 nonbonded pdb=" O ARG J 44 " pdb=" OG1 THR J 47 " model vdw 2.294 3.040 nonbonded pdb=" O LEU X 29 " pdb=" N VAL X 33 " model vdw 2.311 3.120 ... (remaining 64535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'J' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'K' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'L' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'M' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'N' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'O' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'P' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) selection = (chain 'Q' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 44 and (n \ ame N or name CA or name C or name O or name CB )) or resid 45 through 46 or (re \ sid 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 72)) } ncs_group { reference = chain 'T' selection = (chain 'Z' and (resid 31 through 135 or resid 188 through 304)) } ncs_group { reference = (chain 'U' and resid 9 through 45) selection = (chain 'V' and resid 9 through 45) selection = (chain 'Y' and resid 9 through 45) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.680 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.006 0.045 8101 Z= 0.422 Angle : 0.834 7.576 11102 Z= 0.608 Chirality : 0.058 0.261 1451 Planarity : 0.004 0.056 1478 Dihedral : 10.759 87.988 2294 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.21 % Allowed : 1.24 % Favored : 98.55 % 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: 0.17 (0.23), residues: 1284 helix: 0.85 (0.16), residues: 1033 sheet: None (None), residues: 0 loop : -2.92 (0.35), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.014 0.001 PHE Q 62 TYR 0.006 0.001 TYR M 48 ARG 0.001 0.000 ARG N 44 Details of bonding type rmsd hydrogen bonds : bond 0.16026 ( 827) hydrogen bonds : angle 6.12756 ( 2469) covalent geometry : bond 0.00578 ( 8101) covalent geometry : angle 0.83440 (11102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 SER cc_start: 0.9570 (t) cc_final: 0.9140 (p) REVERT: H 50 PHE cc_start: 0.9038 (m-80) cc_final: 0.8739 (t80) REVERT: I 33 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8863 (mm-40) REVERT: I 49 MET cc_start: 0.9764 (ptm) cc_final: 0.9504 (ptt) REVERT: I 50 PHE cc_start: 0.9212 (m-10) cc_final: 0.8894 (m-10) REVERT: I 55 PHE cc_start: 0.9652 (m-80) cc_final: 0.9371 (m-80) REVERT: I 68 PHE cc_start: 0.9561 (m-10) cc_final: 0.8961 (m-80) REVERT: J 11 LEU cc_start: 0.9771 (tt) cc_final: 0.9465 (tt) REVERT: J 27 ILE cc_start: 0.9614 (mm) cc_final: 0.9281 (mm) REVERT: J 48 TYR cc_start: 0.9202 (m-80) cc_final: 0.8644 (m-80) REVERT: J 49 MET cc_start: 0.9896 (ppp) cc_final: 0.9690 (ppp) REVERT: J 50 PHE cc_start: 0.9681 (m-80) cc_final: 0.9183 (m-80) REVERT: J 51 ILE cc_start: 0.9439 (pt) cc_final: 0.9031 (pt) REVERT: J 55 PHE cc_start: 0.9516 (m-10) cc_final: 0.9041 (m-80) REVERT: J 57 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8779 (tm-30) REVERT: J 61 ILE cc_start: 0.9124 (mm) cc_final: 0.8923 (mm) REVERT: J 64 LEU cc_start: 0.9732 (tt) cc_final: 0.9385 (pp) REVERT: J 68 PHE cc_start: 0.9531 (m-80) cc_final: 0.9298 (m-80) REVERT: K 44 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.8954 (mmm160) REVERT: K 45 VAL cc_start: 0.9376 (p) cc_final: 0.8928 (p) REVERT: K 48 TYR cc_start: 0.9073 (m-80) cc_final: 0.8461 (m-80) REVERT: K 51 ILE cc_start: 0.9395 (pt) cc_final: 0.8960 (pt) REVERT: K 55 PHE cc_start: 0.9427 (m-10) cc_final: 0.9126 (m-80) REVERT: L 18 ILE cc_start: 0.9521 (tt) cc_final: 0.9134 (pt) REVERT: L 45 VAL cc_start: 0.9475 (p) cc_final: 0.8993 (p) REVERT: L 48 TYR cc_start: 0.9327 (m-80) cc_final: 0.9043 (m-80) REVERT: L 50 PHE cc_start: 0.9132 (m-10) cc_final: 0.8648 (t80) REVERT: M 48 TYR cc_start: 0.9226 (m-80) cc_final: 0.9016 (m-80) REVERT: N 26 ILE cc_start: 0.9720 (mm) cc_final: 0.9302 (tt) REVERT: N 33 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9000 (mm110) REVERT: N 40 GLU cc_start: 0.9602 (mm-30) cc_final: 0.9296 (mp0) REVERT: N 48 TYR cc_start: 0.9257 (m-10) cc_final: 0.8775 (m-80) REVERT: N 51 ILE cc_start: 0.9777 (tp) cc_final: 0.9510 (tp) REVERT: N 55 PHE cc_start: 0.9442 (m-80) cc_final: 0.8918 (m-80) REVERT: N 62 PHE cc_start: 0.9616 (m-10) cc_final: 0.9276 (m-80) REVERT: N 68 PHE cc_start: 0.9702 (m-10) cc_final: 0.9315 (m-80) REVERT: O 15 LEU cc_start: 0.9307 (mm) cc_final: 0.9047 (mm) REVERT: O 18 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7192 (tp) REVERT: O 26 ILE cc_start: 0.9626 (mm) cc_final: 0.9391 (mm) REVERT: O 27 ILE cc_start: 0.9683 (mt) cc_final: 0.9300 (mt) REVERT: O 29 SER cc_start: 0.9556 (t) cc_final: 0.9175 (p) REVERT: O 62 PHE cc_start: 0.9250 (m-80) cc_final: 0.8973 (m-80) REVERT: P 15 LEU cc_start: 0.9580 (mm) cc_final: 0.8803 (tp) REVERT: P 26 ILE cc_start: 0.9785 (mm) cc_final: 0.9456 (tp) REVERT: P 27 ILE cc_start: 0.8994 (mt) cc_final: 0.8640 (mt) REVERT: P 50 PHE cc_start: 0.8956 (m-80) cc_final: 0.7833 (t80) REVERT: P 51 ILE cc_start: 0.9112 (pt) cc_final: 0.8765 (pt) REVERT: P 59 LEU cc_start: 0.9338 (tp) cc_final: 0.9128 (tp) REVERT: P 62 PHE cc_start: 0.9458 (m-10) cc_final: 0.9215 (m-80) REVERT: Q 11 LEU cc_start: 0.9657 (mt) cc_final: 0.9445 (mt) REVERT: Q 51 ILE cc_start: 0.9474 (mt) cc_final: 0.9113 (mt) REVERT: Q 53 ILE cc_start: 0.9232 (pt) cc_final: 0.9001 (pt) REVERT: Q 55 PHE cc_start: 0.9176 (m-10) cc_final: 0.8844 (m-80) REVERT: Q 56 THR cc_start: 0.9196 (p) cc_final: 0.8869 (t) REVERT: Q 59 LEU cc_start: 0.9609 (mm) cc_final: 0.9333 (mm) REVERT: Q 62 PHE cc_start: 0.8980 (m-80) cc_final: 0.8693 (m-80) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.1357 time to fit residues: 68.2414 Evaluate side-chains 301 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054880 restraints weight = 58625.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.056046 restraints weight = 44774.