Starting phenix.real_space_refine on Sun May 11 23:28:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfs_37498/05_2025/8wfs_37498.cif" } resolution = 3.36 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2864 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 3973 2.51 5 N 1123 2.21 5 O 1124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6274 Number of models: 1 Model: "" Number of chains: 13 Chain: "c" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 884 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 102} Chain: "C" Number of atoms: 882 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102} Conformer: "B" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 102} bond proxies already assigned to first conformer: 894 Chain: "E" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 957 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 113} Chain: "B" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1035 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123} Chain: "b" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1035 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 123} Chain: "X" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1112 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 133} Chain: "a" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 179 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA C 114 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA C 114 " occ=0.50 Time building chain proxies: 5.70, per 1000 atoms: 0.91 Number of scatterers: 6274 At special positions: 0 Unit cell: (83.7876, 97.7522, 134.275, 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 54 16.00 O 1124 8.00 N 1123 7.00 C 3973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS c 1 " - pdb=" SG CYS c 7 " distance=2.03 Simple disulfide: pdb=" SG CYS c 5 " - pdb=" SG CYS c 14 " distance=2.03 Simple disulfide: pdb=" SG CYS c 68 " - pdb=" SG CYS c 93 " distance=2.04 Simple disulfide: pdb=" SG CYS c 70 " - pdb=" SG CYS c 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 1 " - pdb=" SG CYS C 7 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 14 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 70 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 10 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS E 22 " distance=2.03 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 75 " - pdb=" SG CYS E 119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 1 " - pdb=" SG CYS B 7 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 14 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS a 484 " distance=2.03 Simple disulfide: pdb=" SG CYS b 1 " - pdb=" SG CYS b 7 " distance=2.03 Simple disulfide: pdb=" SG CYS b 5 " - pdb=" SG CYS b 14 " distance=2.03 Simple disulfide: pdb=" SG CYS b 68 " - pdb=" SG CYS b 93 " distance=2.03 Simple disulfide: pdb=" SG CYS b 70 " - pdb=" SG CYS b 116 " distance=2.03 Simple disulfide: pdb=" SG CYS b 122 " - pdb=" SG CYS a 485 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 10 " distance=2.03 Simple disulfide: pdb=" SG CYS X 8 " - pdb=" SG CYS X 22 " distance=2.03 Simple disulfide: pdb=" SG CYS X 73 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS X 75 " - pdb=" SG CYS X 119 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 1 " - " ASN c 41 " " NAG D 1 " - " ASN C 41 " " NAG F 1 " - " ASN E 44 " " NAG G 1 " - " ASN B 41 " " NAG H 1 " - " ASN b 41 " " NAG I 1 " - " ASN X 44 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 31.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'c' and resid 49 through 53 removed outlier: 3.545A pdb=" N ALA c 52 " --> pdb=" O LEU c 49 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 71 No H-bonds generated for 'chain 'c' and resid 69 through 71' Processing helix chain 'c' and resid 72 through 81 removed outlier: 4.190A pdb=" N GLY c 81 " --> pdb=" O ALA c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 89 removed outlier: 3.541A pdb=" N TYR c 88 " --> pdb=" O ARG c 85 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG c 89 " --> pdb=" O ALA c 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 85 through 89' Processing helix chain 'c' and resid 96 through 100 removed outlier: 3.662A pdb=" N ARG c 100 " --> pdb=" O PRO c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 115 Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 96 through 100 removed outlier: 3.651A pdb=" N ARG C 100 " --> pdb=" O PRO C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 108 through 115 removed outlier: 3.754A pdb=" N LEU C 112 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 85 Processing helix chain 'E' and resid 88 through 95 removed outlier: 4.089A pdb=" N VAL E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 72 through 80 removed outlier: 3.594A pdb=" N ALA B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.524A