Starting phenix.real_space_refine on Fri Nov 21 05:49:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nvf_49834/11_2025/9nvf_49834.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 14439 2.51 5 N 3721 2.21 5 O 4410 1.98 5 H 23629 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46251 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "B" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1814 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "C" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "D" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "E" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1814 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "F" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "G" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "H" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "I" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1677 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "K" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "L" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1655 Classifications: {'peptide': 104} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "M" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1613 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain: "W" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "X" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1677 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "Y" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "Z" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "a" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "b" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "c" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "d" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "e" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1814 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "f" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "g" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1815 Classifications: {'peptide': 114} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1655 Classifications: {'peptide': 104} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "i" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1677 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Time building chain proxies: 8.94, per 1000 atoms: 0.19 Number of scatterers: 46251 At special positions: 0 Unit cell: (128.75, 142.5, 153.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 4410 8.00 N 3721 7.00 C 14439 6.00 H 23629 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5414 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 54 sheets defined 8.2% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.605A pdb=" N ILE B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.667A pdb=" N ILE D 140 " --> pdb=" O GLU D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 68 removed outlier: 3.752A pdb=" N ILE E 68 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 136 through 140 removed outlier: 3.508A pdb=" N ILE F 140 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 116 through 120 Processing helix chain 'G' and resid 136 through 140 Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.799A pdb=" N ILE I 68 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 136 through 140 removed outlier: 3.503A pdb=" N ILE I 140 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 120 Processing helix chain 'K' and resid 64 through 68 removed outlier: 3.755A pdb=" N ILE K 68 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 120 Processing helix chain 'K' and resid 136 through 140 Processing helix chain 'L' and resid 116 through 120 removed outlier: 4.185A pdb=" N ALA L 120 " --> pdb=" O GLU L 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 120 Processing helix chain 'W' and resid 116 through 120 Processing helix chain 'X' and resid 116 through 120 Processing helix chain 'Y' and resid 116 through 120 Processing helix chain 'Y' and resid 136 through 140 removed outlier: 3.667A pdb=" N ILE Y 140 " --> pdb=" O GLU Y 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 66 No H-bonds generated for 'chain 'Z' and resid 64 through 66' Processing helix chain 'Z' and resid 116 through 120 Processing helix chain 'Z' and resid 136 through 140 Processing helix chain 'a' and resid 116 through 120 Processing helix chain 'a' and resid 136 through 140 Processing helix chain 'b' and resid 116 through 120 Processing helix chain 'b' and resid 136 through 140 removed outlier: 3.631A pdb=" N ILE b 140 " --> pdb=" O GLU b 137 " (cutoff:3.500A) Processing helix chain 'c' and resid 116 through 120 Processing helix chain 'd' and resid 64 through 68 Processing helix chain 'd' and resid 116 through 120 Processing helix chain 'd' and resid 124 through 126 No H-bonds generated for 'chain 'd' and resid 124 through 126' Processing helix chain 'd' and resid 136 through 140 Processing helix chain 'e' and resid 64 through 66 No H-bonds generated for 'chain 'e' and resid 64 through 66' Processing helix chain 'e' and resid 116 through 120 Processing helix chain 'f' and resid 64 through 68 Processing helix chain 'f' and resid 136 through 140 Processing helix chain 'g' and resid 116 through 120 Processing helix chain 'h' and resid 64 through 68 Processing helix chain 'h' and resid 116 through 120 Processing helix chain 'i' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.789A pdb=" N GLN A 36 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 125 removed outlier: 6.670A pdb=" N GLU A 49 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE W 94 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 96 removed outlier: 5.251A pdb=" N ILE A 94 " --> pdb=" O GLU W 49 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU W 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.274A pdb=" N GLU B 49 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE X 94 " --> pdb=" O GLU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 97 removed outlier: 5.253A pdb=" N ILE B 94 " --> pdb=" O GLU X 49 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU X 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 96 " --> pdb=" O ILE X 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 125 removed outlier: 4.312A pdb=" N HIS C 53 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 45 " --> pdb=" O SER Y 97 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER Y 97 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 47 " --> pdb=" O ILE Y 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 93 through 97 removed outlier: 5.369A pdb=" N ILE C 94 " --> pdb=" O GLU Y 49 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU Y 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 96 " --> pdb=" O ILE Y 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.815A pdb=" N GLN D 36 " --> pdb=" O LYS D 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 125 removed outlier: 3.568A pdb=" N TYR Z 96 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D 49 " --> pdb=" O ILE Z 94 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE Z 94 " --> pdb=" O GLU D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 97 removed outlier: 5.642A pdb=" N ILE D 94 " --> pdb=" O GLU Z 49 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU Z 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.890A pdb=" N GLN Y 36 " --> pdb=" O LYS Y 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 36 through 40 removed outlier: 3.798A pdb=" N GLN E 36 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.549A pdb=" N GLU E 49 " --> pdb=" O ILE a 94 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE a 94 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.642A pdb=" N ILE E 94 " --> pdb=" O GLU a 49 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU a 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 36 through 40 removed outlier: 3.841A pdb=" N GLN F 36 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.615A pdb=" N GLU F 49 " --> pdb=" O ILE b 94 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE b 94 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 93 through 97 removed outlier: 6.558A pdb=" N ILE b 47 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N SER F 97 " --> pdb=" O ILE b 45 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE b 45 " --> pdb=" O SER F 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 142 through 143 removed outlier: 3.579A pdb=" N LYS F 142 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN G 36 " --> pdb=" O LYS G 110 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 121 through 125 removed outlier: 7.112A pdb=" N ILE G 45 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER c 97 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE G 47 " --> pdb=" O ILE c 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE c 95 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 93 through 97 removed outlier: 5.561A pdb=" N ILE G 94 " --> pdb=" O GLU c 49 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU c 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 96 " --> pdb=" O ILE c 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 142 through 143 removed outlier: 4.055A pdb=" N GLN d 36 " --> pdb=" O LYS d 110 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 38 removed outlier: 3.580A pdb=" N GLN H 36 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 121 through 124 removed outlier: 5.835A pdb=" N GLU H 49 " --> pdb=" O ILE d 94 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE d 94 " --> pdb=" O GLU H 49 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 93 through 97 removed outlier: 5.341A pdb=" N ILE H 94 " --> pdb=" O GLU d 49 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLU d 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 36 through 40 removed outlier: 3.865A pdb=" N GLN I 36 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.970A pdb=" N GLU I 49 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE e 94 " --> pdb=" O GLU I 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 92 through 97 removed outlier: 5.595A pdb=" N ILE I 94 " --> pdb=" O GLU e 49 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU e 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS e 53 " --> pdb=" O GLY e 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 36 through 40 removed outlier: 3.688A pdb=" N GLN J 36 " --> pdb=" O LYS J 110 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR J 106 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 121 through 125 removed outlier: 6.436A pdb=" N GLU J 49 " --> pdb=" O ILE f 94 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE f 94 " --> pdb=" O GLU J 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 93 through 94 removed outlier: 3.836A pdb=" N ILE f 57 " --> pdb=" O SER f 46 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE f 48 " --> pdb=" O LYS f 55 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LYS f 55 " --> pdb=" O ILE f 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 37 through 40 Processing sheet with id=AD7, first strand: chain 'K' and resid 121 through 125 removed outlier: 6.831A pdb=" N GLU K 49 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE g 94 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 92 through 97 removed outlier: 5.523A pdb=" N ILE K 94 " --> pdb=" O GLU g 49 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU g 49 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS g 53 " --> pdb=" O GLY g 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.906A