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.056890 restraints weight = 36076.681| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8101 Z= 0.233 Angle : 0.647 10.559 11102 Z= 0.375 Chirality : 0.044 0.246 1451 Planarity : 0.004 0.042 1478 Dihedral : 4.366 28.514 1331 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 0.41 % Allowed : 8.49 % Favored : 91.10 % 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: 0.57 (0.23), residues: 1284 helix: 1.08 (0.15), residues: 1068 sheet: None (None), residues: 0 loop : -3.10 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.047 0.002 PHE K 62 TYR 0.023 0.002 TYR O 48 ARG 0.004 0.001 ARG O 44 Details of bonding type rmsd hydrogen bonds : bond 0.05169 ( 827) hydrogen bonds : angle 4.85720 ( 2469) covalent geometry : bond 0.00441 ( 8101) covalent geometry : angle 0.64652 (11102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 PHE cc_start: 0.9325 (m-80) cc_final: 0.8614 (m-80) REVERT: I 49 MET cc_start: 0.9795 (ptm) cc_final: 0.9590 (ptt) REVERT: I 50 PHE cc_start: 0.9072 (m-10) cc_final: 0.8844 (m-10) REVERT: I 55 PHE cc_start: 0.9742 (m-80) cc_final: 0.9362 (m-80) REVERT: I 57 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8752 (pp20) REVERT: I 62 PHE cc_start: 0.9357 (m-80) cc_final: 0.9131 (m-80) REVERT: I 64 LEU cc_start: 0.9707 (mm) cc_final: 0.9487 (mt) REVERT: I 68 PHE cc_start: 0.9510 (m-10) cc_final: 0.8935 (m-80) REVERT: J 11 LEU cc_start: 0.9750 (tt) cc_final: 0.9543 (tt) REVERT: J 41 ILE cc_start: 0.8986 (tp) cc_final: 0.8695 (tp) REVERT: J 48 TYR cc_start: 0.9223 (m-80) cc_final: 0.8707 (m-80) REVERT: J 50 PHE cc_start: 0.9703 (m-80) cc_final: 0.9258 (m-80) REVERT: J 51 ILE cc_start: 0.9488 (pt) cc_final: 0.9080 (pt) REVERT: J 53 ILE cc_start: 0.9856 (mt) cc_final: 0.9610 (mt) REVERT: J 55 PHE cc_start: 0.9488 (m-10) cc_final: 0.8950 (m-80) REVERT: J 57 GLU cc_start: 0.9424 (mt-10) cc_final: 0.8742 (tm-30) REVERT: J 64 LEU cc_start: 0.9821 (tt) cc_final: 0.9454 (pp) REVERT: K 15 LEU cc_start: 0.9352 (mm) cc_final: 0.9123 (mp) REVERT: K 24 ILE cc_start: 0.9493 (mm) cc_final: 0.9223 (mm) REVERT: K 26 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9345 (tt) REVERT: K 27 ILE cc_start: 0.9557 (mt) cc_final: 0.9343 (mt) REVERT: K 44 ARG cc_start: 0.9356 (mmm-85) cc_final: 0.9143 (tpt170) REVERT: K 51 ILE cc_start: 0.9395 (pt) cc_final: 0.9033 (pt) REVERT: K 55 PHE cc_start: 0.9390 (m-10) cc_final: 0.9149 (m-80) REVERT: K 62 PHE cc_start: 0.9408 (m-80) cc_final: 0.9070 (m-80) REVERT: L 18 ILE cc_start: 0.9643 (tt) cc_final: 0.9296 (pt) REVERT: L 26 ILE cc_start: 0.9406 (tp) cc_final: 0.9089 (tt) REVERT: L 32 VAL cc_start: 0.9733 (p) cc_final: 0.9257 (p) REVERT: L 45 VAL cc_start: 0.9363 (p) cc_final: 0.8903 (p) REVERT: L 48 TYR cc_start: 0.9235 (m-80) cc_final: 0.8895 (m-80) REVERT: L 55 PHE cc_start: 0.9427 (m-80) cc_final: 0.8988 (m-80) REVERT: M 46 VAL cc_start: 0.9637 (m) cc_final: 0.9298 (p) REVERT: M 48 TYR cc_start: 0.9238 (m-80) cc_final: 0.9035 (m-80) REVERT: M 49 MET cc_start: 0.9513 (ttp) cc_final: 0.9278 (tmm) REVERT: M 50 PHE cc_start: 0.9494 (m-80) cc_final: 0.9103 (m-80) REVERT: N 11 LEU cc_start: 0.9498 (mm) cc_final: 0.9289 (mm) REVERT: N 40 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9226 (mp0) REVERT: N 48 TYR cc_start: 0.9351 (m-10) cc_final: 0.8941 (m-80) REVERT: N 53 ILE cc_start: 0.9664 (mm) cc_final: 0.9417 (mm) REVERT: N 55 PHE cc_start: 0.9446 (m-80) cc_final: 0.9031 (m-80) REVERT: N 57 GLU cc_start: 0.9237 (pp20) cc_final: 0.8968 (pp20) REVERT: N 59 LEU cc_start: 0.9781 (mt) cc_final: 0.9524 (mt) REVERT: N 62 PHE cc_start: 0.9444 (m-10) cc_final: 0.9068 (m-80) REVERT: N 68 PHE cc_start: 0.9705 (m-10) cc_final: 0.9225 (m-80) REVERT: O 15 LEU cc_start: 0.9635 (mm) cc_final: 0.9292 (tp) REVERT: O 29 SER cc_start: 0.9573 (t) cc_final: 0.9335 (p) REVERT: O 46 VAL cc_start: 0.9217 (t) cc_final: 0.8384 (t) REVERT: O 50 PHE cc_start: 0.9533 (m-80) cc_final: 0.9026 (m-80) REVERT: O 62 PHE cc_start: 0.9273 (m-80) cc_final: 0.8964 (m-80) REVERT: P 15 LEU cc_start: 0.9565 (mm) cc_final: 0.9167 (tp) REVERT: P 49 MET cc_start: 0.9069 (ptp) cc_final: 0.8714 (ptp) REVERT: P 53 ILE cc_start: 0.9610 (pt) cc_final: 0.9243 (tp) REVERT: P 62 PHE cc_start: 0.9571 (m-10) cc_final: 0.9344 (m-80) REVERT: Q 53 ILE cc_start: 0.9382 (pt) cc_final: 0.9145 (pt) REVERT: Q 59 LEU cc_start: 0.9643 (mm) cc_final: 0.9311 (mm) REVERT: Q 62 PHE cc_start: 0.9045 (m-80) cc_final: 0.8753 (m-80) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.1309 time to fit residues: 62.6559 Evaluate side-chains 286 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 106 optimal weight: 0.0970 chunk 100 optimal weight: 20.0000 chunk 27 optimal weight: 0.0670 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.068490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049842 restraints weight = 42308.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051122 restraints weight = 31941.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.051962 restraints weight = 25551.913| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8101 Z= 0.161 Angle : 0.604 8.046 11102 Z= 0.332 Chirality : 0.044 0.198 1451 Planarity : 0.004 0.040 1478 Dihedral : 4.161 20.861 1331 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.14 % Favored : 94.78 % Rotamer: Outliers : 0.21 % Allowed : 2.90 % Favored : 96.89 % 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: 0.78 (0.23), residues: 1284 helix: 1.23 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : -3.09 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.029 0.001 PHE I 62 TYR 0.017 0.002 TYR O 48 ARG 0.003 0.000 ARG O 37 Details of bonding type rmsd hydrogen bonds : bond 0.04651 ( 827) hydrogen bonds : angle 4.47486 ( 2469) covalent geometry : bond 0.00352 ( 8101) covalent geometry : angle 0.60382 (11102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 PHE cc_start: 0.9216 (m-80) cc_final: 0.8907 (m-80) REVERT: H 68 PHE cc_start: 0.9311 (m-80) cc_final: 0.8632 (m-80) REVERT: I 55 PHE cc_start: 0.9785 (m-80) cc_final: 0.9411 (m-80) REVERT: I 64 LEU cc_start: 0.9819 (mm) cc_final: 0.9611 (mm) REVERT: I 68 PHE cc_start: 0.9456 (m-10) cc_final: 0.8951 (m-80) REVERT: J 27 ILE cc_start: 0.9542 (mm) cc_final: 0.9281 (mm) REVERT: J 41 ILE cc_start: 0.8696 (tp) cc_final: 0.8385 (tp) REVERT: J 50 PHE cc_start: 0.9695 (m-80) cc_final: 0.9363 (m-80) REVERT: J 51 ILE cc_start: 0.9467 (pt) cc_final: 0.9193 (pt) REVERT: J 53 ILE cc_start: 0.9790 (mt) cc_final: 0.9527 (mt) REVERT: J 55 PHE cc_start: 0.9283 (m-10) cc_final: 0.8998 (m-80) REVERT: J 57 GLU cc_start: 0.9452 (mt-10) cc_final: 0.8913 (tm-30) REVERT: J 64 LEU cc_start: 0.9849 (tt) cc_final: 0.9574 (pp) REVERT: K 15 LEU cc_start: 0.9224 (mm) cc_final: 0.8928 (mp) REVERT: K 24 ILE cc_start: 0.9494 (mm) cc_final: 0.9203 (mm) REVERT: K 27 ILE cc_start: 0.9329 (mt) cc_final: 0.8926 (mt) REVERT: K 44 ARG cc_start: 0.9316 (mmm-85) cc_final: 0.9073 (tpt170) REVERT: K 50 PHE cc_start: 0.9662 (m-10) cc_final: 0.9274 (m-80) REVERT: L 18 ILE cc_start: 0.9291 (tt) cc_final: 0.8981 (mt) REVERT: L 26 ILE cc_start: 0.8961 (tp) cc_final: 0.8707 (tt) REVERT: L 48 TYR cc_start: 0.9193 (m-80) cc_final: 0.8866 (m-80) REVERT: L 55 PHE cc_start: 0.9360 (m-80) cc_final: 0.9114 (m-80) REVERT: M 40 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8973 (mm-30) REVERT: M 46 VAL cc_start: 0.9612 (m) cc_final: 0.9280 (p) REVERT: M 49 MET cc_start: 0.9627 (ttp) cc_final: 0.9393 (tmm) REVERT: M 50 PHE cc_start: 0.9371 (m-80) cc_final: 0.8932 (m-80) REVERT: M 62 PHE cc_start: 0.9399 (m-80) cc_final: 0.9173 (m-80) REVERT: N 11 LEU cc_start: 0.9408 (mm) cc_final: 0.9195 (mm) REVERT: N 33 GLN cc_start: 0.9342 (mm-40) cc_final: 0.8987 (mm110) REVERT: N 40 GLU cc_start: 0.9524 (mm-30) cc_final: 0.9195 (mp0) REVERT: N 48 TYR cc_start: 0.9340 (m-10) cc_final: 0.8921 (m-80) REVERT: N 55 PHE cc_start: 0.9491 (m-80) cc_final: 0.9177 (m-80) REVERT: N 64 LEU cc_start: 0.9818 (mt) cc_final: 0.9504 (mt) REVERT: N 68 PHE cc_start: 0.9733 (m-10) cc_final: 0.9248 (m-80) REVERT: N 69 LEU cc_start: 0.8923 (tt) cc_final: 0.8717 (pp) REVERT: O 29 SER cc_start: 0.9470 (t) cc_final: 0.9235 (p) REVERT: O 46 VAL cc_start: 0.9145 (t) cc_final: 0.8271 (t) REVERT: O 50 PHE cc_start: 0.9601 (m-80) cc_final: 0.8982 (m-80) REVERT: O 62 PHE cc_start: 0.9313 (m-80) cc_final: 0.8961 (m-80) REVERT: P 53 ILE cc_start: 0.9615 (pt) cc_final: 0.9198 (tp) REVERT: P 62 PHE cc_start: 0.9541 (m-10) cc_final: 0.9315 (m-80) REVERT: Q 53 ILE cc_start: 0.9318 (pt) cc_final: 0.9050 (pt) REVERT: Q 59 LEU cc_start: 0.9669 (mm) cc_final: 0.9434 (mm) REVERT: Q 62 PHE cc_start: 0.9051 (m-80) cc_final: 0.8833 (m-80) outliers start: 1 outliers final: 0 residues processed: 318 average time/residue: 0.1339 time to fit residues: 63.5440 Evaluate side-chains 284 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 127 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 0.0470 chunk 115 optimal weight: 0.0770 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.069842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.050552 restraints weight = 40583.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051869 restraints weight = 31070.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.052716 restraints weight = 25050.949| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8101 Z= 0.149 Angle : 0.602 8.205 11102 Z= 0.333 Chirality : 0.044 0.218 1451 Planarity : 0.004 0.052 1478 Dihedral : 4.083 21.176 1331 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 0.62 % Allowed : 4.55 % Favored : 94.82 % 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: 0.76 (0.23), residues: 1284 helix: 1.23 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -3.17 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.049 0.002 PHE K 62 TYR 0.012 0.001 TYR H 48 ARG 0.004 0.000 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 827) hydrogen bonds : angle 4.25787 ( 2469) covalent geometry : bond 0.00325 ( 8101) covalent geometry : angle 0.60157 (11102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 317 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ILE cc_start: 0.9709 (mt) cc_final: 0.9487 (mt) REVERT: H 55 PHE cc_start: 0.9220 (m-80) cc_final: 0.8794 (m-80) REVERT: H 68 PHE cc_start: 0.9285 (m-80) cc_final: 0.9039 (t80) REVERT: I 41 ILE cc_start: 0.9329 (mm) cc_final: 0.9089 (mt) REVERT: I 49 MET cc_start: 0.9339 (ptt) cc_final: 0.9111 (tmm) REVERT: I 55 PHE cc_start: 0.9770 (m-80) cc_final: 0.9415 (m-80) REVERT: I 64 LEU cc_start: 0.9831 (mm) cc_final: 0.9598 (mm) REVERT: I 68 PHE cc_start: 0.9430 (m-10) cc_final: 0.8919 (m-80) REVERT: J 27 ILE cc_start: 0.9586 (mm) cc_final: 0.9348 (mm) REVERT: J 41 ILE cc_start: 0.8708 (tp) cc_final: 0.8486 (tp) REVERT: J 47 THR cc_start: 0.9628 (p) cc_final: 0.9409 (p) REVERT: J 50 PHE cc_start: 0.9663 (m-80) cc_final: 0.9238 (m-80) REVERT: J 53 ILE cc_start: 0.9775 (mt) cc_final: 0.9469 (mt) REVERT: J 55 PHE cc_start: 0.9243 (m-10) cc_final: 0.8986 (m-80) REVERT: J 56 THR cc_start: 0.9663 (p) cc_final: 0.9106 (p) REVERT: J 57 GLU cc_start: 0.9434 (mt-10) cc_final: 0.8985 (tm-30) REVERT: J 64 LEU cc_start: 0.9854 (tt) cc_final: 0.9610 (pp) REVERT: J 65 VAL cc_start: 0.9679 (m) cc_final: 0.9465 (m) REVERT: K 15 LEU cc_start: 0.9230 (mm) cc_final: 0.9005 (mm) REVERT: K 24 ILE cc_start: 0.9444 (mm) cc_final: 0.9098 (mm) REVERT: K 27 ILE cc_start: 0.9234 (mt) cc_final: 0.8928 (mt) REVERT: K 44 ARG cc_start: 0.9304 (mmm-85) cc_final: 0.9019 (tpt170) REVERT: K 55 PHE cc_start: 0.9395 (m-10) cc_final: 0.9138 (m-80) REVERT: K 62 PHE cc_start: 0.9460 (m-80) cc_final: 0.9060 (m-80) REVERT: L 18 ILE cc_start: 0.9256 (tt) cc_final: 0.8901 (pt) REVERT: L 26 ILE cc_start: 0.8932 (tp) cc_final: 0.8722 (tt) REVERT: L 46 VAL cc_start: 0.9490 (t) cc_final: 0.9120 (m) REVERT: L 48 TYR cc_start: 0.9152 (m-80) cc_final: 0.8698 (m-80) REVERT: L 55 PHE cc_start: 0.9401 (m-80) cc_final: 0.9103 (m-80) REVERT: M 40 GLU cc_start: 0.9287 (mm-30) cc_final: 0.9010 (mm-30) REVERT: M 46 VAL cc_start: 0.9595 (m) cc_final: 0.9277 (p) REVERT: M 50 PHE cc_start: 0.9270 (m-80) cc_final: 0.8941 (m-80) REVERT: M 55 PHE cc_start: 0.9666 (m-80) cc_final: 0.9279 (m-80) REVERT: M 62 PHE cc_start: 0.9407 (m-80) cc_final: 0.9107 (m-80) REVERT: N 11 LEU cc_start: 0.9461 (mm) cc_final: 0.9230 (mm) REVERT: N 33 GLN cc_start: 0.9314 (mm-40) cc_final: 0.8992 (mm110) REVERT: N 40 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9192 (mp0) REVERT: N 48 TYR cc_start: 0.9303 (m-10) cc_final: 0.8904 (m-80) REVERT: N 53 ILE cc_start: 0.9668 (mm) cc_final: 0.9404 (mm) REVERT: N 55 PHE cc_start: 0.9455 (m-80) cc_final: 0.9093 (m-80) REVERT: N 59 LEU cc_start: 0.9617 (mt) cc_final: 0.9399 (mt) REVERT: N 62 PHE cc_start: 0.9302 (m-80) cc_final: 0.8777 (m-80) REVERT: N 64 LEU cc_start: 0.9819 (mt) cc_final: 0.9609 (mt) REVERT: N 68 PHE cc_start: 0.9717 (m-10) cc_final: 0.9213 (m-80) REVERT: O 29 SER cc_start: 0.9456 (t) cc_final: 0.9205 (p) REVERT: O 46 VAL cc_start: 0.9134 (t) cc_final: 0.8331 (t) REVERT: O 50 PHE cc_start: 0.9533 (m-80) cc_final: 0.9048 (m-80) REVERT: O 62 PHE cc_start: 0.9297 (m-80) cc_final: 0.8927 (m-80) REVERT: O 64 LEU cc_start: 0.9754 (mt) cc_final: 0.9530 (mt) REVERT: O 68 PHE cc_start: 0.9237 (m-80) cc_final: 0.8737 (m-80) REVERT: P 49 MET cc_start: 0.9058 (ptp) cc_final: 0.8700 (ptt) REVERT: P 53 ILE cc_start: 0.9558 (pt) cc_final: 0.9098 (tp) REVERT: P 62 PHE cc_start: 0.9535 (m-10) cc_final: 0.9309 (m-80) REVERT: Q 59 LEU cc_start: 0.9661 (mm) cc_final: 0.9384 (mm) REVERT: Q 62 PHE cc_start: 0.9013 (m-80) cc_final: 0.8772 (m-80) outliers start: 3 outliers final: 1 residues processed: 317 average time/residue: 0.1343 time to fit residues: 63.5122 Evaluate side-chains 286 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 97 optimal weight: 20.0000 chunk 14 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.071686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056956 restraints weight = 56874.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.058144 restraints weight = 43865.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.059068 restraints weight = 35584.085| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8101 Z= 0.162 Angle : 0.618 8.127 11102 Z= 0.341 Chirality : 0.045 0.239 1451 Planarity : 0.004 0.048 1478 Dihedral : 4.026 21.349 1331 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.21 % Allowed : 4.14 % Favored : 95.65 % 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: 0.92 (0.24), residues: 1284 helix: 1.36 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : -3.21 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.032 0.001 PHE K 62 TYR 0.021 0.002 TYR M 48 ARG 0.002 0.000 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 827) hydrogen bonds : angle 4.23939 ( 2469) covalent geometry : bond 0.00356 ( 8101) covalent geometry : angle 0.61761 (11102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 GLN cc_start: 0.9238 (pm20) cc_final: 0.8774 (pm20) REVERT: H 55 PHE cc_start: 0.9240 (m-80) cc_final: 0.8794 (m-80) REVERT: H 68 PHE cc_start: 0.9337 (m-80) cc_final: 0.9069 (t80) REVERT: I 55 PHE cc_start: 0.9755 (m-80) cc_final: 0.9381 (m-80) REVERT: I 64 LEU cc_start: 0.9820 (mm) cc_final: 0.9612 (mm) REVERT: I 68 PHE cc_start: 0.9458 (m-10) cc_final: 0.8927 (m-80) REVERT: J 27 ILE cc_start: 0.9640 (mm) cc_final: 0.9403 (mm) REVERT: J 40 GLU cc_start: 0.9210 (mp0) cc_final: 0.8977 (mp0) REVERT: J 41 ILE cc_start: 0.8801 (tp) cc_final: 0.8514 (tp) REVERT: J 50 PHE cc_start: 0.9683 (m-80) cc_final: 0.9329 (m-80) REVERT: J 51 ILE cc_start: 0.9488 (pt) cc_final: 0.9156 (pt) REVERT: J 53 ILE cc_start: 0.9827 (mt) cc_final: 0.9585 (mt) REVERT: J 55 PHE cc_start: 0.9383 (m-10) cc_final: 0.9012 (m-80) REVERT: J 57 GLU cc_start: 0.9444 (mt-10) cc_final: 0.8879 (tm-30) REVERT: J 64 LEU cc_start: 0.9808 (tt) cc_final: 0.9424 (pp) REVERT: J 65 VAL cc_start: 0.9663 (m) cc_final: 0.9388 (m) REVERT: J 68 PHE cc_start: 0.9577 (m-80) cc_final: 0.9286 (m-80) REVERT: K 24 ILE cc_start: 0.9564 (mm) cc_final: 0.9036 (pt) REVERT: K 32 VAL cc_start: 0.9722 (p) cc_final: 0.9434 (p) REVERT: K 44 ARG cc_start: 0.9277 (mmm-85) cc_final: 0.9006 (tpt170) REVERT: K 50 PHE cc_start: 0.9653 (m-10) cc_final: 0.9231 (m-80) REVERT: K 51 ILE cc_start: 0.9352 (pt) cc_final: 0.9146 (pt) REVERT: K 62 PHE cc_start: 0.9448 (m-80) cc_final: 0.9005 (m-80) REVERT: L 18 ILE cc_start: 0.9396 (tt) cc_final: 0.8983 (pt) REVERT: L 48 TYR cc_start: 0.9208 (m-10) cc_final: 0.8910 (m-80) REVERT: L 55 PHE cc_start: 0.9448 (m-80) cc_final: 0.9186 (m-80) REVERT: M 40 GLU cc_start: 0.9308 (mm-30) cc_final: 0.9026 (mm-30) REVERT: N 11 LEU cc_start: 0.9475 (mm) cc_final: 0.9240 (mm) REVERT: N 33 GLN cc_start: 0.9308 (mm-40) cc_final: 0.9060 (mm110) REVERT: N 48 TYR cc_start: 0.9263 (m-10) cc_final: 0.8976 (m-80) REVERT: N 55 PHE cc_start: 0.9500 (m-80) cc_final: 0.9064 (m-80) REVERT: N 62 PHE cc_start: 0.9389 (m-80) cc_final: 0.8933 (m-80) REVERT: N 64 LEU cc_start: 0.9929 (mt) cc_final: 0.9659 (mt) REVERT: N 68 PHE cc_start: 0.9655 (m-10) cc_final: 0.9237 (m-80) REVERT: O 29 SER cc_start: 0.9515 (t) cc_final: 0.9271 (p) REVERT: O 46 VAL cc_start: 0.9122 (t) cc_final: 0.8349 (t) REVERT: O 50 PHE cc_start: 0.9604 (m-80) cc_final: 0.9147 (m-80) REVERT: O 62 PHE cc_start: 0.9285 (m-80) cc_final: 0.8974 (m-80) REVERT: O 64 LEU cc_start: 0.9814 (mt) cc_final: 0.9578 (mt) REVERT: O 68 PHE cc_start: 0.9402 (m-80) cc_final: 0.8907 (m-80) REVERT: P 15 LEU cc_start: 0.9285 (mm) cc_final: 0.8618 (tp) REVERT: P 49 MET cc_start: 0.9120 (ptp) cc_final: 0.8846 (ptt) REVERT: P 62 PHE cc_start: 0.9563 (m-10) cc_final: 0.9314 (m-80) REVERT: Q 59 LEU cc_start: 0.9676 (mm) cc_final: 0.9409 (mm) REVERT: Q 62 PHE cc_start: 0.9053 (m-80) cc_final: 0.8797 (m-80) outliers start: 1 outliers final: 0 residues processed: 310 average time/residue: 0.1276 time to fit residues: 59.2394 Evaluate side-chains 281 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.8142 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.071727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056797 restraints weight = 56957.