pdb=" N TYR B 88 " --> pdb=" O ARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.589A pdb=" N ARG B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 108 through 117 removed outlier: 4.135A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.829A pdb=" N GLN B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 53 removed outlier: 3.908A pdb=" N LEU b 53 " --> pdb=" O LEU b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 71 No H-bonds generated for 'chain 'b' and resid 69 through 71' Processing helix chain 'b' and resid 72 through 81 removed outlier: 3.505A pdb=" N GLY b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 96 through 100 removed outlier: 3.551A pdb=" N ARG b 100 " --> pdb=" O PRO b 97 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 107 Processing helix chain 'b' and resid 108 through 116 removed outlier: 3.798A pdb=" N LEU b 112 " --> pdb=" O ALA b 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS b 116 " --> pdb=" O LEU b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 140 Processing helix chain 'X' and resid 74 through 76 No H-bonds generated for 'chain 'X' and resid 74 through 76' Processing helix chain 'X' and resid 77 through 88 Processing helix chain 'X' and resid 89 through 94 Processing helix chain 'X' and resid 130 through 146 removed outlier: 3.662A pdb=" N ALA X 137 " --> pdb=" O LEU X 133 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY X 145 " --> pdb=" O VAL X 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU X 146 " --> pdb=" O ALA X 142 " (cutoff:3.500A) Processing helix chain 'a' and resid 483 through 503 removed outlier: 3.688A pdb=" N LEU a 487 " --> pdb=" O PHE a 483 " (cutoff:3.500A) Proline residue: a 488 - end of helix removed outlier: 4.359A pdb=" N PHE a 491 " --> pdb=" O LEU a 487 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL a 493 " --> pdb=" O LEU a 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'c' and resid 66 through 67 removed outlier: 7.480A pdb=" N TRP c 66 " --> pdb=" O VAL c 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 8 removed outlier: 3.658A pdb=" N VAL C 36 " --> pdb=" O VAL C 12 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67 removed outlier: 7.132A pdb=" N TRP C 66 " --> pdb=" O VAL C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.660A pdb=" N GLY E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU E 18 " --> pdb=" O HIS E 39 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU E 41 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 20 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E 40 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 72 removed outlier: 7.077A pdb=" N TRP E 71 " --> pdb=" O ALA E 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 6 through 8 removed outlier: 6.827A pdb=" N LEU B 35 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 6 through 8 removed outlier: 3.522A pdb=" N VAL b 36 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU b 35 " --> pdb=" O HIS b 60 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 66 through 67 removed outlier: 7.041A pdb=" N TRP b 66 " --> pdb=" O VAL b 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'X' and resid 9 through 13 removed outlier: 6.947A pdb=" N LEU X 18 " --> pdb=" O ARG X 38 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU X 40 " --> pdb=" O LEU X 18 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL X 20 " --> pdb=" O LEU X 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 71 through 72 removed outlier: 6.640A pdb=" N TRP X 71 " --> pdb=" O ALA X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 149 hydrogen bonds defined for protein. 351 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: 1.50 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2060 1.34 - 1.47: 1427 1.47 - 1.59: 2898 1.59 - 1.71: 1 1.71 - 1.83: 56 Bond restraints: 6442 Sorted by residual: bond pdb=" CB PRO c 29 " pdb=" CG PRO c 29 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" CB PRO C 2 " pdb=" CG PRO C 2 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.54e+00 bond pdb=" C ALA B 86 " pdb=" N PRO B 87 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.38e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" CG PRO C 2 " pdb=" CD PRO C 2 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 1.95e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 8639 2.61 - 5.22: 181 5.22 - 7.83: 18 7.83 - 10.45: 9 10.45 - 13.06: 1 Bond angle restraints: 8848 Sorted by residual: angle pdb=" CA PRO c 29 " pdb=" N PRO c 29 " pdb=" CD PRO c 29 " ideal model delta sigma weight residual 112.00 98.94 13.06 1.40e+00 5.10e-01 8.70e+01 angle pdb=" N GLY b 124 " pdb=" CA GLY b 124 " pdb=" C GLY b 124 " ideal model delta sigma weight residual 115.66 105.40 10.26 1.56e+00 4.11e-01 4.33e+01 angle pdb=" CA PRO C 2 " pdb=" N PRO C 2 " pdb=" CD