Starting phenix.real_space_refine on Wed Jan 15 15:14:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wfs_37498/01_2025/8wfs_37498.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wfs_37498/01_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_37498/01_2025/8wfs_37498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wfs_37498/01_2025/8wfs_37498.map" model { file = "/net/cci-nas-00/data/ceres_data/8wfs_37498/01_2025/8wfs_37498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wfs_37498/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.26, per 1000 atoms: 0.84 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: 1.74 Conformation dependent library (CDL) restraints added in 997.4 milliseconds 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: 0.70 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: 1.41 Time building geometry restraints manager: 2.01 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.160 Find NCS groups from input model: 0.240 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 6442 Z= 0.293 Angle : 0.866 13.057 8848 Z= 0.414 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 *********************** 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 : 0.685 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: 0.3954 time to fit residues: 60.6060 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 : 0.652 ------------------------------------------------------------------------------- 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 6442 Z= 0.278 Angle : 0.802 9.761 8848 Z= 0.367 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 *********************** 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 : 0.708 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: 0.3817 time to fit residues: 64.6150 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 : 0.645 ------------------------------------------------------------------------------- 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: 0.0010 chunk 4 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 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: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3769 r_free = 0.3769 target = 0.136473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120096 restraints weight = 10164.167| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.53 r_work: 0.3435 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 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 = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6442 Z= 0.283 Angle : 0.776 9.648 8848 Z= 0.354 Chirality : 0.046 0.198 1060 Planarity : 0.006 0.057 1129 Dihedral : 10.109 74.332 1176 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.97 % Allowed : 28.26 % Favored : 65.78 % 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: -1.27 (0.30), residues: 797 helix: -0.00 (0.41), residues: 165 sheet: -1.58 (0.67), residues: 68 loop : -1.05 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP b 123 HIS 0.003 0.001 HIS B 60 PHE 0.005 0.001 PHE a 491 TYR 0.028 0.002 TYR a 492 ARG 0.011 0.001 ARG C 89 *********************** 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: 38 poor density : 129 time to evaluate : 0.655 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: 0.8837 (tp) cc_final: 0.8544 (tp) REVERT: E 36 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7877 (ptt90) REVERT: E 95 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7865 (t) REVERT: b 138 LEU cc_start: -0.2881 (OUTLIER) cc_final: -0.3403 (tp) REVERT: X 124 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.6872 (pp30) outliers start: 38 outliers final: 20 residues processed: 155 average time/residue: 0.3605 time to fit residues: 64.8025 Evaluate side-chains 148 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 7 CYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain E residue 36 ARG 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 11 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 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: 0.2980 chunk 64 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 46 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 overall best weight: 0.3258 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.137591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.121183 restraints weight = 10211.696| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.55 r_work: 0.3448 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 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 = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6442 Z= 0.219 Angle : 0.750 9.257 8848 Z= 0.342 Chirality : 0.044 0.225 1060 Planarity : 0.006 0.052 1129 Dihedral : 8.888 64.369 1176 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.02 % Allowed : 29.67 % Favored : 65.31 % 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: -1.27 (0.30), residues: 797 helix: 0.05 (0.41), residues: 165 sheet: -1.58 (0.66), residues: 68 loop : -1.06 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 123 HIS 0.002 0.000 HIS B 60 PHE 0.003 0.001 PHE c 28 TYR 0.027 0.002 TYR a 492 ARG 0.009 0.001 ARG C 89 *********************** 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 164 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.696 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: 0.7463 (OUTLIER) cc_final: 0.7093 (t70) REVERT: E 95 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7859 (t) REVERT: b 21 TRP cc_start: 0.8391 (OUTLIER) cc_final: 0.7950 (t-100) REVERT: b 113 ARG cc_start: 0.7725 (mtp85) cc_final: 0.7456 (mtp85) REVERT: b 138 LEU cc_start: -0.2954 (OUTLIER) cc_final: -0.3491 (tp) REVERT: X 124 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6880 (pp30) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.3845 time to fit residues: 69.6491 Evaluate side-chains 148 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 chunk 75 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 chunk 67 optimal weight: 0.0770 chunk 27 optimal weight: 0.0870 chunk 45 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.1612 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.139474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123051 restraints weight = 10191.763| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.55 r_work: 0.3478 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 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 = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6442 Z= 0.177 Angle : 0.725 9.297 8848 Z= 0.331 Chirality : 0.042 0.224 1060 Planarity : 0.006 0.049 1129 Dihedral : 7.619 59.944 1176 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.40 % Allowed : 30.77 % Favored : 64.84 % 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: -1.21 (0.30), residues: 797 helix: 0.35 (0.42), residues: 159 sheet: -1.63 (0.66), residues: 68 loop : -1.08 (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 B 60 PHE 0.004 0.001 PHE c 28 TYR 0.026 0.001 TYR a 492 ARG 0.010 0.001 ARG C 89 *********************** 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 152 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7011 (t70) REVERT: B 17 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7482 (mtm-85) REVERT: B 72 LEU cc_start: 0.8727 (tt) cc_final: 0.8521 (tp) REVERT: B 109 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7800 (mt-10) REVERT: b 113 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7309 (mtp85) REVERT: b 138 LEU cc_start: -0.3179 (OUTLIER) cc_final: -0.3910 (tp) REVERT: X 124 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6854 (pp30) outliers start: 28 outliers final: 18 residues processed: 143 average time/residue: 0.3922 time to fit residues: 64.2895 Evaluate side-chains 143 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.3566 > 50: distance: 66 - 67: 6.518 distance: 66 - 69: 6.026 distance: 67 - 68: 5.420 distance: 67 - 75: 15.211 distance: 69 - 70: 3.094 distance: 73 - 74: 3.441 distance: 75 - 76: 13.190 distance: 76 - 77: 22.206 distance: 76 - 79: 16.341 distance: 77 - 78: 13.340 distance: 77 - 83: 16.519 distance: 79 - 80: 4.195 distance: 80 - 81: 15.915 distance: 83 - 84: 13.311 distance: 84 - 85: 15.109 distance: 85 - 86: 11.665 distance: 85 - 87: 9.285 distance: 87 - 88: 18.753 distance: 88 - 89: 13.774 distance: 88 - 91: 4.517 distance: 89 - 90: 11.655 distance: 89 - 92: 8.733 distance: 92 - 93: 17.298 distance: 93 - 94: 10.398 distance: 93 - 96: 10.783 distance: 94 - 95: 12.144 distance: 94 - 100: 13.013 distance: 96 - 97: 5.365 distance: 97 - 98: 8.107 distance: 100 - 101: 11.718 distance: 100 - 106: 12.540 distance: 101 - 102: 4.646 distance: 101 - 104: 16.356 distance: 102 - 103: 10.964 distance: 102 - 107: 6.840 distance: 104 - 105: 22.094 distance: 105 - 106: 17.318 distance: 107 - 108: 5.908 distance: 108 - 111: 3.423 distance: 109 - 110: 4.137 distance: 112 - 113: 4.612 distance: 114 - 116: 4.194 distance: 114 - 117: 4.365 distance: 115 - 116: 3.480 distance: 116 - 118: 4.575 distance: 117 - 119: 3.528 distance: 118 - 120: 5.277 distance: 119 - 120: 4.889 distance: 121 - 122: 6.587 distance: 122 - 123: 3.891 distance: 122 - 125: 7.541 distance: 123 - 124: 3.859 distance: 123 - 132: 4.480 distance: 125 - 126: 13.415 distance: 126 - 127: 11.108 distance: 127 - 128: 16.908 distance: 128 - 129: 13.563 distance: 129 - 130: 13.944 distance: 129 - 131: 15.591 distance: 132 - 133: 3.350 distance: 133 - 134: 7.180 distance: 133 - 136: 3.931 distance: 134 - 135: 4.693 distance: 134 - 138: 6.529 distance: 136 - 137: 5.901 distance: 137 - 182: 11.286 distance: 138 - 139: 15.102 distance: 139 - 140: 23.513 distance: 139 - 142: 16.732 distance: 140 - 141: 20.162 distance: 140 - 146: 11.579 distance: 142 - 143: 7.502 distance: 143 - 145: 18.625