pdb=" N SER L 38 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 106 " --> pdb=" O LYS L 40 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 121 through 125 removed outlier: 3.863A pdb=" N TYR h 96 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU L 49 " --> pdb=" O ILE h 94 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE h 94 " --> pdb=" O GLU L 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 92 through 96 removed outlier: 3.866A pdb=" N ILE L 95 " --> pdb=" O ILE h 47 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE h 47 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS h 53 " --> pdb=" O GLY h 50 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 92 through 96 removed outlier: 3.866A pdb=" N ILE L 95 " --> pdb=" O ILE h 47 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE h 47 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS h 53 " --> pdb=" O GLY h 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 121 through 125 removed outlier: 6.339A pdb=" N GLU M 49 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE i 94 " --> pdb=" O GLU M 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 69 through 73 Processing sheet with id=AE6, first strand: chain 'M' and resid 93 through 97 removed outlier: 5.571A pdb=" N ILE M 94 " --> pdb=" O GLU i 49 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU i 49 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR M 96 " --> pdb=" O ILE i 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 37 through 38 Processing sheet with id=AE8, first strand: chain 'W' and resid 142 through 143 removed outlier: 3.891A pdb=" N GLN Z 36 " --> pdb=" O LYS Z 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 37 through 40 Processing sheet with id=AF1, first strand: chain 'Y' and resid 142 through 143 removed outlier: 3.530A pdb=" N LYS Y 142 " --> pdb=" O ALA b 72 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN b 36 " --> pdb=" O LYS b 110 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 142 through 143 removed outlier: 3.530A pdb=" N LYS Y 142 " --> pdb=" O ALA b 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 36 through 40 removed outlier: 3.827A pdb=" N GLN a 36 " --> pdb=" O LYS a 110 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU a 78 " --> pdb=" O ASN a 71 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN a 71 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 142 through 143 removed outlier: 3.913A pdb=" N GLN c 36 " --> pdb=" O LYS c 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 36 through 40 Processing sheet with id=AF6, first strand: chain 'f' and resid 36 through 38 removed outlier: 3.933A pdb=" N GLN f 36 " --> pdb=" O LYS f 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS f 110 " --> pdb=" O GLN f 36 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER f 38 " --> pdb=" O THR f 108 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR f 108 " --> pdb=" O SER f 38 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE f 109 " --> pdb=" O LEU f 77 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU f 77 " --> pdb=" O ILE f 109 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 142 through 143 Processing sheet with id=AF8, first strand: chain 'h' and resid 37 through 40 Processing sheet with id=AF9, first strand: chain 'i' and resid 37 through 40 974 hydrogen bonds defined for protein. 2355 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: 13.61 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 23629 1.00 - 1.20: 0 1.20 - 1.40: 8412 1.40 - 1.60: 14418 1.60 - 1.81: 104 Bond restraints: 46563 Sorted by residual: bond pdb=" N ASP B 51 " pdb=" H ASP B 51 " ideal model delta sigma weight residual 0.860 0.954 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C ARG J 93 " pdb=" N ILE J 94 " ideal model delta sigma weight residual 1.335 1.378 -0.044 1.22e-02 6.72e+03 1.28e+01 bond pdb=" N ILE b 79 " pdb=" CA ILE b 79 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" C GLU J 92 " pdb=" N ARG J 93 " ideal model delta sigma weight residual 1.331 1.372 -0.041 1.38e-02 5.25e+03 8.77e+00 bond pdb=" ND2 ASN B 145 " pdb="HD22 ASN B 145 " ideal model delta sigma weight residual 0.860 0.802 0.058 2.00e-02 2.50e+03 8.52e+00 ... (remaining 46558 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 85257 3.53 - 7.07: 39 7.07 - 10.60: 3 10.60 - 14.13: 1 14.13 - 17.67: 5 Bond angle restraints: 85305 Sorted by residual: angle pdb=" C ASN W 71 " pdb=" CA ASN W 71 " pdb=" CB ASN W 71 " ideal model delta sigma weight residual 110.79 93.12 17.67 1.39e+00 5.18e-01 1.62e+02 angle pdb=" N ASN W 71 " pdb=" CA ASN W 71 " pdb=" C ASN W 71 " ideal model delta sigma weight residual 107.61 123.64 -16.03 1.74e+00 3.30e-01 8.49e+01 angle pdb=" N ASP B 51 " pdb=" CA ASP B 51 " pdb=" C ASP B 51 " ideal model delta sigma weight residual 112.45 102.50 9.95 1.39e+00 5.18e-01 5.12e+01 angle pdb=" CA ALA b 81 " pdb=" C ALA b 81 " pdb=" O ALA b 81 " ideal model delta sigma weight residual 121.26 114.40 6.86 1.12e+00 7.97e-01 3.75e+01 angle pdb=" CA ARG W 80 " pdb=" C ARG W 80 " pdb=" O ARG W 80 " ideal model delta sigma weight residual 121.40 115.28 6.12 1.13e+00 7.83e-01 2.93e+01 ... (remaining 85300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19713 17.91 - 35.81: 1233 35.81 - 53.72: 292 53.72 - 71.62: 110 71.62 - 89.53: 53 Dihedral angle restraints: 21401 sinusoidal: 12351 harmonic: 9050 Sorted by residual: dihedral pdb=" CD ARG J 93 " pdb=" NE ARG J 93 " pdb=" CZ ARG J 93 " pdb=" NH1 ARG J 93 " ideal model delta sinusoidal sigma weight residual 0.00 61.38 -61.38 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" C ASN W 71 " pdb=" N ASN W 71 " pdb=" CA ASN W 71 " pdb=" CB ASN W 71 " ideal model delta harmonic sigma weight residual -122.60 -109.18 -13.42 0 2.50e+00 1.60e-01 2.88e+01 dihedral pdb=" CA ASN W 71 " pdb=" C ASN W 71 " pdb=" N ALA W 72 " pdb=" CA ALA W 72 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 21398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2944 0.054 - 0.108: 385 0.108 - 0.162: 317 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 3649 Sorted by residual: chirality pdb=" CA ILE W 79 " pdb=" N ILE W 79 " pdb=" C ILE W 79 " pdb=" CB ILE W 79 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE b 69 " pdb=" N ILE b 69 " pdb=" C ILE b 69 " pdb=" CB ILE b 69 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASP e 75 " pdb=" N ASP e 75 " pdb=" C ASP e 75 " pdb=" CB ASP e 75 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 3646 not shown) Planarity restraints: 6678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 80 " 0.134 9.50e-02 1.11e+02 3.15e-01 2.18e+03 pdb=" NE ARG b 80 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG b 80 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG b 80 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG b 80 " 0.065 2.00e-02 2.50e+03 pdb="HH11 ARG b 80 " 0.463 2.00e-02 2.50e+03 pdb="HH12 ARG b 80 " -0.601 2.00e-02 2.50e+03 pdb="HH21 ARG b 80 " -0.291 2.00e-02 2.50e+03 pdb="HH22 ARG b 80 " 0.452 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 80 " -0.019 9.50e-02 1.11e+02 2.97e-01 1.98e+03 pdb=" NE ARG W 80 " -0.104 2.00e-02 2.50e+03 pdb=" CZ ARG W 80 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG W 80 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG W 80 " 0.059 2.00e-02 2.50e+03 pdb="HH11 ARG W 80 " 0.553 2.00e-02 2.50e+03 pdb="HH12 ARG W 80 " -0.618 2.00e-02 2.50e+03 pdb="HH21 ARG W 80 " -0.112 2.00e-02 2.50e+03 pdb="HH22 ARG W 80 " 0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 93 " -1.172 9.50e-02 1.11e+02 4.20e-01 6.87e+02 pdb=" NE ARG J 93 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG J 93 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG J 93 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 93 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG J 93 " 0.305 2.00e-02 2.50e+03 pdb="HH12 ARG J 93 " -0.319 2.00e-02 2.50e+03 pdb="HH21 ARG J 93 " -0.008 2.00e-02 2.50e+03 pdb="HH22 ARG J 93 " 0.115 2.00e-02 2.50e+03 ... (remaining 6675 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1286 2.16 - 2.77: 94117 2.77 - 3.38: 125844 3.38 - 3.99: 166689 3.99 - 4.60: 254726 Nonbonded interactions: 642662 Sorted by model distance: nonbonded pdb=" OE1 GLU Y 117 " pdb=" H GLU Y 117 " model vdw 1.548 2.450 nonbonded pdb=" OE1 GLU d 118 " pdb=" H GLU d 118 " model vdw 1.550 2.450 nonbonded pdb=" OE1 GLU A 118 " pdb=" H GLU A 118 " model vdw 1.552 2.450 nonbonded pdb=" OE1 GLU K 117 " pdb=" H GLU K 117 " model vdw 1.567 2.450 nonbonded pdb=" OE1 GLU c 102 " pdb=" H GLU c 102 " model vdw 1.569 2.450 ... (remaining 642657 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' and resid 38 through 137) selection = (chain 'B' and resid 38 through 137) selection = (chain 'C' and resid 38 through 137) selection = (chain 'D' and resid 38 through 137) selection = (chain 'E' and resid 38 through 137) selection = (chain 'F' and resid 38 through 137) selection = (chain 'G' and resid 38 through 137) selection = (chain 'H' and resid 38 through 137) selection = (chain 'I' and resid 38 through 137) selection = (chain 'J' and resid 38 through 137) selection = (chain 'K' and resid 38 through 137) selection = (chain 'L' and resid 38 through 137) selection = (chain 'M' and resid 38 through 137) selection = (chain 'W' and resid 38 through 137) selection = (chain 'X' and resid 38 through 137) selection = (chain 'Y' and resid 38 through 137) selection = (chain 'Z' and resid 38 through 137) selection = (chain 'a' and resid 38 through 137) selection = (chain 'b' and resid 38 through 137) selection = (chain 'c' and resid 38 through 137) selection = (chain 'd' and resid 38 through 137) selection = (chain 'e' and resid 38 through 137) selection = (chain 'f' and resid 38 through 137) selection = (chain 'g' and resid 38 through 137) selection = (chain 'h' and resid 38 through 137) selection = (chain 'i' and resid 38 through 137) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.320 Extract box with map and model: 0.630 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 46.610 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 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 : 0.003 0.044 22934 Z= 0.148 Angle : 0.464 17.667 30951 Z= 0.255 Chirality : 0.052 0.271 3649 Planarity : 0.008 0.434 3952 Dihedral : 9.737 81.960 8962 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 1.39 (0.14), residues: 1262 loop : 0.09 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 80 TYR 0.007 0.001 TYR X 106 PHE 0.005 0.001 PHE W 124 TRP 0.003 0.001 TRP K 59 HIS 0.002 0.001 HIS W 53 Details of bonding type rmsd covalent geometry : bond 0.00291 (22934) covalent geometry : angle 0.46361 (30951) hydrogen bonds : bond 0.24262 ( 960) hydrogen bonds : angle 10.11660 ( 2355) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.8703 (ptm) cc_final: 0.8380 (ppp) REVERT: E 90 GLU cc_start: 0.9379 (mp0) cc_final: 0.9131 (pm20) REVERT: G 110 LYS cc_start: 0.9655 (tttt) cc_final: 0.9305 (tptp) REVERT: H 77 LEU cc_start: 0.9671 (tp) cc_final: 0.9301 (mt) REVERT: I 51 ASP cc_start: 0.9278 (m-30) cc_final: 0.9046 (p0) REVERT: K 87 MET cc_start: 0.8597 (mmm) cc_final: 0.8321 (mmt) REVERT: W 49 GLU cc_start: 0.8982 (tt0) cc_final: 0.8780 (tm-30) REVERT: W 87 MET cc_start: 0.8967 (ptm) cc_final: 0.8321 (ppp) REVERT: Z 43 MET cc_start: 0.8916 (ttm) cc_final: 0.8639 (ttp) REVERT: b 49 GLU cc_start: 0.8284 (tt0) cc_final: 0.8020 (tt0) REVERT: b 75 ASP cc_start: 0.9210 (p0) cc_final: 0.8420 (p0) REVERT: b 110 LYS cc_start: 0.9446 (tttt) cc_final: 0.9098 (tppt) REVERT: c 49 GLU cc_start: 0.8629 (tt0) cc_final: 0.8158 (tm-30) REVERT: e 63 VAL cc_start: 0.9080 (t) cc_final: 0.8803 (p) REVERT: e 79 ILE cc_start: 0.9354 (mt) cc_final: 0.9016 (mm) REVERT: f 83 ARG cc_start: 0.8931 (ptp90) cc_final: 0.8496 (ptm-80) REVERT: h 75 ASP cc_start: 0.9197 (p0) cc_final: 0.8885 (t70) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5246 time to fit residues: 230.0108 Evaluate side-chains 194 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 145 ASN a 36 GLN h 71 ASN h 119 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.097518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062090 restraints weight = 316602.