PRO C 2 " ideal model delta sigma weight residual 112.00 106.47 5.53 1.40e+00 5.10e-01 1.56e+01 angle pdb=" N PRO c 29 " pdb=" CD PRO c 29 " pdb=" CG PRO c 29 " ideal model delta sigma weight residual 103.20 98.14 5.06 1.50e+00 4.44e-01 1.14e+01 angle pdb=" N PRO c 29 " pdb=" CA PRO c 29 " pdb=" C PRO c 29 " ideal model delta sigma weight residual 111.68 116.99 -5.31 1.67e+00 3.59e-01 1.01e+01 ... (remaining 8843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 3602 22.26 - 44.52: 419 44.52 - 66.78: 71 66.78 - 89.03: 20 89.03 - 111.29: 16 Dihedral angle restraints: 4128 sinusoidal: 1818 harmonic: 2310 Sorted by residual: dihedral pdb=" CB CYS X 73 " pdb=" SG CYS X 73 " pdb=" SG CYS X 97 " pdb=" CB CYS X 97 " ideal model delta sinusoidal sigma weight residual 93.00 14.03 78.97 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS b 122 " pdb=" SG CYS b 122 " pdb=" SG CYS a 485 " pdb=" CB CYS a 485 " ideal model delta sinusoidal sigma weight residual 93.00 171.92 -78.92 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS B 122 " pdb=" SG CYS B 122 " pdb=" SG CYS a 484 " pdb=" CB CYS a 484 " ideal model delta sinusoidal sigma weight residual 93.00 168.07 -75.07 1 1.00e+01 1.00e-02 7.13e+01 ... (remaining 4125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 870 0.056 - 0.111: 160 0.111 - 0.167: 22 0.167 - 0.223: 3 0.223 - 0.278: 5 Chirality restraints: 1060 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO c 29 " pdb=" N PRO c 29 " pdb=" C PRO c 29 " pdb=" CB PRO c 29 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1057 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE c 28 " 0.089 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO c 29 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO c 29 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO c 29 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 1 " -0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 2 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 2 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 2 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO X 51 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO X 52 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO X 52 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO X 52 " -0.044 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1511 2.79 - 3.32: 5736 3.32 - 3.84: 10220 3.84 - 4.37: 11281 4.37 - 4.90: 19207 Nonbonded interactions: 47955 Sorted by model distance: nonbonded pdb=" NH2 ARG c 102 " pdb=" OE2 GLU c 111 " model vdw 2.261 3.120 nonbonded pdb=" NH1 ARG c 67 " pdb=" OD2 ASP c 69 " model vdw 2.273 3.120 nonbonded pdb=" O SER X 126 " pdb=" OG SER X 126 " model vdw 2.289 3.040 nonbonded pdb=" NH1 ARG C 89 " pdb=" OD1 ASP E 86 " model vdw 2.319 3.120 nonbonded pdb=" O CYS b 122 " pdb=" N GLY b 124 " model vdw 2.330 3.120 ... (remaining 47950 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 'A' selection = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = (chain 'C' and (resid 1 through 113 or resid 115 through 117)) selection = (chain 'c' and (resid 1 through 113 or resid 115 through 117)) } ncs_group { reference = chain 'E' selection = (chain 'X' and resid 1 through 125) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.470 Find NCS groups from input model: 0.250 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 6482 Z= 0.198 Angle : 0.891 13.057 8942 Z= 0.421 Chirality : 0.048 0.278 1060 Planarity : 0.008 0.124 1129 Dihedral : 19.138 111.292 2556 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.94 % Allowed : 32.97 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.77 (0.29), residues: 797 helix: -1.26 (0.39), residues: 161 sheet: -1.45 (0.69), residues: 68 loop : -1.15 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP b 123 HIS 0.002 0.001 HIS E 72 PHE 0.008 0.001 PHE c 28 TYR 0.032 0.002 TYR a 492 ARG 0.008 0.001 ARG b 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 6) link_NAG-ASN : angle 2.88739 ( 18) link_BETA1-4 : bond 0.00334 ( 8) link_BETA1-4 : angle 2.74733 ( 24) hydrogen bonds : bond 0.23842 ( 149) hydrogen bonds : angle 8.41223 ( 351) SS BOND : bond 0.00246 ( 26) SS BOND : angle 1.63006 ( 52) covalent geometry : bond 0.00484 ( 6442) covalent geometry : angle 0.86553 ( 8848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 113 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7257 (mtp85) outliers start: 6 outliers final: 2 residues processed: 134 average time/residue: 0.3862 time to fit residues: 59.4417 Evaluate side-chains 132 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.0020 chunk 70 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 64 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN B 64 ASN b 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120867 restraints weight = 10031.327| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.50 