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.057954 restraints weight = 44230.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058890 restraints weight = 36123.575| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8101 Z= 0.148 Angle : 0.614 8.284 11102 Z= 0.337 Chirality : 0.045 0.233 1451 Planarity : 0.004 0.055 1478 Dihedral : 3.970 22.556 1331 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer: Outliers : 0.21 % Allowed : 2.48 % Favored : 97.31 % 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: 1.06 (0.24), residues: 1284 helix: 1.45 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -3.23 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.049 0.001 PHE I 50 TYR 0.012 0.001 TYR M 48 ARG 0.001 0.000 ARG J 37 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 827) hydrogen bonds : angle 4.15611 ( 2469) covalent geometry : bond 0.00332 ( 8101) covalent geometry : angle 0.61394 (11102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 55 PHE cc_start: 0.9163 (m-80) cc_final: 0.8757 (m-80) REVERT: H 68 PHE cc_start: 0.9265 (m-80) cc_final: 0.8955 (t80) REVERT: I 55 PHE cc_start: 0.9715 (m-80) cc_final: 0.9344 (m-80) REVERT: I 64 LEU cc_start: 0.9711 (mm) cc_final: 0.9479 (mm) REVERT: I 68 PHE cc_start: 0.9470 (m-10) cc_final: 0.8905 (m-80) REVERT: J 47 THR cc_start: 0.9501 (p) cc_final: 0.9198 (p) REVERT: J 50 PHE cc_start: 0.9716 (m-80) cc_final: 0.9126 (m-80) REVERT: J 51 ILE cc_start: 0.9498 (pt) cc_final: 0.9152 (pt) REVERT: J 55 PHE cc_start: 0.9450 (m-10) cc_final: 0.9045 (m-80) REVERT: J 57 GLU cc_start: 0.9411 (mt-10) cc_final: 0.8838 (tm-30) REVERT: J 61 ILE cc_start: 0.9037 (mm) cc_final: 0.8804 (mm) REVERT: J 64 LEU cc_start: 0.9802 (tt) cc_final: 0.9369 (pp) REVERT: J 65 VAL cc_start: 0.9650 (m) cc_final: 0.9383 (m) REVERT: J 68 PHE cc_start: 0.9407 (m-80) cc_final: 0.9207 (m-80) REVERT: K 15 LEU cc_start: 0.9350 (mm) cc_final: 0.9098 (mt) REVERT: K 24 ILE cc_start: 0.9542 (mm) cc_final: 0.9303 (mm) REVERT: K 32 VAL cc_start: 0.9848 (p) cc_final: 0.9569 (p) REVERT: K 33 GLN cc_start: 0.9445 (mp-120) cc_final: 0.9222 (mm-40) REVERT: K 44 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8996 (tpt170) REVERT: K 55 PHE cc_start: 0.9314 (m-80) cc_final: 0.9103 (m-80) REVERT: K 62 PHE cc_start: 0.9483 (m-80) cc_final: 0.9223 (m-80) REVERT: L 26 ILE cc_start: 0.9434 (tp) cc_final: 0.9178 (tt) REVERT: L 48 TYR cc_start: 0.9071 (m-10) cc_final: 0.8775 (m-80) REVERT: L 55 PHE cc_start: 0.9462 (m-80) cc_final: 0.9175 (m-80) REVERT: M 40 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8884 (mm-30) REVERT: M 55 PHE cc_start: 0.9585 (m-80) cc_final: 0.9153 (m-80) REVERT: M 59 LEU cc_start: 0.9727 (mt) cc_final: 0.9446 (mt) REVERT: M 62 PHE cc_start: 0.9350 (m-80) cc_final: 0.8929 (m-80) REVERT: N 11 LEU cc_start: 0.9514 (mm) cc_final: 0.9281 (mm) REVERT: N 33 GLN cc_start: 0.9305 (mm-40) cc_final: 0.9089 (mm110) REVERT: N 48 TYR cc_start: 0.9283 (m-10) cc_final: 0.8845 (m-80) REVERT: N 53 ILE cc_start: 0.9642 (mm) cc_final: 0.9428 (mm) REVERT: N 55 PHE cc_start: 0.9478 (m-80) cc_final: 0.9052 (m-80) REVERT: N 62 PHE cc_start: 0.9320 (m-80) cc_final: 0.8879 (m-80) REVERT: N 64 LEU cc_start: 0.9810 (mt) cc_final: 0.9514 (mt) REVERT: N 68 PHE cc_start: 0.9428 (m-10) cc_final: 0.9042 (m-80) REVERT: O 29 SER cc_start: 0.9596 (t) cc_final: 0.9333 (p) REVERT: O 62 PHE cc_start: 0.9229 (m-80) cc_final: 0.8845 (m-80) REVERT: O 64 LEU cc_start: 0.9719 (mt) cc_final: 0.9508 (mt) REVERT: O 68 PHE cc_start: 0.9360 (m-80) cc_final: 0.8763 (m-80) REVERT: P 15 LEU cc_start: 0.9484 (mm) cc_final: 0.8778 (tp) REVERT: P 49 MET cc_start: 0.9193 (ptp) cc_final: 0.8810 (ptt) REVERT: P 62 PHE cc_start: 0.9501 (m-10) cc_final: 0.9279 (m-80) REVERT: Q 59 LEU cc_start: 0.9566 (mm) cc_final: 0.9195 (mm) REVERT: Q 62 PHE cc_start: 0.8967 (m-80) cc_final: 0.8712 (m-80) outliers start: 1 outliers final: 1 residues processed: 315 average time/residue: 0.1305 time to fit residues: 61.5799 Evaluate side-chains 283 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 111 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** 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 = 0.3422 r_free = 0.3422 target = 0.068088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050691 restraints weight = 42212.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051722 restraints weight = 33156.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052530 restraints weight = 27539.537| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8101 Z= 0.152 Angle : 0.648 7.933 11102 Z= 0.355 Chirality : 0.046 0.263 1451 Planarity : 0.004 0.072 1478 Dihedral : 3.935 21.812 1331 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: 1.03 (0.24), residues: 1284 helix: 1.42 (0.16), residues: 1073 sheet: None (None), residues: 0 loop : -3.17 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.046 0.002 PHE I 62 TYR 0.008 0.001 TYR H 48 ARG 0.010 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 827) hydrogen bonds : angle 4.21410 ( 2469) covalent geometry : bond 0.00346 ( 8101) covalent geometry : angle 0.64814 (11102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 GLN cc_start: 0.9454 (pm20) cc_final: 0.8782 (pm20) REVERT: H 68 PHE cc_start: 0.9283 (m-80) cc_final: 0.8971 (t80) REVERT: I 55 PHE cc_start: 0.9729 (m-80) cc_final: 0.9379 (m-80) REVERT: I 62 PHE cc_start: 0.9283 (m-80) cc_final: 0.9042 (m-80) REVERT: I 64 LEU cc_start: 0.9824 (mm) cc_final: 0.9539 (mm) REVERT: I 68 PHE cc_start: 0.9436 (m-10) cc_final: 0.8896 (m-80) REVERT: J 27 ILE cc_start: 0.9611 (mm) cc_final: 0.9366 (mm) REVERT: J 48 TYR cc_start: 0.9288 (m-80) cc_final: 0.8736 (m-80) REVERT: J 50 PHE cc_start: 0.9655 (m-80) cc_final: 0.9193 (m-80) REVERT: J 51 ILE cc_start: 0.9493 (pt) cc_final: 0.9273 (pt) REVERT: J 53 ILE cc_start: 0.9782 (mt) cc_final: 0.9529 (mt) REVERT: J 55 PHE cc_start: 0.9315 (m-10) cc_final: 0.8862 (m-80) REVERT: J 57 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8793 (tm-30) REVERT: J 61 ILE cc_start: 0.8782 (mm) cc_final: 0.8558 (mm) REVERT: J 64 LEU cc_start: 0.9858 (tt) cc_final: 0.9496 (pp) REVERT: J 65 VAL cc_start: 0.9633 (m) cc_final: 0.9352 (m) REVERT: J 68 PHE cc_start: 0.9516 (m-80) cc_final: 0.9274 (m-80) REVERT: K 15 LEU cc_start: 0.9208 (mm) cc_final: 0.9005 (mt) REVERT: K 24 ILE cc_start: 0.9524 (mm) cc_final: 0.9224 (mm) REVERT: K 27 ILE cc_start: 0.9391 (mt) cc_final: 0.9089 (mt) REVERT: K 44 ARG cc_start: 0.9255 (mmm-85) cc_final: 0.9033 (tpt170) REVERT: K 62 PHE cc_start: 0.9503 (m-80) cc_final: 0.9217 (m-80) REVERT: L 26 ILE cc_start: 0.8996 (tp) cc_final: 0.8796 (tt) REVERT: L 48 TYR cc_start: 0.9076 (m-10) cc_final: 0.8759 (m-80) REVERT: L 50 PHE cc_start: 0.8574 (m-10) cc_final: 0.8042 (t80) REVERT: L 55 PHE cc_start: 0.9439 (m-80) cc_final: 0.9184 (m-80) REVERT: M 40 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8928 (mm-30) REVERT: M 55 PHE cc_start: 0.9643 (m-80) cc_final: 0.9225 (m-80) REVERT: M 59 LEU cc_start: 0.9751 (mt) cc_final: 0.9476 (mt) REVERT: M 62 PHE cc_start: 0.9423 (m-80) cc_final: 0.8925 (m-80) REVERT: N 11 LEU cc_start: 0.9508 (mm) cc_final: 0.9279 (mm) REVERT: N 40 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9208 (mp0) REVERT: N 48 TYR cc_start: 0.9232 (m-10) cc_final: 0.8785 (m-80) REVERT: N 53 ILE cc_start: 0.9638 (mm) cc_final: 0.9378 (mm) REVERT: N 55 PHE cc_start: 0.9453 (m-80) cc_final: 0.9052 (m-80) REVERT: N 62 PHE cc_start: 0.9386 (m-80) cc_final: 0.8911 (m-80) REVERT: N 64 LEU cc_start: 0.9884 (mt) cc_final: 0.9579 (mt) REVERT: N 68 PHE cc_start: 0.9589 (m-10) cc_final: 0.9151 (m-80) REVERT: O 29 SER cc_start: 0.9559 (t) cc_final: 0.9321 (p) REVERT: O 62 PHE cc_start: 0.9250 (m-80) cc_final: 0.8855 (m-80) REVERT: O 64 LEU cc_start: 0.9759 (mt) cc_final: 0.9526 (mt) REVERT: O 68 PHE cc_start: 0.9378 (m-80) cc_final: 0.8793 (m-80) REVERT: P 15 LEU cc_start: 0.9452 (mm) cc_final: 0.8730 (tp) REVERT: P 50 PHE cc_start: 0.9208 (m-80) cc_final: 0.9005 (m-10) REVERT: P 62 PHE cc_start: 0.9500 (m-10) cc_final: 0.9261 (m-80) REVERT: Q 27 ILE cc_start: 0.9717 (mt) cc_final: 0.9497 (mt) REVERT: Q 33 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8825 (tm-30) REVERT: Q 62 PHE cc_start: 0.8898 (m-80) cc_final: 0.8619 (m-80) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.1371 time to fit residues: 64.2078 Evaluate side-chains 285 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 120 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** 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 = 0.3429 r_free = 0.3429 target = 0.073007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.057878 restraints weight = 56170.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059189 restraints weight = 43085.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060187 restraints weight = 34682.630| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8101 Z= 0.152 Angle : 0.652 8.292 11102 Z= 0.357 Chirality : 0.047 0.253 1451 Planarity : 0.004 0.053 1478 Dihedral : 3.902 19.441 1331 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: 1.05 (0.24), residues: 1284 helix: 1.43 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -3.23 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.045 0.002 PHE I 62 TYR 0.010 0.001 TYR O 48 ARG 0.006 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 827) hydrogen bonds : angle 4.15991 ( 2469) covalent geometry : bond 0.00345 ( 8101) covalent geometry : angle 0.65209 (11102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 GLN cc_start: 0.9498 (pm20) cc_final: 0.8834 (mp10) REVERT: H 68 PHE cc_start: 0.9261 (m-80) cc_final: 0.8950 (t80) REVERT: I 33 GLN cc_start: 0.9258 (mp10) cc_final: 0.9033 (mp10) REVERT: I 55 PHE cc_start: 0.9721 (m-80) cc_final: 0.9388 (m-80) REVERT: I 62 PHE cc_start: 0.9148 (m-80) cc_final: 0.8874 (m-80) REVERT: J 48 TYR cc_start: 0.9106 (m-80) cc_final: 0.8560 (m-80) REVERT: J 50 PHE cc_start: 0.9690 (m-80) cc_final: 0.9100 (m-80) REVERT: J 51 ILE cc_start: 0.9499 (pt) cc_final: 0.9085 (pt) REVERT: J 55 PHE cc_start: 0.9424 (m-10) cc_final: 0.9034 (m-80) REVERT: J 57 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8698 (tm-30) REVERT: J 61 ILE cc_start: 0.8977 (mm) cc_final: 0.8700 (mm) REVERT: J 64 LEU cc_start: 0.9818 (tt) cc_final: 0.9465 (pp) REVERT: J 65 VAL cc_start: 0.9637 (m) cc_final: 0.9403 (m) REVERT: J 68 PHE cc_start: 0.9540 (m-80) cc_final: 0.9278 (m-80) REVERT: K 15 LEU cc_start: 0.9268 (mm) cc_final: 0.9063 (mt) REVERT: K 24 ILE cc_start: 0.9435 (mm) cc_final: 0.9006 (pt) REVERT: K 44 ARG cc_start: 0.9210 (mmm-85) cc_final: 0.8977 (tpt170) REVERT: K 51 ILE cc_start: 0.9371 (pt) cc_final: 0.8992 (pt) REVERT: K 62 PHE cc_start: 0.9476 (m-80) cc_final: 0.9161 (m-80) REVERT: L 26 ILE cc_start: 0.9416 (tp) cc_final: 0.9153 (tt) REVERT: L 48 TYR cc_start: 0.9072 (m-10) cc_final: 0.8782 (m-80) REVERT: L 50 PHE cc_start: 0.8538 (m-10) cc_final: 0.8003 (t80) REVERT: L 55 PHE cc_start: 0.9464 (m-80) cc_final: 0.9210 (m-80) REVERT: M 40 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8910 (mm-30) REVERT: M 48 TYR cc_start: 0.9017 (m-80) cc_final: 0.8761 (m-80) REVERT: M 50 PHE cc_start: 0.9289 (m-80) cc_final: 0.8689 (m-80) REVERT: M 51 ILE cc_start: 0.9841 (mt) cc_final: 0.9638 (mm) REVERT: M 55 PHE cc_start: 0.9554 (m-80) cc_final: 0.9182 (m-80) REVERT: M 59 LEU cc_start: 0.9683 (mt) cc_final: 0.9362 (mt) REVERT: M 62 PHE cc_start: 