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064433 restraints weight = 122028.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.065866 restraints weight = 69288.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066710 restraints weight = 49096.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067136 restraints weight = 40160.794| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22934 Z= 0.203 Angle : 0.581 6.474 30951 Z= 0.308 Chirality : 0.054 0.197 3649 Planarity : 0.004 0.087 3952 Dihedral : 5.602 85.273 3055 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.67 % Allowed : 8.24 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.84 (0.13), residues: 1334 loop : 0.04 (0.17), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 93 TYR 0.018 0.001 TYR X 96 PHE 0.007 0.001 PHE c 42 TRP 0.006 0.001 TRP I 59 HIS 0.004 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00422 (22934) covalent geometry : angle 0.58111 (30951) hydrogen bonds : bond 0.04645 ( 960) hydrogen bonds : angle 7.38610 ( 2355) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8969 (tp) REVERT: G 110 LYS cc_start: 0.9654 (tttt) cc_final: 0.9344 (tptp) REVERT: H 49 GLU cc_start: 0.9670 (tt0) cc_final: 0.9430 (tt0) REVERT: H 77 LEU cc_start: 0.9729 (tp) cc_final: 0.9366 (mt) REVERT: I 43 MET cc_start: 0.8617 (ttm) cc_final: 0.8373 (ttm) REVERT: K 87 MET cc_start: 0.8524 (mmm) cc_final: 0.7838 (tmm) REVERT: W 49 GLU cc_start: 0.8951 (tt0) cc_final: 0.8732 (pp20) REVERT: W 87 MET cc_start: 0.8856 (ptm) cc_final: 0.8399 (ppp) REVERT: X 93 ARG cc_start: 0.7604 (mtm-85) cc_final: 0.7383 (ptp90) REVERT: Y 49 GLU cc_start: 0.8490 (tt0) cc_final: 0.8148 (tm-30) REVERT: Z 43 MET cc_start: 0.9135 (ttm) cc_final: 0.8911 (ttp) REVERT: b 75 ASP cc_start: 0.9163 (p0) cc_final: 0.8361 (p0) REVERT: b 110 LYS cc_start: 0.9432 (tttt) cc_final: 0.9143 (tppt) REVERT: c 49 GLU cc_start: 0.8508 (tt0) cc_final: 0.8138 (tm-30) REVERT: e 63 VAL cc_start: 0.9116 (t) cc_final: 0.8794 (p) REVERT: f 83 ARG cc_start: 0.8761 (ptp90) cc_final: 0.8301 (ptm-80) REVERT: h 75 ASP cc_start: 0.9127 (p0) cc_final: 0.8906 (t0) outliers start: 17 outliers final: 12 residues processed: 205 average time/residue: 0.5090 time to fit residues: 147.4710 Evaluate side-chains 187 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 67 ASP Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 48 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 243 optimal weight: 0.3980 chunk 188 optimal weight: 20.0000 chunk 159 optimal weight: 30.0000 chunk 50 optimal weight: 8.9990 chunk 272 optimal weight: 50.0000 chunk 26 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 20.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.097825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062404 restraints weight = 312883.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.064689 restraints weight = 120267.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066103 restraints weight = 68791.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.066955 restraints weight = 49089.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067402 restraints weight = 40237.645| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 22934 Z= 0.147 Angle : 0.518 6.955 30951 Z= 0.268 Chirality : 0.053 0.186 3649 Planarity : 0.003 0.032 3952 Dihedral : 5.505 89.952 3055 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 0.51 % Allowed : 9.47 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.74 (0.14), residues: 1330 loop : 0.04 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 107 TYR 0.010 0.001 TYR X 96 PHE 0.006 0.001 PHE c 42 TRP 0.005 0.001 TRP g 59 HIS 0.004 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00319 (22934) covalent geometry : angle 0.51788 (30951) hydrogen bonds : bond 0.03876 ( 960) hydrogen bonds : angle 6.66721 ( 2355) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 110 LYS cc_start: 0.9634 (tttt) cc_final: 0.9343 (tptp) REVERT: H 77 LEU cc_start: 0.9748 (tp) cc_final: 0.9394 (mt) REVERT: K 87 MET cc_start: 0.8505 (mmm) cc_final: 0.7816 (tmm) REVERT: L 107 ARG cc_start: 0.5751 (mmt-90) cc_final: 0.5433 (tpp-160) REVERT: W 49 GLU cc_start: 0.8923 (tt0) cc_final: 0.8712 (pp20) REVERT: W 87 MET cc_start: 0.8861 (ptm) cc_final: 0.8428 (ppp) REVERT: Y 49 GLU cc_start: 0.8566 (tt0) cc_final: 0.8106 (tm-30) REVERT: b 75 ASP cc_start: 0.9117 (p0) cc_final: 0.8504 (p0) REVERT: c 49 GLU cc_start: 0.8535 (tt0) cc_final: 0.8193 (tm-30) REVERT: e 63 VAL cc_start: 0.9117 (t) cc_final: 0.8764 (p) REVERT: e 87 MET cc_start: 0.8417 (pmm) cc_final: 0.8013 (pmm) REVERT: f 83 ARG cc_start: 0.8783 (ptp90) cc_final: 0.8317 (ptm-80) REVERT: h 75 ASP cc_start: 0.9182 (p0) cc_final: 0.8961 (t0) outliers start: 13 outliers final: 12 residues processed: 192 average time/residue: 0.4690 time to fit residues: 128.7314 Evaluate side-chains 181 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 114 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 241 optimal weight: 8.9990 chunk 269 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 126 ASN f 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.094949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.055861 restraints weight = 311067.