r_work: 0.3449 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6482 Z= 0.180 Angle : 0.822 9.761 8942 Z= 0.373 Chirality : 0.046 0.179 1060 Planarity : 0.006 0.064 1129 Dihedral : 12.657 87.122 1177 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.61 % Allowed : 30.14 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.39 (0.30), residues: 797 helix: -0.25 (0.41), residues: 165 sheet: -1.48 (0.68), residues: 68 loop : -1.10 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP b 123 HIS 0.003 0.001 HIS c 60 PHE 0.005 0.001 PHE X 55 TYR 0.035 0.002 TYR a 492 ARG 0.010 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 6) link_NAG-ASN : angle 2.24908 ( 18) link_BETA1-4 : bond 0.00377 ( 8) link_BETA1-4 : angle 2.67516 ( 24) hydrogen bonds : bond 0.05177 ( 149) hydrogen bonds : angle 5.83728 ( 351) SS BOND : bond 0.00283 ( 26) SS BOND : angle 1.30883 ( 52) covalent geometry : bond 0.00424 ( 6442) covalent geometry : angle 0.80221 ( 8848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7080 (t70) REVERT: E 36 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7816 (ptt90) REVERT: b 76 ARG cc_start: 0.8331 (tpt90) cc_final: 0.8109 (tmt170) REVERT: b 113 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7621 (mtp85) REVERT: b 138 LEU cc_start: -0.2574 (OUTLIER) cc_final: -0.3133 (tp) REVERT: X 62 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8166 (pt0) outliers start: 23 outliers final: 7 residues processed: 147 average time/residue: 0.3665 time to fit residues: 62.2158 Evaluate side-chains 138 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 62 GLN Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120930 restraints weight = 10180.542| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.53 r_work: 0.3447 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6482 Z= 0.160 Angle : 0.782 9.347 8942 Z= 0.353 Chirality : 0.045 0.206 1060 Planarity : 0.006 0.056 1129 Dihedral : 10.172 74.933 1176 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.49 % Allowed : 28.41 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.30), residues: 797 helix: 0.04 (0.41), residues: 165 sheet: -1.58 (0.66), residues: 68 loop : -1.04 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP b 123 HIS 0.002 0.001 HIS B 60 PHE 0.004 0.001 PHE a 491 TYR 0.029 0.002 TYR a 492 ARG 0.011 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 6) link_NAG-ASN : angle 2.30228 ( 18) link_BETA1-4 : bond 0.00322 ( 8) link_BETA1-4 : angle 2.65922 ( 24) hydrogen bonds : bond 0.04581 ( 149) hydrogen bonds : angle 5.43037 ( 351) SS BOND : bond 0.00249 ( 26) SS BOND : angle 1.26500 ( 52) covalent geometry : bond 0.00378 ( 6442) covalent geometry : angle 0.76068 ( 8848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 LEU cc_start: 0.8833 (tp) cc_final: 0.8533 (tp) REVERT: E 21 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7057 (t70) REVERT: E 95 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7856 (t) REVERT: B 17 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7653 (mtm180) REVERT: b 76 ARG cc_start: 0.8342 (tpt90) cc_final: 0.8131 (tmt170) REVERT: b 138 LEU cc_start: -0.2907 (OUTLIER) cc_final: -0.3417 (tp) REVERT: X 124 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.6942 (pp30) outliers start: 35 outliers final: 17 residues processed: 157 average time/residue: 0.3440 time to fit residues: 62.3792 Evaluate side-chains 144 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 46 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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 = 0.3776 r_free = 0.3776 target = 0.136914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120632 restraints weight = 10217.194| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.52 r_work: 0.3442 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6482 Z= 0.173 Angle : 0.786 9.730 8942 Z= 0.354 Chirality : 0.045 0.216 1060 Planarity : 0.006 0.053 1129 Dihedral : 9.146 66.586 1176 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.34 % Allowed : 29.20 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.28 (0.30), residues: 797 helix: -0.00 (0.41), residues: 165 sheet: -1.59 (0.66), residues: 68 loop : -1.05 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 123 HIS 0.002 0.001 HIS E 72 PHE 0.004 0.001 PHE c 28 TYR 0.027 0.002 TYR a 492 ARG 0.010 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 6) link_NAG-ASN : angle 2.32236 ( 18) link_BETA1-4 : bond 0.00298 ( 8) link_BETA1-4 : angle 2.57882 ( 24) hydrogen bonds : bond 0.04344 ( 149) hydrogen bonds : angle 5.34726 ( 351) SS BOND : bond 0.00268 ( 26) SS BOND : angle 1.27359 ( 52) covalent geometry : bond 0.00407 ( 6442) covalent geometry : angle 0.76546 ( 8848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7060 (t70) REVERT: E 95 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7863 (t) REVERT: b 21 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7947 (t-100) REVERT: b 76 ARG cc_start: 0.8332 (tpt90) cc_final: 0.8131 (tmt170) REVERT: b 113 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7455 (mtp85) REVERT: b 138 LEU cc_start: -0.3023 (OUTLIER) cc_final: -0.3567 (tp) REVERT: X 124 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.6854 (pp30) outliers start: 34 outliers final: 23 residues processed: 153 average time/residue: 0.3618 time to fit residues: 64.2560 Evaluate side-chains 151 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain b residue 21 TRP Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 chunk 67 optimal weight: 0.0570 chunk 27 optimal weight: 0.0270 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 0.0670 chunk 57 optimal weight: 0.4980 overall best weight: 0.1232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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 = 0.3814 r_free = 0.3814 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124308 restraints weight = 10171.205| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.46 r_work: 0.3485 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6482 Z= 0.111 Angle : 0.736 8.931 8942 Z= 0.334 Chirality : 0.042 0.227 1060 Planarity : 0.006 0.048 1129 Dihedral : 7.691 58.932 1176 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.40 % Allowed : 31.08 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.22 (0.29), residues: 797 helix: 0.32 (0.42), residues: 159 sheet: -1.57 (0.67), residues: 68 loop : -1.09 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP b 123 HIS 0.001 0.000 HIS X 105 PHE 0.004 0.001 PHE c 28 TYR 0.026 0.001 TYR a 492 ARG 0.011 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 6) link_NAG-ASN : angle 2.28769 ( 18) link_BETA1-4 : bond 0.00412 ( 8) link_BETA1-4 : angle 2.46206 ( 24) hydrogen bonds : bond 0.03618 ( 149) hydrogen bonds : angle 5.04336 ( 351) SS BOND : bond 0.00349 ( 26) SS BOND : angle 1.14311 ( 52) covalent geometry : bond 0.00257 ( 6442) covalent geometry : angle 0.71615 ( 8848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7037 (t70) REVERT: B 17 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7247 (mtm180) REVERT: b 109 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7211 (mm-30) REVERT: b 113 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7407 (mtp85) REVERT: b 138 LEU cc_start: -0.3194 (OUTLIER) cc_final: -0.3919 (tp) REVERT: X 124 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6848 (pp30) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 0.3822 time to fit residues: 64.1971 Evaluate side-chains 144 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120020 restraints weight = 10145.229| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.52 r_work: 0.3432 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6482 Z= 0.214 Angle : 0.798 9.352 8942 Z= 0.358 Chirality : 0.046 0.252 1060 Planarity : 0.006 0.049 1129 Dihedral : 7.401 59.005 1175 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.81 % Allowed : 29.51 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.31 (0.29), residues: 797 helix: 0.15 (0.41), residues: 159 sheet: -1.55 (0.67), residues: 68 loop : -1.13 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 123 HIS 0.003 0.001 HIS B 60 PHE 0.006 0.001 PHE C 28 TYR 0.027 0.002 TYR a 492 ARG 0.010 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 6) link_NAG-ASN : angle 2.31221 ( 18) link_BETA1-4 : bond 0.00273 ( 8) link_BETA1-4 : angle 2.40653 ( 24) hydrogen bonds : bond 0.04216 ( 149) hydrogen bonds : angle 5.22478 ( 351) SS BOND : bond 0.00310 ( 26) SS BOND : angle 1.32280 ( 52) covalent geometry : bond 0.00498 ( 6442) covalent geometry : angle 0.77846 ( 8848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6999 (t70) REVERT: E 95 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7835 (t) REVERT: B 109 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7813 (mt-10) REVERT: b 21 TRP cc_start: 0.8382 (OUTLIER) cc_final: 0.7911 (t-100) REVERT: b 138 LEU cc_start: -0.3166 (OUTLIER) cc_final: -0.3920 (tp) REVERT: X 124 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6812 (pp30) outliers start: 37 outliers final: 22 residues processed: 157 average time/residue: 0.3383 time to fit residues: 61.5106 Evaluate side-chains 156 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain b residue 21 TRP Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 0.0040 chunk 58 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 65 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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 = 0.3784 r_free = 0.3784 target = 0.137641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121336 restraints weight = 10105.308| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.53 