0.9361 (m-80) cc_final: 0.8875 (m-80) REVERT: N 11 LEU cc_start: 0.9506 (mm) cc_final: 0.9261 (mm) REVERT: N 40 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9163 (mp0) REVERT: N 48 TYR cc_start: 0.9268 (m-10) cc_final: 0.8816 (m-80) REVERT: N 53 ILE cc_start: 0.9618 (mm) cc_final: 0.9355 (mm) REVERT: N 55 PHE cc_start: 0.9505 (m-80) cc_final: 0.9200 (m-80) REVERT: N 59 LEU cc_start: 0.9583 (mt) cc_final: 0.9379 (mt) REVERT: N 62 PHE cc_start: 0.9342 (m-80) cc_final: 0.8865 (m-80) REVERT: N 64 LEU cc_start: 0.9846 (mt) cc_final: 0.9555 (mt) REVERT: N 68 PHE cc_start: 0.9455 (m-10) cc_final: 0.9050 (m-80) REVERT: O 29 SER cc_start: 0.9622 (t) cc_final: 0.9352 (p) REVERT: O 62 PHE cc_start: 0.9192 (m-80) cc_final: 0.8821 (m-80) REVERT: O 64 LEU cc_start: 0.9732 (mt) cc_final: 0.9505 (mt) REVERT: O 68 PHE cc_start: 0.9421 (m-80) cc_final: 0.8855 (m-80) REVERT: P 49 MET cc_start: 0.9206 (ptp) cc_final: 0.8755 (ptt) REVERT: P 50 PHE cc_start: 0.9210 (m-80) cc_final: 0.8996 (m-10) REVERT: P 59 LEU cc_start: 0.9283 (tp) cc_final: 0.9022 (tp) REVERT: P 62 PHE cc_start: 0.9473 (m-10) cc_final: 0.9213 (m-80) REVERT: Q 33 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8911 (tm-30) REVERT: Q 37 ARG cc_start: 0.8534 (ttm170) cc_final: 0.7832 (ttm170) REVERT: Q 59 LEU cc_start: 0.9502 (mm) cc_final: 0.9252 (mm) REVERT: Q 62 PHE cc_start: 0.8884 (m-80) cc_final: 0.8501 (m-80) REVERT: Q 66 ILE cc_start: 0.9827 (mm) cc_final: 0.9585 (tp) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1373 time to fit residues: 63.3375 Evaluate side-chains 280 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.068629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050017 restraints weight = 42714.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.051213 restraints weight = 32137.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.052180 restraints weight = 26039.829| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8101 Z= 0.152 Angle : 0.655 8.172 11102 Z= 0.355 Chirality : 0.047 0.254 1451 Planarity : 0.004 0.078 1478 Dihedral : 3.914 21.570 1331 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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: 1.03 (0.24), residues: 1284 helix: 1.41 (0.16), residues: 1076 sheet: None (None), residues: 0 loop : -3.22 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.038 0.002 PHE I 62 TYR 0.007 0.001 TYR O 48 ARG 0.007 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 827) hydrogen bonds : angle 4.14431 ( 2469) covalent geometry : bond 0.00349 ( 8101) covalent geometry : angle 0.65533 (11102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 GLN cc_start: 0.9221 (pm20) cc_final: 0.8713 (pm20) REVERT: H 68 PHE cc_start: 0.9234 (m-80) cc_final: 0.8910 (t80) REVERT: I 40 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8660 (mp0) REVERT: I 55 PHE cc_start: 0.9722 (m-80) cc_final: 0.9353 (m-80) REVERT: I 62 PHE cc_start: 0.9245 (m-80) cc_final: 0.8980 (m-80) REVERT: J 27 ILE cc_start: 0.9654 (mm) cc_final: 0.9397 (mm) REVERT: J 48 TYR cc_start: 0.9333 (m-80) cc_final: 0.8711 (m-80) REVERT: J 50 PHE cc_start: 0.9630 (m-80) cc_final: 0.9295 (m-80) REVERT: J 51 ILE cc_start: 0.9517 (pt) cc_final: 0.9301 (pt) REVERT: J 53 ILE cc_start: 0.9753 (mt) cc_final: 0.9491 (mt) REVERT: J 55 PHE cc_start: 0.9311 (m-10) cc_final: 0.9108 (m-80) REVERT: J 56 THR cc_start: 0.9584 (p) cc_final: 0.9342 (p) REVERT: J 57 GLU cc_start: 0.9366 (mt-10) cc_final: 0.8978 (tm-30) REVERT: J 59 LEU cc_start: 0.9691 (mm) cc_final: 0.9436 (pp) REVERT: J 64 LEU cc_start: 0.9877 (tt) cc_final: 0.9528 (pp) REVERT: J 65 VAL cc_start: 0.9632 (m) cc_final: 0.9416 (m) REVERT: J 68 PHE cc_start: 0.9597 (m-80) cc_final: 0.9310 (m-80) REVERT: K 24 ILE cc_start: 0.9464 (mm) cc_final: 0.8987 (pt) REVERT: K 27 ILE cc_start: 0.9385 (mt) cc_final: 0.9177 (mt) REVERT: K 44 ARG cc_start: 0.9258 (mmm-85) cc_final: 0.9024 (tpt170) REVERT: K 62 PHE cc_start: 0.9469 (m-80) cc_final: 0.9146 (m-80) REVERT: L 26 ILE cc_start: 0.9056 (tp) cc_final: 0.8839 (tt) REVERT: L 48 TYR cc_start: 0.9056 (m-10) cc_final: 0.8749 (m-80) REVERT: L 50 PHE cc_start: 0.8583 (m-10) cc_final: 0.8035 (t80) REVERT: L 55 PHE cc_start: 0.9473 (m-80) cc_final: 0.9182 (m-80) REVERT: M 40 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8940 (mm-30) REVERT: M 48 TYR cc_start: 0.9024 (m-80) cc_final: 0.8793 (m-80) REVERT: M 50 PHE cc_start: 0.9139 (m-80) cc_final: 0.8631 (m-80) REVERT: M 55 PHE cc_start: 0.9625 (m-80) cc_final: 0.9257 (m-80) REVERT: M 59 LEU cc_start: 0.9723 (mt) cc_final: 0.9416 (mt) REVERT: M 62 PHE cc_start: 0.9441 (m-80) cc_final: 0.8901 (m-80) REVERT: N 11 LEU cc_start: 0.9527 (mm) cc_final: 0.9299 (mm) REVERT: N 40 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9220 (mp0) REVERT: N 48 TYR cc_start: 0.9191 (m-10) cc_final: 0.8756 (m-80) REVERT: N 53 ILE cc_start: 0.9594 (mm) cc_final: 0.9309 (mm) REVERT: N 55 PHE cc_start: 0.9454 (m-80) cc_final: 0.9102 (m-80) REVERT: N 59 LEU cc_start: 0.9591 (mt) cc_final: 0.9369 (mt) REVERT: N 62 PHE cc_start: 0.9387 (m-80) cc_final: 0.8968 (m-80) REVERT: N 64 LEU cc_start: 0.9887 (mt) cc_final: 0.9574 (mt) REVERT: N 68 PHE cc_start: 0.9583 (m-10) cc_final: 0.9117 (m-80) REVERT: O 29 SER cc_start: 0.9595 (t) cc_final: 0.9367 (p) REVERT: O 62 PHE cc_start: 0.9233 (m-80) cc_final: 0.8886 (m-80) REVERT: O 64 LEU cc_start: 0.9756 (mt) cc_final: 0.9528 (mt) REVERT: O 68 PHE cc_start: 0.9413 (m-80) cc_final: 0.8871 (m-80) REVERT: P 49 MET cc_start: 0.9172 (ptp) cc_final: 0.8972 (ptt) REVERT: P 59 LEU cc_start: 0.9220 (tp) cc_final: 0.8971 (tp) REVERT: P 62 PHE cc_start: 0.9477 (m-10) cc_final: 0.9210 (m-80) REVERT: Q 59 LEU cc_start: 0.9557 (mm) cc_final: 0.9355 (mm) REVERT: Q 62 PHE cc_start: 0.8883 (m-80) cc_final: 0.8531 (m-80) REVERT: Q 66 ILE cc_start: 0.9853 (mm) cc_final: 0.9581 (tp) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1401 time to fit residues: 63.9196 Evaluate side-chains 280 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 104 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 33 GLN ** 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 = 0.3417 r_free = 0.3417 target = 0.067995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051093 restraints weight = 43220.