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.058047 restraints weight = 118509.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059283 restraints weight = 68517.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059951 restraints weight = 49600.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060269 restraints weight = 41659.172| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22934 Z= 0.184 Angle : 0.514 6.630 30951 Z= 0.265 Chirality : 0.053 0.178 3649 Planarity : 0.004 0.052 3952 Dihedral : 5.460 89.549 3055 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 0.83 % Allowed : 9.90 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.56 (0.14), residues: 1335 loop : -0.07 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 93 TYR 0.012 0.001 TYR Z 96 PHE 0.008 0.001 PHE c 42 TRP 0.004 0.001 TRP G 59 HIS 0.003 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00393 (22934) covalent geometry : angle 0.51356 (30951) hydrogen bonds : bond 0.03357 ( 960) hydrogen bonds : angle 6.31368 ( 2355) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 87 MET cc_start: 0.8256 (pmm) cc_final: 0.7874 (ppp) REVERT: G 110 LYS cc_start: 0.9617 (tttt) cc_final: 0.9346 (tptp) REVERT: H 77 LEU cc_start: 0.9722 (tp) cc_final: 0.9351 (mt) REVERT: K 87 MET cc_start: 0.8554 (mmm) cc_final: 0.8025 (tmm) REVERT: L 107 ARG cc_start: 0.5891 (mmt-90) cc_final: 0.5680 (tpp-160) REVERT: M 43 MET cc_start: 0.0539 (mtp) cc_final: 0.0207 (mtp) REVERT: W 49 GLU cc_start: 0.8933 (tt0) cc_final: 0.8719 (pp20) REVERT: W 87 MET cc_start: 0.8857 (ptm) cc_final: 0.8457 (ppp) REVERT: Y 49 GLU cc_start: 0.8549 (tt0) cc_final: 0.8167 (tm-30) REVERT: b 110 LYS cc_start: 0.9437 (tttt) cc_final: 0.9220 (tppt) REVERT: e 63 VAL cc_start: 0.9156 (t) cc_final: 0.8791 (p) REVERT: f 83 ARG cc_start: 0.8863 (ptp90) cc_final: 0.8448 (ptm-80) REVERT: h 75 ASP cc_start: 0.9257 (p0) cc_final: 0.9035 (t70) outliers start: 21 outliers final: 16 residues processed: 181 average time/residue: 0.4193 time to fit residues: 109.6368 Evaluate side-chains 180 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 59 TRP Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 132 optimal weight: 0.3980 chunk 184 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 123 optimal weight: 50.0000 chunk 163 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 50.0000 chunk 23 optimal weight: 1.9990 chunk 122 optimal weight: 50.0000 chunk 129 optimal weight: 40.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.095031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.055986 restraints weight = 311348.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.058188 restraints weight = 118576.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059407 restraints weight = 68147.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.060032 restraints weight = 49529.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060389 restraints weight = 42019.990| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22934 Z= 0.154 Angle : 0.495 8.024 30951 Z= 0.253 Chirality : 0.053 0.175 3649 Planarity : 0.004 0.036 3952 Dihedral : 5.302 88.590 3055 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 0.75 % Allowed : 10.46 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.53 (0.14), residues: 1337 loop : -0.02 (0.17), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.011 0.001 TYR Z 96 PHE 0.006 0.001 PHE B 124 TRP 0.004 0.001 TRP Y 59 HIS 0.003 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00331 (22934) covalent geometry : angle 0.49471 (30951) hydrogen bonds : bond 0.03098 ( 960) hydrogen bonds : angle 6.00789 ( 2355) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7672 (ppp) cc_final: 0.7427 (tmm) REVERT: G 87 MET cc_start: 0.8227 (pmm) cc_final: 0.7874 (ppp) REVERT: G 110 LYS cc_start: 0.9597 (tttt) cc_final: 0.9350 (tptp) REVERT: H 77 LEU cc_start: 0.9720 (tp) cc_final: 0.9358 (mt) REVERT: K 87 MET cc_start: 0.8534 (mmm) cc_final: 0.7946 (tmm) REVERT: M 43 MET cc_start: 0.1057 (mtp) cc_final: 0.0689 (mtp) REVERT: W 49 GLU cc_start: 0.8910 (tt0) cc_final: 0.8681 (pp20) REVERT: W 87 MET cc_start: 0.8863 (ptm) cc_final: 0.8574 (ppp) REVERT: Y 49 GLU cc_start: 0.8548 (tt0) cc_final: 0.8175 (tm-30) REVERT: Y 101 GLU cc_start: 0.7580 (tp30) cc_final: 0.7368 (tp30) REVERT: b 110 LYS cc_start: 0.9436 (tttt) cc_final: 0.9210 (tppt) REVERT: e 63 VAL cc_start: 0.9152 (t) cc_final: 0.8765 (p) REVERT: f 83 ARG cc_start: 0.8883 (ptp90) cc_final: 0.8536 (ptm-80) REVERT: h 75 ASP cc_start: 0.9246 (p0) cc_final: 0.9037 (t70) outliers start: 19 outliers final: 15 residues processed: 176 average time/residue: 0.4183 time to fit residues: 107.5810 Evaluate side-chains 177 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 59 TRP Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 159 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 chunk 144 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 264 optimal weight: 50.0000 chunk 115 optimal weight: 8.9990 chunk 221 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.094657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057438 restraints weight = 319668.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.059596 restraints weight = 153295.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.059499 restraints weight = 84184.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059696 restraints weight = 74936.