r_work: 0.3454 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6482 Z= 0.145 Angle : 0.777 9.119 8942 Z= 0.348 Chirality : 0.044 0.256 1060 Planarity : 0.006 0.049 1129 Dihedral : 6.858 58.466 1175 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 5.34 % Allowed : 30.46 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.29 (0.30), residues: 797 helix: 0.12 (0.42), residues: 159 sheet: -1.48 (0.68), residues: 68 loop : -1.12 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP a 498 HIS 0.005 0.001 HIS B 139 PHE 0.005 0.001 PHE c 28 TYR 0.026 0.002 TYR a 492 ARG 0.010 0.000 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 6) link_NAG-ASN : angle 2.37562 ( 18) link_BETA1-4 : bond 0.00338 ( 8) link_BETA1-4 : angle 2.32945 ( 24) hydrogen bonds : bond 0.03938 ( 149) hydrogen bonds : angle 5.17547 ( 351) SS BOND : bond 0.00244 ( 26) SS BOND : angle 1.44175 ( 52) covalent geometry : bond 0.00346 ( 6442) covalent geometry : angle 0.75580 ( 8848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6964 (t70) REVERT: B 70 CYS cc_start: 0.7528 (t) cc_final: 0.7287 (t) REVERT: b 138 LEU cc_start: -0.3258 (OUTLIER) cc_final: -0.3893 (tp) REVERT: X 124 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6948 (pp30) outliers start: 34 outliers final: 24 residues processed: 153 average time/residue: 0.3363 time to fit residues: 59.8508 Evaluate side-chains 151 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 71 ARG Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 18 LEU Chi-restraints excluded: chain X residue 47 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 44 optimal weight: 0.0980 chunk 57 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.1980 chunk 8 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 0.0030 chunk 15 optimal weight: 1.9990 overall best weight: 0.0608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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 = 0.3828 r_free = 0.3828 target = 0.141041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124843 restraints weight = 10165.437| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.55 r_work: 0.3503 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6482 Z= 0.109 Angle : 0.738 8.764 8942 Z= 0.332 Chirality : 0.041 0.272 1060 Planarity : 0.006 0.048 1129 Dihedral : 6.083 56.328 1175 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.08 % Allowed : 30.46 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.30), residues: 797 helix: -0.01 (0.41), residues: 171 sheet: -1.76 (0.64), residues: 73 loop : -0.99 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 498 HIS 0.002 0.000 HIS B 139 PHE 0.004 0.001 PHE a 501 TYR 0.027 0.001 TYR a 492 ARG 0.010 0.000 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 6) link_NAG-ASN : angle 2.34200 ( 18) link_BETA1-4 : bond 0.00406 ( 8) link_BETA1-4 : angle 2.32565 ( 24) hydrogen bonds : bond 0.03345 ( 149) hydrogen bonds : angle 5.16095 ( 351) SS BOND : bond 0.00222 ( 26) SS BOND : angle 1.18433 ( 52) covalent geometry : bond 0.00252 ( 6442) covalent geometry : angle 0.71817 ( 8848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 LEU cc_start: 0.8712 (tp) cc_final: 0.8269 (tp) REVERT: E 21 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6612 (t70) REVERT: B 17 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7132 (mtm-85) REVERT: b 109 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7136 (mm-30) REVERT: b 138 LEU cc_start: -0.3252 (OUTLIER) cc_final: -0.3821 (tp) REVERT: X 124 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6799 (pp30) outliers start: 26 outliers final: 16 residues processed: 145 average time/residue: 0.3558 time to fit residues: 59.5696 Evaluate side-chains 143 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 16 MET Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.0670 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 44 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123039 restraints weight = 10208.413| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.52 r_work: 0.3477 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6482 Z= 0.139 Angle : 0.770 8.986 8942 Z= 0.344 Chirality : 0.044 0.302 1060 Planarity : 0.006 0.046 1129 Dihedral : 5.969 53.451 1175 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.77 % Allowed : 31.08 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -1.24 (0.30), residues: 797 helix: -0.05 (0.40), residues: 171 sheet: -1.56 (0.67), residues: 68 loop : -1.00 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP a 498 HIS 0.002 0.000 HIS B 60 PHE 0.004 0.001 PHE c 28 TYR 0.028 0.002 TYR a 492 ARG 0.010 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 6) link_NAG-ASN : angle 2.37291 ( 18) link_BETA1-4 : bond 0.00312 ( 8) link_BETA1-4 : angle 2.23913 ( 24) hydrogen bonds : bond 0.03608 ( 149) hydrogen bonds : angle 5.08936 ( 