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.051948 restraints weight = 34192.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052744 restraints weight = 29085.745| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8101 Z= 0.167 Angle : 0.673 8.312 11102 Z= 0.370 Chirality : 0.047 0.249 1451 Planarity : 0.004 0.053 1478 Dihedral : 3.888 22.257 1331 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.96 (0.24), residues: 1284 helix: 1.35 (0.16), residues: 1077 sheet: None (None), residues: 0 loop : -3.20 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.040 0.002 PHE I 62 TYR 0.011 0.001 TYR O 48 ARG 0.006 0.000 ARG P 37 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 827) hydrogen bonds : angle 4.25713 ( 2469) covalent geometry : bond 0.00379 ( 8101) covalent geometry : angle 0.67298 (11102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 PHE cc_start: 0.9245 (m-80) cc_final: 0.8880 (t80) REVERT: I 39 PRO cc_start: 0.7788 (Cg_endo) cc_final: 0.7326 (Cg_exo) REVERT: I 40 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8602 (mp0) REVERT: I 55 PHE cc_start: 0.9727 (m-80) cc_final: 0.9366 (m-80) REVERT: I 62 PHE cc_start: 0.9234 (m-80) cc_final: 0.8993 (m-80) REVERT: J 26 ILE cc_start: 0.9571 (tp) cc_final: 0.9255 (pt) REVERT: J 27 ILE cc_start: 0.9629 (mm) cc_final: 0.9342 (mm) REVERT: J 48 TYR cc_start: 0.9302 (m-80) cc_final: 0.8718 (m-80) REVERT: J 50 PHE cc_start: 0.9651 (m-80) cc_final: 0.9268 (m-80) REVERT: J 51 ILE cc_start: 0.9518 (pt) cc_final: 0.9296 (pt) REVERT: J 53 ILE cc_start: 0.9779 (mt) cc_final: 0.9527 (mt) REVERT: J 55 PHE cc_start: 0.9318 (m-10) cc_final: 0.9018 (m-80) REVERT: J 56 THR cc_start: 0.9575 (p) cc_final: 0.9263 (p) REVERT: J 57 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8902 (tm-30) REVERT: J 59 LEU cc_start: 0.9642 (mm) cc_final: 0.9417 (pp) REVERT: J 61 ILE cc_start: 0.8966 (mm) cc_final: 0.8747 (mm) REVERT: J 64 LEU cc_start: 0.9869 (tt) cc_final: 0.9533 (pp) REVERT: J 68 PHE cc_start: 0.9587 (m-80) cc_final: 0.9321 (m-80) REVERT: K 24 ILE cc_start: 0.9446 (mm) cc_final: 0.9227 (mm) REVERT: K 27 ILE cc_start: 0.9440 (mt) cc_final: 0.9148 (mt) REVERT: K 44 ARG cc_start: 0.9247 (mmm-85) cc_final: 0.9027 (tpt170) REVERT: K 51 ILE cc_start: 0.9323 (pt) cc_final: 0.9111 (pt) REVERT: K 55 PHE cc_start: 0.9510 (m-10) cc_final: 0.9305 (m-80) REVERT: K 62 PHE cc_start: 0.9486 (m-80) cc_final: 0.9139 (m-80) REVERT: L 18 ILE cc_start: 0.9251 (tt) cc_final: 0.8880 (pt) REVERT: L 48 TYR cc_start: 0.9017 (m-10) cc_final: 0.8713 (m-80) REVERT: L 55 PHE cc_start: 0.9459 (m-80) cc_final: 0.9170 (m-80) REVERT: M 40 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8921 (mm-30) REVERT: M 48 TYR cc_start: 0.8984 (m-80) cc_final: 0.8749 (m-80) REVERT: M 55 PHE cc_start: 0.9599 (m-80) cc_final: 0.9238 (m-80) REVERT: M 59 LEU cc_start: 0.9724 (mt) cc_final: 0.9393 (mt) REVERT: M 62 PHE cc_start: 0.9360 (m-80) cc_final: 0.8833 (m-80) REVERT: N 11 LEU cc_start: 0.9544 (mm) cc_final: 0.9296 (mm) REVERT: N 40 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9199 (mp0) REVERT: N 48 TYR cc_start: 0.9224 (m-10) cc_final: 0.8783 (m-80) REVERT: N 53 ILE cc_start: 0.9630 (mm) cc_final: 0.9306 (mm) REVERT: N 55 PHE cc_start: 0.9472 (m-80) cc_final: 0.9066 (m-80) REVERT: N 59 LEU cc_start: 0.9587 (mt) cc_final: 0.9357 (mt) REVERT: N 62 PHE cc_start: 0.9374 (m-80) cc_final: 0.8955 (m-80) REVERT: N 64 LEU cc_start: 0.9878 (mt) cc_final: 0.9576 (mt) REVERT: N 68 PHE cc_start: 0.9570 (m-10) cc_final: 0.9125 (m-80) REVERT: O 29 SER cc_start: 0.9644 (t) cc_final: 0.9409 (p) REVERT: O 48 TYR cc_start: 0.9487 (m-10) cc_final: 0.9267 (m-80) REVERT: O 62 PHE cc_start: 0.9197 (m-80) cc_final: 0.8939 (m-80) REVERT: O 68 PHE cc_start: 0.9433 (m-80) cc_final: 0.8863 (m-80) REVERT: P 49 MET cc_start: 0.9356 (ptp) cc_final: 0.8935 (ptt) REVERT: P 62 PHE cc_start: 0.9449 (m-10) cc_final: 0.9163 (m-80) REVERT: Q 27 ILE cc_start: 0.9627 (mt) cc_final: 0.9384 (mt) REVERT: Q 53 ILE cc_start: 0.9043 (pt) cc_final: 0.8625 (pt) REVERT: Q 59 LEU cc_start: 0.9542 (mm) cc_final: 0.9326 (mm) REVERT: Q 62 PHE cc_start: 0.8900 (m-80) cc_final: 0.8558 (m-80) REVERT: Q 66 ILE cc_start: 0.9845 (mm) cc_final: 0.9594 (tp) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1356 time to fit residues: 61.3001 Evaluate side-chains 274 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 33 GLN ** 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 = 0.3370 r_free = 0.3370 target = 0.065957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050085 restraints weight = 40957.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050955 restraints weight = 33426.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051520 restraints weight = 28536.037| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8101 Z= 0.176 Angle : 0.668 8.001 11102 Z= 0.369 Chirality : 0.046 0.259 1451 Planarity : 0.004 0.051 1478 Dihedral : 3.911 22.484 1331 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 0.98 (0.24), residues: 1284 helix: 1.37 (0.16), residues: 1076 sheet: None (None), residues: 0 loop : -3.20 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP T 122 PHE 0.040 0.002 PHE I 62 TYR 0.010 0.001 TYR O 48 ARG 0.002 0.000 ARG Q 37 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 827) hydrogen bonds : angle 4.29869 ( 2469) covalent geometry : bond 0.00385 ( 8101) covalent geometry : angle 0.66823 (11102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2751.22 seconds wall clock time: 48 minutes 7.22 seconds (2887.22 seconds total)