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059726 restraints weight = 68629.445| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22934 Z= 0.232 Angle : 0.520 7.564 30951 Z= 0.268 Chirality : 0.052 0.171 3649 Planarity : 0.004 0.032 3952 Dihedral : 5.381 87.652 3055 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 0.87 % Allowed : 11.13 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.63 (0.14), residues: 1204 loop : -0.20 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.014 0.001 TYR Z 96 PHE 0.009 0.001 PHE W 124 TRP 0.005 0.001 TRP K 59 HIS 0.004 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00497 (22934) covalent geometry : angle 0.51956 (30951) hydrogen bonds : bond 0.03204 ( 960) hydrogen bonds : angle 5.99504 ( 2355) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 MET cc_start: 0.8382 (mmm) cc_final: 0.8082 (tmm) REVERT: M 43 MET cc_start: 0.0416 (mtp) cc_final: 0.0161 (mtp) REVERT: W 87 MET cc_start: 0.8832 (ptm) cc_final: 0.8552 (ppp) REVERT: Y 49 GLU cc_start: 0.8279 (tt0) cc_final: 0.8055 (tm-30) REVERT: e 63 VAL cc_start: 0.9168 (t) cc_final: 0.8737 (p) REVERT: f 83 ARG cc_start: 0.8882 (ptp90) cc_final: 0.8558 (ptm-80) REVERT: g 82 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (pttp) REVERT: h 75 ASP cc_start: 0.9230 (p0) cc_final: 0.8975 (t70) outliers start: 22 outliers final: 18 residues processed: 173 average time/residue: 0.3979 time to fit residues: 99.5146 Evaluate side-chains 170 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 59 TRP Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 82 LYS Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 193 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.094831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057777 restraints weight = 323468.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.059908 restraints weight = 150496.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.060100 restraints weight = 78743.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060232 restraints weight = 74273.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.060254 restraints weight = 68784.181| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22934 Z= 0.194 Angle : 0.509 7.123 30951 Z= 0.261 Chirality : 0.052 0.168 3649 Planarity : 0.004 0.035 3952 Dihedral : 5.311 86.939 3055 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 0.95 % Allowed : 11.60 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.58 (0.14), residues: 1283 loop : -0.17 (0.17), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 83 TYR 0.013 0.001 TYR Z 96 PHE 0.008 0.001 PHE L 42 TRP 0.004 0.001 TRP D 59 HIS 0.006 0.001 HIS h 53 Details of bonding type rmsd covalent geometry : bond 0.00414 (22934) covalent geometry : angle 0.50880 (30951) hydrogen bonds : bond 0.03073 ( 960) hydrogen bonds : angle 5.90727 ( 2355) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 MET cc_start: 0.8368 (mmm) cc_final: 0.8101 (tmm) REVERT: M 43 MET cc_start: 0.0361 (mtp) cc_final: 0.0157 (mtp) REVERT: W 87 MET cc_start: 0.8843 (ptm) cc_final: 0.8567 (ppp) REVERT: c 80 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: e 63 VAL cc_start: 0.9175 (t) cc_final: 0.8738 (p) REVERT: f 83 ARG cc_start: 0.8885 (ptp90) cc_final: 0.8585 (ptm-80) REVERT: h 75 ASP cc_start: 0.9222 (p0) cc_final: 0.8969 (t70) outliers start: 24 outliers final: 20 residues processed: 174 average time/residue: 0.3587 time to fit residues: 91.1198 Evaluate side-chains 176 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 59 TRP Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain c residue 80 ARG Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 204 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 138 optimal weight: 50.0000 chunk 243 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.098308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063644 restraints weight = 321350.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066450 restraints weight = 159323.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066741 restraints weight = 80882.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066969 restraints weight = 75853.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.067141 restraints weight = 70539.245| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22934 Z= 0.090 Angle : 0.483 7.384 30951 Z= 0.243 Chirality : 0.054 0.166 3649 Planarity : 0.004 0.035 3952 Dihedral : 5.018 85.496 3055 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.71 % Favored : 96.25 % Rotamer: Outliers : 0.79 % Allowed : 11.80 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.71 (0.14), residues: 1292 loop : 0.06 (0.17), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 93 TYR 0.008 0.001 TYR Z 96 PHE 0.006 0.001 PHE B 124 TRP 0.003 0.000 TRP G 59 HIS 0.002 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00200 (22934) covalent geometry : angle 0.48334 (30951) hydrogen bonds : bond 0.02722 ( 960) hydrogen bonds : angle 5.63459 ( 2355) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 MET cc_start: 0.8338 (mmm) cc_final: 0.7984 (tmm) REVERT: W 87 MET cc_start: 0.8962 (ptm) cc_final: 0.8702 (ppp) REVERT: c 80 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: e 63 VAL cc_start: 0.9082 (t) cc_final: 0.8621 (p) REVERT: f 83 ARG cc_start: 0.8874 (ptp90) cc_final: 0.8522 (ptm-80) REVERT: h 75 ASP cc_start: 0.9199 (p0) cc_final: 0.8980 (t70) REVERT: i 43 MET cc_start: -0.3332 (mtp) cc_final: -0.3595 (mtp) outliers start: 20 outliers final: 17 residues processed: 169 average time/residue: 0.3549 time to fit residues: 86.3816 Evaluate side-chains 174 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain c residue 80 ARG Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain f residue 133 LEU Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 120 optimal weight: 50.0000 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.093959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.055068 restraints weight = 327447.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.056935 restraints weight = 141738.