351) SS BOND : bond 0.00261 ( 26) SS BOND : angle 1.50716 ( 52) covalent geometry : bond 0.00332 ( 6442) covalent geometry : angle 0.74925 ( 8848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 113 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.8169 (tpp80) REVERT: C 72 LEU cc_start: 0.8823 (tp) cc_final: 0.8403 (tp) REVERT: E 21 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6861 (t70) REVERT: B 17 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7413 (mtm-85) REVERT: b 21 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.7857 (t-100) REVERT: b 100 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7472 (tpt170) REVERT: b 138 LEU cc_start: -0.3110 (OUTLIER) cc_final: -0.3707 (tp) REVERT: X 124 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.6886 (pp30) outliers start: 24 outliers final: 19 residues processed: 145 average time/residue: 0.3539 time to fit residues: 59.5095 Evaluate side-chains 148 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain b residue 21 TRP Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 4 CYS Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 60 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.4980 chunk 23 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 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 = 0.3817 r_free = 0.3817 target = 0.140286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124137 restraints weight = 10310.661| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.55 r_work: 0.3490 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6482 Z= 0.118 Angle : 0.755 8.998 8942 Z= 0.336 Chirality : 0.043 0.302 1060 Planarity : 0.005 0.045 1129 Dihedral : 5.613 47.670 1175 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.45 % Allowed : 31.08 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % 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: -1.17 (0.30), residues: 797 helix: 0.07 (0.41), residues: 171 sheet: -1.50 (0.68), residues: 68 loop : -0.99 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 498 HIS 0.001 0.000 HIS B 139 PHE 0.004 0.001 PHE a 491 TYR 0.030 0.001 TYR a 492 ARG 0.011 0.000 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 6) link_NAG-ASN : angle 2.40224 ( 18) link_BETA1-4 : bond 0.00359 ( 8) link_BETA1-4 : angle 2.23645 ( 24) hydrogen bonds : bond 0.03366 ( 149) hydrogen bonds : angle 5.04773 ( 351) SS BOND : bond 0.00232 ( 26) SS BOND : angle 1.38699 ( 52) covalent geometry : bond 0.00284 ( 6442) covalent geometry : angle 0.73468 ( 8848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 LEU cc_start: 0.8699 (tp) cc_final: 0.8250 (tp) REVERT: E 21 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6579 (t70) REVERT: b 138 LEU cc_start: -0.3324 (OUTLIER) cc_final: -0.3924 (tp) REVERT: X 124 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6735 (pp30) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.3627 time to fit residues: 58.9343 Evaluate side-chains 142 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 6 SER Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 91 LEU Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain b residue 138 LEU Chi-restraints excluded: chain X residue 14 GLU Chi-restraints excluded: chain X residue 15 THR Chi-restraints excluded: chain X residue 20 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 110 ARG Chi-restraints excluded: chain X residue 112 THR Chi-restraints excluded: chain X residue 124 GLN Chi-restraints excluded: chain X residue 146 LEU Chi-restraints excluded: chain a residue 485 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121663 restraints weight = 10480.278| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.57 r_work: 0.3450 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6482 Z= 0.181 Angle : 0.807 9.082 8942 Z= 0.361 Chirality : 0.047 0.330 1060 Planarity : 0.006 0.046 1129 Dihedral : 5.722 40.509 1175 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.71 % Allowed : 30.61 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.06 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.30), residues: 797 helix: 0.16 (0.41), residues: 165 sheet: -1.55 (0.67), residues: 68 loop : -1.09 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP a 498 HIS 0.002 0.001 HIS B 60 PHE 0.006 0.001 PHE a 491 TYR 0.031 0.002 TYR a 492 ARG 0.010 0.001 ARG C 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 6) link_NAG-ASN : angle 2.50258 ( 18) link_BETA1-4 : bond 0.00247 ( 8) link_BETA1-4 : angle 2.19438 ( 24) hydrogen bonds : bond 0.03867 ( 149) hydrogen bonds : angle 5.20351 ( 351) SS BOND : bond 0.00316 ( 26) SS BOND : angle 1.54779 ( 52) covalent geometry : bond 0.00426 ( 6442) covalent geometry : angle 0.78663 ( 8848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4006.57 seconds wall clock time: 69 minutes 40.59 seconds (4180.59 seconds total)