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.058087 restraints weight = 85688.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058608 restraints weight = 63414.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.058971 restraints weight = 54693.306| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 22934 Z= 0.352 Angle : 0.599 7.795 30951 Z= 0.313 Chirality : 0.052 0.168 3649 Planarity : 0.004 0.044 3952 Dihedral : 5.477 85.484 3055 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 1.03 % Allowed : 11.68 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.45 (0.15), residues: 1224 loop : -0.39 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 80 TYR 0.016 0.002 TYR Z 96 PHE 0.014 0.001 PHE W 124 TRP 0.012 0.001 TRP K 59 HIS 0.007 0.001 HIS W 53 Details of bonding type rmsd covalent geometry : bond 0.00764 (22934) covalent geometry : angle 0.59905 (30951) hydrogen bonds : bond 0.03489 ( 960) hydrogen bonds : angle 5.95792 ( 2355) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 MET cc_start: 0.8254 (mmm) cc_final: 0.8018 (tmm) REVERT: f 83 ARG cc_start: 0.8866 (ptp90) cc_final: 0.8497 (ptm-80) REVERT: h 75 ASP cc_start: 0.9119 (p0) cc_final: 0.8838 (t70) REVERT: i 43 MET cc_start: -0.4343 (mtp) cc_final: -0.4555 (mtp) outliers start: 26 outliers final: 23 residues processed: 163 average time/residue: 0.3152 time to fit residues: 74.4324 Evaluate side-chains 167 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 59 TRP Chi-restraints excluded: chain K residue 67 ASP Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain e residue 87 MET Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain g residue 82 LYS Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 201 optimal weight: 0.8980 chunk 271 optimal weight: 50.0000 chunk 164 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 218 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.097807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.063348 restraints weight = 320321.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.065369 restraints weight = 163587.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.066691 restraints weight = 89555.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066899 restraints weight = 81243.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.066741 restraints weight = 67708.404| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22934 Z= 0.115 Angle : 0.494 8.270 30951 Z= 0.249 Chirality : 0.054 0.165 3649 Planarity : 0.004 0.034 3952 Dihedral : 5.126 84.520 3055 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.75 % Allowed : 12.00 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.53 (0.14), residues: 1306 loop : -0.08 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.011 0.001 TYR Z 96 PHE 0.007 0.001 PHE B 124 TRP 0.003 0.001 TRP b 59 HIS 0.003 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00248 (22934) covalent geometry : angle 0.49374 (30951) hydrogen bonds : bond 0.02830 ( 960) hydrogen bonds : angle 5.69502 ( 2355) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 87 MET cc_start: 0.8328 (mmm) cc_final: 0.8024 (tmm) REVERT: f 83 ARG cc_start: 0.8898 (ptp90) cc_final: 0.8491 (ptm-80) REVERT: h 75 ASP cc_start: 0.9174 (p0) cc_final: 0.8920 (t70) REVERT: i 43 MET cc_start: -0.3384 (mtp) cc_final: -0.3620 (mtp) outliers start: 19 outliers final: 18 residues processed: 158 average time/residue: 0.2904 time to fit residues: 66.9536 Evaluate side-chains 167 residues out of total 2525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 106 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain L residue 106 TYR Chi-restraints excluded: chain W residue 133 LEU Chi-restraints excluded: chain Z residue 115 VAL Chi-restraints excluded: chain c residue 45 ILE Chi-restraints excluded: chain d residue 60 LEU Chi-restraints excluded: chain d residue 129 LEU Chi-restraints excluded: chain e residue 77 LEU Chi-restraints excluded: chain e residue 87 MET Chi-restraints excluded: chain f residue 79 ILE Chi-restraints excluded: chain g residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 56 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 199 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 217 optimal weight: 40.0000 chunk 201 optimal weight: 0.7980 chunk 16 optimal weight: 50.0000 chunk 213 optimal weight: 5.9990 overall best weight: 2.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.098373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063669 restraints weight = 318895.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.065764 restraints weight = 147728.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.067042 restraints weight = 91122.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067863 restraints weight = 67591.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068285 restraints weight = 56054.091| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22934 Z= 0.131 Angle : 0.494 8.078 30951 Z= 0.250 Chirality : 0.053 0.164 3649 Planarity : 0.004 0.034 3952 Dihedral : 5.074 83.668 3055 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.79 % Allowed : 12.12 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2856 helix: None (None), residues: 0 sheet: 0.59 (0.14), residues: 1306 loop : -0.03 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 80 TYR 0.010 0.001 TYR Z 96 PHE 0.007 0.001 PHE B 124 TRP 0.002 0.001 TRP a 59 HIS 0.003 0.001 HIS c 53 Details of bonding type rmsd covalent geometry : bond 0.00286 (22934) covalent geometry : angle 0.49425 (30951) hydrogen bonds : bond 0.02783 ( 960) hydrogen bonds : angle 5.58672 ( 2355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7243.47 seconds wall clock time: 123 minutes 23.18 seconds (7403.18 seconds total)